101
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Toyoshima K, Ohsugi Y, Lin P, Komatsu K, Shiba T, Takeuchi Y, Hirota T, Shimohira T, Tsuchiya Y, Katagiri S, Iwata T, Aoki A. Blue Light-Emitting Diode Irradiation Without a Photosensitizer Alters Oral Microbiome Composition of Ligature-Induced Periodontitis in Mice. Photobiomodul Photomed Laser Surg 2023; 41:549-559. [PMID: 37788456 DOI: 10.1089/photob.2023.0061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023] Open
Abstract
Objective: This study investigated the suppressive effects of blue light-emitting diode (LED) irradiation on bone resorption and changes in the oral microbiome of mice with ligature-induced periodontitis. Background: Wavelength of blue light has antimicrobial effects; however, whether blue LED irradiation alone inhibits the progression of periodontitis remains unclear. Methods: Nine-week-old male mice ligated ligature around the right maxillary second molar was divided into ligation alone (Li) and ligation with blue LED irradiation (LiBL) groups. The LiBL group underwent blue LED (wavelength, 455 nm) irradiation four times in a week at 150 mW/cm2 without a photosensitizer on the gingival tissue around the ligated tooth at a distance of 5 mm for 5 min. The total energy density per day was 45 J/cm2. Bone resorption was evaluated using micro-computed tomography at 8 days. Differences in the oral microbiome composition of the collected ligatures between the Li and LiBL groups were analyzed using next-generation sequencing based on the 16S rRNA gene from the ligatures. Results: Blue LED irradiation did not suppress bone resorption caused by ligature-induced periodontitis. However, in the LiBL group, the α-diversity, number of observed features, and Chao1 were significantly decreased. The relative abundances in phylum Myxococcota and Bacteroidota were underrepresented, and the genera Staphylococcus, Lactococcus, and Lactobacillus were significantly overrepresented by blue LED exposure. Metagenomic function prediction indicated an increase in the downregulated pathways related to microbial energy metabolism after irradiation. The co-occurrence network was altered to a simpler structure in the LiBL group, and the number of core genera decreased. Conclusions: Blue LED irradiation altered the composition and network of the oral microbiome of ligature-induced periodontitis in mice.
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Affiliation(s)
- Keita Toyoshima
- Department of Periodontology and Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yujin Ohsugi
- Department of Periodontology and Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Peiya Lin
- Department of Periodontology and Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Keiji Komatsu
- Department of Lifetime Oral Health Care Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takahiko Shiba
- Department of Periodontology and Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Yasuo Takeuchi
- Department of Periodontology and Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Lifetime Oral Health Care Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tomomitsu Hirota
- Division of Molecular Genetics, Research Center for Medical Science, The Jikei University School of Medicine, Tokyo, Japan
| | - Tsuyoshi Shimohira
- Department of Periodontology and Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yosuke Tsuchiya
- Department of Periodontology and Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Sayaka Katagiri
- Department of Periodontology and Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takanori Iwata
- Department of Periodontology and Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Akira Aoki
- Department of Periodontology and Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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102
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Benton L, Lopez-Galvez N, Herman C, Caporaso G, Cope E, Rosales C, Gameros M, Lothrop N, Martínez F, Wright A, Carr T, Beamer P. Environmental and Structural Factors Associated with Bacterial Diversity in Household Dust Across the Arizona-Sonora Border. RESEARCH SQUARE 2023:rs.3.rs-3325336. [PMID: 37841844 PMCID: PMC10571632 DOI: 10.21203/rs.3.rs-3325336/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
We previously reported that asthma prevalence was higher in the United States (US) compared to Mexico (MX) (25.8% vs 8.4%). This investigation assessed differences in microbial dust composition in relation to demographic and housing characteristics on both sides of the US-MX Border. Forty homes were recruited in the US and MX. Home visits collected floor dust and documented occupants' demographics, asthma prevalence, and housing structure and use characteristics. US households were more likely to have inhabitants who reported asthma when compared with MX households (30% vs 5%) and had significantly different flooring types. The percentage of households on paved roads, with flushing toilets, with piped water and with air conditioning was higher in the US, while dust load was higher in MX. Significant differences exist between countries in the microbial composition of the floor dust. Dust from US homes was enriched with Geodermatophilus, whereas dust from Mexican homes was enriched with Alishewanella and Chryseomicrobium. A predictive metagenomics analysis identified 68 significantly differentially abundant functional pathways between US and MX. This study documented multiple structural, environmental, and demographic differences between homes in the US and MX that may contribute to significantly different microbial composition of dust observed in these two countries.
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103
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Feng E, Yang X, Zhao K, Li Y, Zhu H, Wang Z, Zhang Z. Gut microbiota is associated with spatial memory and seed-hoarding behavior of South China field mice ( Apodemus draco). Front Microbiol 2023; 14:1236359. [PMID: 37771706 PMCID: PMC10525317 DOI: 10.3389/fmicb.2023.1236359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/25/2023] [Indexed: 09/30/2023] Open
Abstract
Background Scatter-hoarding animals store food in multiple locations within their home range and rely on spatial memory for subsequent localization and retrieval. The relationship between memory and scatter-hoarding behavior has been widely demonstrated, but the association of gut microbiota with spatial memory and seed-hoarding behavior of animals remains unclear. Methods In this study, by using enclosure behavior tests, memory tests including an object location test (OLT) and a novel object recognition test (NORT), and fecal microbiota transplantation (FMT) experiment, we evaluated the role of gut microbiota in affecting the memory and seed-hoarding behavior of rodents. According to their scatter-hoarding intensity, South China field mice (Apodemus draco) were divided into scatter-hoarding group (SG) and non-scatter-hoarding group (NG). Results We found that the SG performed better than the NG in the NORT. FMT from SG donor mice altered the NG recipient mice's gut microbiota structure. Further tests demonstrated FMT from SG donor mice increased memory of NG recipient mice in laboratory tests and seed larder hoarding intensity of NG recipient mice in enclosures. Conclusion Our results suggest gut microbiota could modulate the memory and seed-hoarding behavior of animals.
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Affiliation(s)
- Enping Feng
- College of Life Science, Hebei University, Baoding, Hebei Province, China
- State Key Laboratory of Integrated Management on Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xifu Yang
- State Key Laboratory of Integrated Management on Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Kunming Zhao
- State Key Laboratory of Integrated Management on Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, China
| | - Ying Li
- State Key Laboratory of Integrated Management on Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Hanyi Zhu
- State Key Laboratory of Integrated Management on Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Zhenshan Wang
- College of Life Science, Hebei University, Baoding, Hebei Province, China
| | - Zhibin Zhang
- State Key Laboratory of Integrated Management on Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
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104
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Wuyts S, Alves R, Zimmermann‐Kogadeeva M, Nishijima S, Blasche S, Driessen M, Geyer PE, Hercog R, Kartal E, Maier L, Müller JB, Garcia Santamarina S, Schmidt TSB, Sevin DC, Telzerow A, Treit PV, Wenzel T, Typas A, Patil KR, Mann M, Kuhn M, Bork P. Consistency across multi-omics layers in a drug-perturbed gut microbial community. Mol Syst Biol 2023; 19:e11525. [PMID: 37485738 PMCID: PMC10495815 DOI: 10.15252/msb.202311525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/25/2023] Open
Abstract
Multi-omics analyses are used in microbiome studies to understand molecular changes in microbial communities exposed to different conditions. However, it is not always clear how much each omics data type contributes to our understanding and whether they are concordant with each other. Here, we map the molecular response of a synthetic community of 32 human gut bacteria to three non-antibiotic drugs by using five omics layers (16S rRNA gene profiling, metagenomics, metatranscriptomics, metaproteomics and metabolomics). We find that all the omics methods with species resolution are highly consistent in estimating relative species abundances. Furthermore, different omics methods complement each other for capturing functional changes. For example, while nearly all the omics data types captured that the antipsychotic drug chlorpromazine selectively inhibits Bacteroidota representatives in the community, the metatranscriptome and metaproteome suggested that the drug induces stress responses related to protein quality control. Metabolomics revealed a decrease in oligosaccharide uptake, likely caused by Bacteroidota depletion. Our study highlights how multi-omics datasets can be utilized to reveal complex molecular responses to external perturbations in microbial communities.
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Affiliation(s)
- Sander Wuyts
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Renato Alves
- European Molecular Biology LaboratoryHeidelbergGermany
| | | | | | - Sonja Blasche
- European Molecular Biology LaboratoryHeidelbergGermany
- Medical Research Council Toxicology UnitCambridgeUK
| | | | - Philipp E Geyer
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Rajna Hercog
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Ece Kartal
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Lisa Maier
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Johannes B Müller
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Sarela Garcia Santamarina
- European Molecular Biology LaboratoryHeidelbergGermany
- Present address:
MOSTMICRO Unit, Instituto de Tecnologia Quimica e BiologicaUniversidade Nova de LisboaOeirasPortugal
| | | | | | - Anja Telzerow
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Peter V Treit
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Tobias Wenzel
- European Molecular Biology LaboratoryHeidelbergGermany
- Present address:
Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological SciencesPontificia Universidad Catolica de ChileSantiagoChile
| | | | - Kiran R Patil
- European Molecular Biology LaboratoryHeidelbergGermany
- Medical Research Council Toxicology UnitCambridgeUK
| | - Matthias Mann
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
- Proteomics Program, NNF Center for Protein Research, Faculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Michael Kuhn
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Peer Bork
- European Molecular Biology LaboratoryHeidelbergGermany
- Max Delbrück Centre for Molecular MedicineBerlinGermany
- Yonsei Frontier Lab (YFL)Yonsei UniversitySeoulSouth Korea
- Department of Bioinformatics, BiocenterUniversity of WürzburgWürzburgGermany
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105
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Kang D, Wang X, Wang J. Intervention study of tai chi training on the intestinal flora of college student basketball players. Medicine (Baltimore) 2023; 102:e35044. [PMID: 37682169 PMCID: PMC10489434 DOI: 10.1097/md.0000000000035044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 08/11/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND In recent years, the interactions between host and host-associated gut flora have received increasingly widespread attention. Tai chi is a traditional Chinese exercise, which can significantly benefit adults with health condition. But the studies on the function of intestinal flora and its correlation with tai chi exercise, are limited. In addition, the influence of tai chi on intestinal flora has largely been understudied. In this study, we investigated the changes in intestinal microflora by 16S rRNA sequencing to clarify the specific mechanism of tai chi on the regulation of intestinal flora and seek to formulate a reasonable "exercise prescription." METHODS Design: randomized controlled trial. Participants: thirty college basketball players randomly divided into control (n = 15) and test (n = 15) groups. Intervention: experimental group practiced 24-style simplified tai chi ≥ 6 times/week for 20 weeks. Outcomes: serum biochemical markers, blood pressure, and intestinal microbial composition measured post-intervention. Analysis: intent-to-treat analysis. RESULTS Primary outcomes: after tai chi intervention, the level of high-density lipoprotein cholesterol (1.22 mmol/L) and triglycerides (0.64 mmol/L) were significantly decreased. Secondary outcomes: aspartate transaminase, alanine aminotransferase, total cholesterol, and low-density lipoprotein remained unchanged. Microbiota: α-diversity index significantly increased, particularly with increased Blautia. Blood pressure: test group showed significantly lower diastolic blood pressure (83-95 mm Hg) compared to control. DISCUSSION Considering other markers, increased gut flora diversity during exercise may imply a healthier gut environment. Physical exercise promotes a decrease in the inflammatory process by reducing the levels of bacteria associated with pro-inflammation, such as Proteobacteria. Further research is required to understand the nuanced link between gut flora diversity and exercise intensity. CONCLUSION 24-style simplified tai chi enhances human intestinal flora diversity. Improvements observed in blood lipid profiles and blood pressure levels.
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Affiliation(s)
- Dongyang Kang
- Chengdu Sport University, Chengdu, Sichuan Province, China
- Department of Physical Education, Henan University of Science and Technology, Luoyang, China
| | - Xiaorong Wang
- Department of Physical Education, Luoyang Polytechnic, Luoyang, China
| | - Jiahong Wang
- Department of Physical Education, Soochow University, Suzhou, China
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106
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Baker JL. Illuminating the oral microbiome and its host interactions: recent advancements in omics and bioinformatics technologies in the context of oral microbiome research. FEMS Microbiol Rev 2023; 47:fuad051. [PMID: 37667515 PMCID: PMC10503653 DOI: 10.1093/femsre/fuad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 08/02/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023] Open
Abstract
The oral microbiota has an enormous impact on human health, with oral dysbiosis now linked to many oral and systemic diseases. Recent advancements in sequencing, mass spectrometry, bioinformatics, computational biology, and machine learning are revolutionizing oral microbiome research, enabling analysis at an unprecedented scale and level of resolution using omics approaches. This review contains a comprehensive perspective of the current state-of-the-art tools available to perform genomics, metagenomics, phylogenomics, pangenomics, transcriptomics, proteomics, metabolomics, lipidomics, and multi-omics analysis on (all) microbiomes, and then provides examples of how the techniques have been applied to research of the oral microbiome, specifically. Key findings of these studies and remaining challenges for the field are highlighted. Although the methods discussed here are placed in the context of their contributions to oral microbiome research specifically, they are pertinent to the study of any microbiome, and the intended audience of this includes researchers would simply like to get an introduction to microbial omics and/or an update on the latest omics methods. Continued research of the oral microbiota using omics approaches is crucial and will lead to dramatic improvements in human health, longevity, and quality of life.
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Affiliation(s)
- Jonathon L Baker
- Department of Oral Rehabilitation & Biosciences, School of Dentistry, Oregon Health & Science University, 3181 Sam Jackson Park Road, Portland, OR 97202, United States
- Genomic Medicine Group, J. Craig Venter Institute, La Jolla, CA 92037, United States
- Department of Pediatrics, UC San Diego School of Medicine, La Jolla, CA 92093, United States
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107
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Hou M, Zhao X, Wang Y, Lv X, Chen Y, Jiao X, Sui Y. Pedogenesis of typical zonal soil drives belowground bacterial communities of arable land in the Northeast China Plain. Sci Rep 2023; 13:14555. [PMID: 37666914 PMCID: PMC10477331 DOI: 10.1038/s41598-023-41401-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/25/2023] [Indexed: 09/06/2023] Open
Abstract
Belowground bacterial communities play essential roles in maintaining ecosystem multifunction, while our understanding of how and why their distribution patterns and community compositions may change with the distinct pedogenetic conditions of different soil types is still limited. Here, we evaluated the roles of soil physiochemical properties and biotic interactions in driving belowground bacterial community composition across three typical zonal soil types, including black calcium soil (QS), typical black soil (HL) and dark brown soil (BQL), with distinct pedogenesis on the Northeast China Plain. Changes in soil bacterial diversity and community composition in these three zonal soil types were strongly correlated with soil pedogenetic features. SOC concentrations in HL were higher than in QS and BQL, but bacterial diversity was low, and the network structure revealed greater stability and connectivity. The composition of the bacterial community correlated significantly with soil pH in QS but with soil texture in BQL. The bacterial co-occurrence network of HL had higher density and clustering coefficients but lower edges, and different keystone species of networks were also detected. This work provides a basic understanding of the driving mechanisms responsible for belowground bacterial biodiversity and distribution patterns over different pedogenetic conditions in agroecosystems.
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Affiliation(s)
- Meng Hou
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, People's Republic of China
- University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China
| | - Xiaorui Zhao
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, People's Republic of China
| | - Yao Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, People's Republic of China
- University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China
| | - Xuemei Lv
- College of Modern Agriculture and Eco-Environment, Heilongjiang University, 150080, Harbin, People's Republic of China
| | - Yimin Chen
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, People's Republic of China
| | - Xiaoguang Jiao
- College of Modern Agriculture and Eco-Environment, Heilongjiang University, 150080, Harbin, People's Republic of China.
| | - Yueyu Sui
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, People's Republic of China.
- University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China.
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108
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Berdan EL, Roger F, Wellenreuther M, Kinnby A, Cervin G, Pereyra R, Töpel M, Johannesson K, Butlin RK, André C. A metabarcoding analysis of the wrackbed microbiome indicates a phylogeographic break along the North Sea-Baltic Sea transition zone. Environ Microbiol 2023; 25:1659-1673. [PMID: 37032322 DOI: 10.1111/1462-2920.16379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 03/18/2023] [Indexed: 04/11/2023]
Abstract
Sandy beaches are biogeochemical hotspots that bridge marine and terrestrial ecosystems via the transfer of organic matter, such as seaweed (termed wrack). A keystone of this unique ecosystem is the microbial community, which helps to degrade wrack and re-mineralize nutrients. However, little is known about this community. Here, we characterize the wrackbed microbiome as well as the microbiome of a primary consumer, the seaweed fly Coelopa frigida, and examine how they change along one of the most studied ecological gradients in the world, the transition from the marine North Sea to the brackish Baltic Sea. We found that polysaccharide degraders dominated both microbiomes, but there were still consistent differences between wrackbed and fly samples. Furthermore, we observed a shift in both microbial communities and functionality between the North and Baltic Sea driven by changes in the frequency of different groups of known polysaccharide degraders. We hypothesize that microbes were selected for their abilities to degrade different polysaccharides corresponding to a shift in polysaccharide content in the different seaweed communities. Our results reveal the complexities of both the wrackbed microbial community, with different groups specialized to different roles, and the cascading trophic consequences of shifts in the near shore algal community.
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Affiliation(s)
- Emma L Berdan
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
| | - Fabian Roger
- Lund University, Centre for Environmental and Climate Science, Sölvegatan 37, 223 62, Lund, Sweden
| | - Maren Wellenreuther
- The New Zealand Institute for Plant & Food Research Ltd, Nelson, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Alexandra Kinnby
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
| | - Gunnar Cervin
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
| | - Ricardo Pereyra
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
| | - Mats Töpel
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
| | - Kerstin Johannesson
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
| | - Roger K Butlin
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Carl André
- Department of Marine Sciences, The University of Gothenburg, Tjärnö Marine Laboratory, 452 96, Strömstad, Sweden
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109
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Mascardi MF, Mazzini FN, Suárez B, Ruda VM, Marciano S, Casciato P, Narvaez A, Haddad L, Anders M, Orozco F, Tamaroff AJ, Cook F, Gounarides J, Gutt S, Gadano A, García CM, Marro ML, Penas Steinhardt A, Trinks J. Integrated analysis of the transcriptome and its interaction with the metabolome in metabolic associated fatty liver disease: Gut microbiome signatures, correlation networks, and effect of PNPLA3 genotype. Proteomics 2023; 23:e2200414. [PMID: 37525333 DOI: 10.1002/pmic.202200414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 08/02/2023]
Abstract
Interactions between communities of the gut microbiome and with the host could affect the onset and progression of metabolic associated fatty liver disease (MAFLD), and can be useful as new diagnostic and prognostic biomarkers. In this study, we performed a multi-omics approach to unravel gut microbiome signatures from 32 biopsy-proven patients (10 simple steatosis -SS- and 22 steatohepatitis -SH-) and 19 healthy volunteers (HV). Human and microbial transcripts were differentially identified between groups (MAFLD vs. HV/SH vs. SS), and analyzed for weighted correlation networks together with previously detected metabolites from the same set of samples. We observed that expression of Desulfobacteraceae bacterium, methanogenic archaea, Mushu phage, opportunistic pathogenic fungi Fusarium proliferatum and Candida sorbophila, protozoa Blastocystis spp. and Fonticula alba were upregulated in MAFLD and SH. Desulfobacteraceae bacterium and Mushu phage were hub species in the onset of MAFLD, whereas the activity of Fonticula alba, Faecalibacterium prausnitzii, and Mushu phage act as key regulators of the progression to SH. A combination of clinical, metabolomic, and transcriptomic parameters showed the highest predictive capacity for MAFLD and SH (AUC = 0.96). In conclusion, faecal microbiome markers from several community members contribute to the switch in signatures characteristic of MAFLD and its progression towards SH.
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Affiliation(s)
- María Florencia Mascardi
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI) - Hospital Italiano de Buenos Aires (HIBA), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Flavia Noelia Mazzini
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI) - Hospital Italiano de Buenos Aires (HIBA), Buenos Aires, Argentina
| | - Bárbara Suárez
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI) - Hospital Italiano de Buenos Aires (HIBA), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Vera M Ruda
- Biotherapeutic and Analytical Technologies, Novartis Institutes for Biomedical Research (NIBR), Cambridge, Massachusetts, USA
| | - Sebastián Marciano
- Liver Unit of Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Paola Casciato
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Liver Unit of Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Adrián Narvaez
- Liver Unit of Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Leila Haddad
- Liver Unit of Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | | | | | - Ana Jesica Tamaroff
- Nutrition Department of Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Frank Cook
- Analytical Sciences & Imaging Department, NIBR, Cambridge, Massachusetts, USA
| | - John Gounarides
- Analytical Sciences & Imaging Department, NIBR, Cambridge, Massachusetts, USA
| | - Susana Gutt
- Nutrition Department of Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Adrián Gadano
- Liver Unit of Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Celia Méndez García
- Chemical Biology & Therapeutics Department, NIBR, Cambridge, Massachusetts, USA
| | - Martin L Marro
- Cardiovascular and Metabolic Disease Area, NIBR, Cambridge, Massachusetts, USA
| | - Alberto Penas Steinhardt
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Departamento de Ciencias Básicas, Laboratorio de Genómica Computacional, Universidad Nacional de Luján, Lujan, Buenos Aires, Argentina
| | - Julieta Trinks
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI) - Hospital Italiano de Buenos Aires (HIBA), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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110
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Lowman ME, Tipton CD, Labordère AL, Brown JA. Equine sinusitis aetiology is linked to sinus microbiome by amplicon sequencing. Equine Vet J 2023; 55:798-807. [PMID: 36199163 DOI: 10.1111/evj.13884] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 09/23/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Information regarding the microbiome in sinusitis using genetic sequencing is lacking and more-in-depth understanding of the microbiome could improve antimicrobial selection and treatment outcomes for cases of primary sinusitis. OBJECTIVES To describe sinus microbiota in samples from horses with sinusitis and compare microbiota and the presence of antimicrobial resistance genes between primary, dental-related and other secondary causes of sinusitis. STUDY DESIGN Retrospective case series. METHODS Records of equine sinusitis from 2017 to 2021 were reviewed and historical microbial amplicon sequence data were obtained from clinical diagnostic testing of sinus secretions. Following bioinformatic processing of bacterial and fungal sequence data, the sinus microbiota and importance of sinusitis aetiology among other factors were investigated from the perspectives of alpha diversity (e.g., number of operational taxonomic units [OTUs], Hill1 Diversity), beta diversity, and differentially abundant taxa. Quantitative PCR allowed for comparisons of estimated bacterial abundance and detection rate of common antibiotic resistance-associated genes. In a smaller subset, longitudinal analysis was performed to evaluate similarity in samples over time. RESULTS Of 81 samples analysed from 70 horses, the bacterial microbiome was characterised in 66, and fungal in five. Only sinusitis aetiology was shown to significantly influence microbiome diversity and composition (p < 0.05). Dental-related sinusitis (n = 44) was associated with a significantly higher proportion of obligate anaerobic bacteria, whereas primary sinusitis (n = 12) and other (n = 10) groups were associated with fewer bacteria and higher proportions of facultative anaerobic and aerobic genera. Antimicrobial resistance genes and fungal components were exclusively identified in dental-related sinusitis. MAIN LIMITATIONS Retrospective nature, incomplete prior antimicrobial administration data. CONCLUSIONS Molecular characterisation in sinusitis identifies microbial species which may be difficult to isolate via culture, and microbiome profiling can differentiate sinusitis aetiology, which may inform further treatment, including antimicrobial therapy.
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Affiliation(s)
- Megan E Lowman
- Marion duPont Scott Equine Medical Center, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Leesburg, VA, USA
| | | | - Alexandra L Labordère
- Marion duPont Scott Equine Medical Center, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Leesburg, VA, USA
| | - James A Brown
- Marion duPont Scott Equine Medical Center, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Leesburg, VA, USA
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111
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Villoslada-Blanco P, Pérez-Matute P, Recio-Fernández E, Íñiguez M, Blanco-Navarrete P, Metola L, Ibarra V, Alba J, de Toro M, Oteo JA. Beyond the effects of HIV infection and integrase inhibitors-based therapies on oral bacteriome. Sci Rep 2023; 13:14327. [PMID: 37653055 PMCID: PMC10471600 DOI: 10.1038/s41598-023-41434-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 08/26/2023] [Indexed: 09/02/2023] Open
Abstract
Oral microbiome is the second largest microbial community in humans after gut. Human immunodeficiency virus (HIV) infection triggers an impairment of the immune system which could favour the growth and the colonization of pathogens in the oral cavity, and this dysbiosis has been associated with oral manifestations that worsen the quality of life of these patients. Antiretroviral therapy (ART) could also drive changes in specific oral bacterial taxa associated with such periodontal diseases. Integrase strand transfer inhibitors (INSTIs), therapy of choice in the treatment of naive HIV-patients, are able to reverse the impact of HIV infection on systemic inflammation, gut permeability, and gut bacterial diversity/richness. The objective of this study was to analyse the effects of HIV infection per se and INSTIs on salivary bacteriome composition, taking into consideration other factors such as smoking, that could also have a significant impact on oral microbiome. To accomplish this objective, 26 non-HIV-infected volunteers and 30 HIV-infected patients (15 naive and 15 under INSTIs-regimen) were recruited. Salivary samples were collected to measure lysozyme levels. Oral bacteriome composition was analysed using 16S rRNA gene sequencing. Naive HIV-infected patients showed statistically higher levels of lysozyme compared to controls (p < 0.001) and INSTIs-treated patients (p < 0.05). Our study was unable to detect differences in α nor β-diversity among the three groups analysed, although significant differences in the abundance of some bacterial taxonomical orders were detected (higher abundance in the phylum Pseudomonadota, in the order Acholeplasmatales, and in the genera Ezakiella and Acholeplasma in the naive group compared to controls; and higher abundance in the phylum Mycoplasmatota, in the order Acholeplasmatales, and in the genera Acholeplasma and uncultured Eubacteriaceae bacterium in the INTIs-treated HIV-infected patients compared to controls). These differences seem to be partially independent of smoking habit. HIV infection and INSTIs effects on oral microbiota seem not to be very potent, probably due to the modulation of other factors such as smoking and the greatest outward exposure of the oral cavity.
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Affiliation(s)
- Pablo Villoslada-Blanco
- Infectious Diseases, Microbiota and Metabolism Unit, Infectious Diseases Department, Center for Biomedical Research of La Rioja (CIBIR), C/Piqueras 98, CIBIR Building, Third Floor, 26006, Logroño, La Rioja, Spain
| | - Patricia Pérez-Matute
- Infectious Diseases, Microbiota and Metabolism Unit, Infectious Diseases Department, Center for Biomedical Research of La Rioja (CIBIR), C/Piqueras 98, CIBIR Building, Third Floor, 26006, Logroño, La Rioja, Spain.
| | - Emma Recio-Fernández
- Infectious Diseases, Microbiota and Metabolism Unit, Infectious Diseases Department, Center for Biomedical Research of La Rioja (CIBIR), C/Piqueras 98, CIBIR Building, Third Floor, 26006, Logroño, La Rioja, Spain
| | - María Íñiguez
- Infectious Diseases, Microbiota and Metabolism Unit, Infectious Diseases Department, Center for Biomedical Research of La Rioja (CIBIR), C/Piqueras 98, CIBIR Building, Third Floor, 26006, Logroño, La Rioja, Spain
| | | | - Luis Metola
- Infectious Diseases Department, Hospital Universitario San Pedro, Logroño, La Rioja, Spain
| | - Valvanera Ibarra
- Infectious Diseases Department, Hospital Universitario San Pedro, Logroño, La Rioja, Spain
| | - Jorge Alba
- Infectious Diseases Department, Hospital Universitario San Pedro, Logroño, La Rioja, Spain
| | - María de Toro
- Genomics and Bioinformatics Platform, Center for Biomedical Research of La Rioja (CIBIR), Logroño, La Rioja, Spain
| | - José A Oteo
- Infectious Diseases, Microbiota and Metabolism Unit, Infectious Diseases Department, Center for Biomedical Research of La Rioja (CIBIR), C/Piqueras 98, CIBIR Building, Third Floor, 26006, Logroño, La Rioja, Spain
- Infectious Diseases Department, Hospital Universitario San Pedro, Logroño, La Rioja, Spain
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112
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Sweeny AR, Lemon H, Ibrahim A, Watt KA, Wilson K, Childs DZ, Nussey DH, Free A, McNally L. A mixed-model approach for estimating drivers of microbiota community composition and differential taxonomic abundance. mSystems 2023; 8:e0004023. [PMID: 37489890 PMCID: PMC10469806 DOI: 10.1128/msystems.00040-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/08/2023] [Indexed: 07/26/2023] Open
Abstract
Next-generation sequencing (NGS) and metabarcoding approaches are increasingly applied to wild animal populations, but there is a disconnect between the widely applied generalized linear mixed model (GLMM) approaches commonly used to study phenotypic variation and the statistical toolkit from community ecology typically applied to metabarcoding data. Here, we describe the suitability of a novel GLMM-based approach for analyzing the taxon-specific sequence read counts derived from standard metabarcoding data. This approach allows decomposition of the contribution of different drivers to variation in community composition (e.g., age, season, individual) via interaction terms in the model random-effects structure. We provide guidance to implementing this approach and show how these models can identify how responsible specific taxonomic groups are for the effects attributed to different drivers. We applied this approach to two cross-sectional data sets from the Soay sheep population of St. Kilda. GLMMs showed agreement with dissimilarity-based approaches highlighting the substantial contribution of age and minimal contribution of season to microbiota community compositions, and simultaneously estimated the contribution of other technical and biological factors. We further used model predictions to show that age effects were principally due to increases in taxa of the phylum Bacteroidetes and declines in taxa of the phylum Firmicutes. This approach offers a powerful means for understanding the influence of drivers of community structure derived from metabarcoding data. We discuss how our approach could be readily adapted to allow researchers to estimate contributions of additional factors such as host or microbe phylogeny to answer emerging questions surrounding the ecological and evolutionary roles of within-host communities. IMPORTANCE NGS and fecal metabarcoding methods have provided powerful opportunities to study the wild gut microbiome. A wealth of data is, therefore, amassing across wild systems, generating the need for analytical approaches that can appropriately investigate simultaneous factors at the host and environmental scale that determine the composition of these communities. Here, we describe a generalized linear mixed-effects model (GLMM) approach to analyze read count data from metabarcoding of the gut microbiota, allowing us to quantify the contributions of multiple host and environmental factors to within-host community structure. Our approach provides outputs that are familiar to a majority of field ecologists and can be run using any standard mixed-effects modeling packages. We illustrate this approach using two metabarcoding data sets from the Soay sheep population of St. Kilda investigating age and season effects as worked examples.
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Affiliation(s)
- Amy R. Sweeny
- Institute of Ecology & Evolution, University of Edinburgh, Edinburgh, United Kingdom
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Hannah Lemon
- Institute of Ecology & Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Anan Ibrahim
- Biochemistry and Biotechnology, Institute of Quantitative Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Kathryn A. Watt
- Institute of Ecology & Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Kenneth Wilson
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | - Dylan Z. Childs
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Daniel H. Nussey
- Institute of Ecology & Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew Free
- Biochemistry and Biotechnology, Institute of Quantitative Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Luke McNally
- Institute of Ecology & Evolution, University of Edinburgh, Edinburgh, United Kingdom
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113
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Rothman JA, Riis JL, Hamilton KR, Blair C, Granger DA, Whiteson KL. Oral microbial communities in children, caregivers, and associations with salivary biomeasures and environmental tobacco smoke exposure. mSystems 2023; 8:e0003623. [PMID: 37338237 PMCID: PMC10470043 DOI: 10.1128/msystems.00036-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/19/2023] [Indexed: 06/21/2023] Open
Abstract
Human oral microbial communities are diverse, with implications for oral and systemic health. Oral microbial communities change over time; thus, it is important to understand how healthy versus dysbiotic oral microbiomes differ, especially within and between families. There is also a need to understand how the oral microbiome composition is changed within an individual including by factors such as environmental tobacco smoke (ETS) exposure, metabolic regulation, inflammation, and antioxidant potential. Using archived saliva samples collected from caregivers and children during a 90-month follow-up assessment in a longitudinal study of child development in the context of rural poverty, we used 16S rRNA gene sequencing to determine the salivary microbiome. A total of 724 saliva samples were available, 448 of which were from caregiver/child dyads, an additional 70 from children and 206 from adults. We compared children's and caregivers' oral microbiomes, performed "stomatotype" analyses, and examined microbial relations with concentrations of salivary markers associated with ETS exposure, metabolic regulation, inflammation, and antioxidant potential (i.e., salivary cotinine, adiponectin, C-reactive protein, and uric acid) assayed from the same biospecimens. Our results indicate that children and caregivers share much of their oral microbiome diversity, but there are distinct differences. Microbiomes from intrafamily individuals are more similar than microbiomes from nonfamily individuals, with child/caregiver dyad explaining 52% of overall microbial variation. Notably, children harbor fewer potential pathogens than caregivers, and participants' microbiomes clustered into two groups, with major differences being driven by Streptococcus spp. Differences in salivary microbiome composition associated with ETS exposure, and taxa associated with salivary analytes representing potential associations between antioxidant potential, metabolic regulation, and the oral microbiome. IMPORTANCE The human oral cavity is a multi-environment habitat that harbors a diversity of microorganisms. This oral microbiome is often transmitted between cohabitating individuals, which may associate oral and systemic health within family members. Furthermore, family social ecology plays a significant role in childhood development, which may be associated with lifelong health outcomes. In this study, we collected saliva from children and their caregivers and used 16S rRNA gene sequencing to characterize their oral microbiomes. We also analyzed salivary biomeasures of environmental tobacco smoke exposure, metabolic regulation, inflammation, and antioxidant potential. We show there are differences in individuals' oral microbiomes mainly due to Streptococcus spp. that family members share much of their microbes, and several bacterial taxa associate with the selected salivary biomeasures. Our results suggest there are large-scale oral microbiome patterns, and there are likely relationships between oral microbiomes and the social ecology of families.
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Affiliation(s)
- Jason A. Rothman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
- Institute for Interdisciplinary Salivary Bioscience Research, University of California, Irvine, California, USA
| | - Jenna L. Riis
- Institute for Interdisciplinary Salivary Bioscience Research, University of California, Irvine, California, USA
- Department of Psychological Science, University of California, Irvine, California, USA
| | - Katrina R. Hamilton
- Institute for Interdisciplinary Salivary Bioscience Research, University of California, Irvine, California, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Clancy Blair
- Department of Population Health, New York University, New York, New York, USA
- Department of Applied Psychology, New York University, New York, New York, USA
| | - Douglas A. Granger
- Institute for Interdisciplinary Salivary Bioscience Research, University of California, Irvine, California, USA
- Department of Acute and Chronic Care, Johns Hopkins University School of Nursing, Baltimore, Maryland, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Salivary Bioscience Laboratory, University of Nebraska, Lincoln, Nebraska, USA
- Department of Psychology, University of Nebraska, Lincoln, Nebraska, USA
| | - Katrine L. Whiteson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
- Institute for Interdisciplinary Salivary Bioscience Research, University of California, Irvine, California, USA
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114
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Katagiri S, Ohsugi Y, Shiba T, Yoshimi K, Nakagawa K, Nagasawa Y, Uchida A, Liu A, Lin P, Tsukahara Y, Iwata T, Tohara H. Homemade blenderized tube feeding improves gut microbiome communities in children with enteral nutrition. Front Microbiol 2023; 14:1215236. [PMID: 37680532 PMCID: PMC10482415 DOI: 10.3389/fmicb.2023.1215236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 08/09/2023] [Indexed: 09/09/2023] Open
Abstract
Enteral nutrition for children is supplied through nasogastric or gastrostomy tubes. Diet not only influences nutritional intake but also interacts with the composition and function of the gut microbiota. Homemade blenderized tube feeding has been administered to children receiving enteral nutrition, in addition to ready-made tube feeding. The purpose of this study was to evaluate the oral/gut microbial communities in children receiving enteral nutrition with or without homemade blenderized tube feeding. Among a total of 30 children, 6 receiving mainly ready-made tube feeding (RTF) and 5 receiving mainly homemade blenderized tube feeding (HBTF) were analyzed in this study. Oral and gut microbiota community profiles were evaluated through 16S rRNA sequencing of saliva and fecal samples. The α-diversity representing the number of observed features, Shannon index, and Chao1 in the gut were significantly increased in HBTF only in the gut microbiome but not in the oral microbiome. In addition, the relative abundances of the phylum Proteobacteria, class Gammaproteobacteria, and genus Escherichia-Shigella were significantly low, whereas that of the genus Ruminococcus was significantly high in the gut of children with HBTF, indicating HBTF altered the gut microbial composition and reducing health risks. Metagenome prediction showed enrichment of carbon fixation pathways in prokaryotes at oral and gut microbiomes in children receiving HBTF. In addition, more complex network structures were observed in the oral cavity and gut in the HBTF group than in the RTF group. In conclusion, HBTF not only provides satisfaction and enjoyment during meals with the family but also alters the gut microbial composition to a healthy state.
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Affiliation(s)
- Sayaka Katagiri
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yujin Ohsugi
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Takahiko Shiba
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, MA, United States
| | - Kanako Yoshimi
- Department of Dysphagia Rehabilitation, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kazuharu Nakagawa
- Department of Dysphagia Rehabilitation, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yuki Nagasawa
- Department of Dysphagia Rehabilitation, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Aritoshi Uchida
- Department of Dysphagia Rehabilitation, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Anhao Liu
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Peiya Lin
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yuta Tsukahara
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Takanori Iwata
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Haruka Tohara
- Department of Dysphagia Rehabilitation, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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115
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Evans JS, Paul VJ, Ushijima B, Pitts KA, Kellogg CA. Investigating microbial size classes associated with the transmission of stony coral tissue loss disease (SCTLD). PeerJ 2023; 11:e15836. [PMID: 37637172 PMCID: PMC10460154 DOI: 10.7717/peerj.15836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 07/11/2023] [Indexed: 08/29/2023] Open
Abstract
Effective treatment and prevention of any disease necessitates knowledge of the causative agent, yet the causative agents of most coral diseases remain unknown, in part due to the difficulty of distinguishing the pathogenic microbe(s) among the complex microbial backdrop of coral hosts. Stony coral tissue loss disease (SCTLD) is a particularly destructive disease of unknown etiology, capable of transmitting through the water column and killing entire colonies within a matter of weeks. Here we used a previously described method to (i) isolate diseased and apparently healthy coral colonies within individual mesocosms containing filtered seawater with low microbial background levels; (ii) incubate for several days to enrich the water with coral-shed microbes; (iii) use tangential-flow filtration to concentrate the microbial community in the mesocosm water; and then (iv) filter the resulting concentrate through a sequential series of different pore-sized filters. To investigate the size class of microorganism(s) associated with SCTLD transmission, we used 0.8 µm pore size filters to capture microeukaryotes and expelled zooxanthellae, 0.22 µm pore size filters to capture bacteria and large viruses, and 0.025 µm pore size filters to capture smaller viruses. In an attempt to further refine which size fraction(s) contained the transmissible element of SCTLD, we then applied these filters to healthy "receiver" coral fragments and monitored them for the onset of SCTLD signs over three separate experimental runs. However, several factors outside of our control confounded the transmission results, rendering them inconclusive. As the bulk of prior studies of SCTLD in coral tissues have primarily investigated the associated bacterial community, we chose to characterize the prokaryotic community associated with all mesocosm 0.22 µm pore size filters using Illumina sequencing of the V4 region of the 16S rRNA gene. We identified overlaps with prior SCTLD studies, including the presence of numerous previously identified SCTLD bioindicators within our mesocosms. The identification in our mesocosms of specific bacterial amplicon sequence variants that also appear across prior studies spanning different collection years, geographic regions, source material, and coral species, suggests that bacteria may play some role in the disease.
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Affiliation(s)
- James S. Evans
- St. Petersburg Coastal and Marine Science Center, U.S. Geological Survey, St. Petersburg, Florida, United States of America
| | - Valerie J. Paul
- Smithsonian Marine Station, Ft. Pierce, Florida, United States of America
| | - Blake Ushijima
- Smithsonian Marine Station, Ft. Pierce, Florida, United States of America
- Department of Biology & Marine Biology, University of North Carolina at Wilmington, Wilmington, North Carolina, United States of America
| | - Kelly A. Pitts
- Smithsonian Marine Station, Ft. Pierce, Florida, United States of America
| | - Christina A. Kellogg
- St. Petersburg Coastal and Marine Science Center, U.S. Geological Survey, St. Petersburg, Florida, United States of America
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116
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Kollár J, Kopalová K, Kavan J, Vrbická K, Nývlt D, Nedbalová L, Stibal M, Kohler TJ. Recently formed Antarctic lakes host less diverse benthic bacterial and diatom communities than their older counterparts. FEMS Microbiol Ecol 2023; 99:fiad087. [PMID: 37516444 PMCID: PMC10446143 DOI: 10.1093/femsec/fiad087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 07/24/2023] [Accepted: 07/28/2023] [Indexed: 07/31/2023] Open
Abstract
Glacier recession is creating new water bodies in proglacial forelands worldwide, including Antarctica. Yet, it is unknown how microbial communities of recently formed "young" waterbodies (originating decades to a few centuries ago) compare with established "old" counterparts (millennia ago). Here, we compared benthic microbial communities of different lake types on James Ross Island, Antarctic Peninsula, using 16S rDNA metabarcoding and light microscopy to explore bacterial and diatom communities, respectively. We found that the older lakes host significantly more diverse bacterial and diatom communities compared to the young ones. To identify potential mechanisms for these differences, linear models and dbRDA analyses suggested combinations of water temperature, pH, and conductivity to be the most important factors for diversity and community structuring, while differences in geomorphological and hydrological stability, though more difficult to quantify, are likely also influential. These results, along with an indicator species analysis, suggest that physical and chemical constraints associated with individual lakes histories are likely more influential to the assembly of the benthic microbial communities than lake age alone. Collectively, these results improve our understanding of microbial community drivers in Antarctic freshwaters, and help predict how the microbial landscape may shift with future habitat creation within a changing environment.
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Affiliation(s)
- Jan Kollár
- Faculty of Science, Department of Ecology, Charles University, Viničná 7, Prague 2, CZ-12844, Czech Republic
| | - Kateřina Kopalová
- Faculty of Science, Department of Ecology, Charles University, Viničná 7, Prague 2, CZ-12844, Czech Republic
| | - Jan Kavan
- Polar-Geo-Lab, Faculty of Science, Department of Geography, Masaryk University, Kotlářská 2, Brno, CZ-61137, Czech Republic
- Alfred Jahn Cold Regions Research Centre, University of Wroclaw, pl. Uniwersytecki 1, Wroclaw 50-137, Poland
| | - Kristýna Vrbická
- Faculty of Science, Department of Ecology, Charles University, Viničná 7, Prague 2, CZ-12844, Czech Republic
| | - Daniel Nývlt
- Polar-Geo-Lab, Faculty of Science, Department of Geography, Masaryk University, Kotlářská 2, Brno, CZ-61137, Czech Republic
| | - Linda Nedbalová
- Faculty of Science, Department of Ecology, Charles University, Viničná 7, Prague 2, CZ-12844, Czech Republic
| | - Marek Stibal
- Faculty of Science, Department of Ecology, Charles University, Viničná 7, Prague 2, CZ-12844, Czech Republic
| | - Tyler J Kohler
- Faculty of Science, Department of Ecology, Charles University, Viničná 7, Prague 2, CZ-12844, Czech Republic
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117
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Romero R, Theis KR, Gomez-Lopez N, Winters AD, Panzer JJ, Lin H, Galaz J, Greenberg JM, Shaffer Z, Kracht DJ, Chaiworapongsa T, Jung E, Gotsch F, Ravel J, Peddada SD, Tarca AL. The Vaginal Microbiota of Pregnant Women Varies with Gestational Age, Maternal Age, and Parity. Microbiol Spectr 2023; 11:e0342922. [PMID: 37486223 PMCID: PMC10434204 DOI: 10.1128/spectrum.03429-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 06/25/2023] [Indexed: 07/25/2023] Open
Abstract
The composition of the vaginal microbiota is heavily influenced by pregnancy and may factor into pregnancy complications, including spontaneous preterm birth. However, results among studies have been inconsistent due, in part, to variation in sample sizes and ethnicity. Thus, an association between the vaginal microbiota and preterm labor continues to be debated. Yet, before assessing associations between the composition of the vaginal microbiota and preterm labor, a robust and in-depth characterization of the vaginal microbiota throughout pregnancy in the specific study population under investigation is required. Here, we report a large longitudinal study (n = 474 women, 1,862 vaginal samples) of a predominantly African-American cohort-a population that experiences a relatively high rate of pregnancy complications-evaluating associations between individual identity, gestational age, and other maternal characteristics with the composition of the vaginal microbiota throughout gestation resulting in term delivery. The principal factors influencing the composition of the vaginal microbiota in pregnancy are individual identity and gestational age at sampling. Other factors are maternal age, parity, obesity, and self-reported Cannabis use. The general pattern across gestation is for the vaginal microbiota to remain or transition to a state of Lactobacillus dominance. This pattern can be modified by maternal parity and obesity. Regardless, network analyses reveal dynamic associations among specific bacterial taxa within the vaginal ecosystem, which shift throughout the course of pregnancy. This study provides a robust foundational understanding of the vaginal microbiota in pregnancy and sets the stage for further investigation of this microbiota in obstetrical disease. IMPORTANCE There is debate regarding links between the vaginal microbiota and pregnancy complications, especially spontaneous preterm birth. Inconsistencies in results among studies are likely due to differences in sample sizes and cohort ethnicity. Ethnicity is a complicating factor because, although all bacterial taxa commonly inhabiting the vagina are present among all ethnicities, the frequencies of these taxa vary among ethnicities. Therefore, an in-depth characterization of the vaginal microbiota throughout pregnancy in the specific study population under investigation is required prior to evaluating associations between the vaginal microbiota and obstetrical disease. This initial investigation is a large longitudinal study of the vaginal microbiota throughout gestation resulting in a term delivery in a predominantly African-American cohort, a population that experiences disproportionally negative maternal-fetal health outcomes. It establishes the magnitude of associations between maternal characteristics, such as age, parity, body mass index, and self-reported Cannabis use, on the vaginal microbiota in pregnancy.
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Affiliation(s)
- Roberto Romero
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan, USA
| | - Kevin R. Theis
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Nardhy Gomez-Lopez
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Andrew D. Winters
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Jonathan J. Panzer
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Huang Lin
- Biostatistics and Bioinformatics Branch, National Institute of Child Health and Human Development, Bethesda, Maryland, USA
| | - Jose Galaz
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Division of Obstetrics and Gynecology, School of Medicine, Faculty of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Jonathan M. Greenberg
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Zachary Shaffer
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - David J. Kracht
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Tinnakorn Chaiworapongsa
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Eunjung Jung
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Busan Paik Hospital, Inje University College of Medicine, Busan, Republic of Korea
| | - Francesca Gotsch
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Shyamal D. Peddada
- Biostatistics and Bioinformatics Branch, National Institute of Child Health and Human Development, Bethesda, Maryland, USA
| | - Adi L. Tarca
- Pregnancy Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
- Department of Computer Science, Wayne State University College of Engineering, Detroit, Michigan, USA
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Núñez-Gómez D, Melgarejo P, Martínez-Nicolás JJ, Hernández F, Martínez-Font R, Lidón V, Legua P. Effects of marine sediment as agricultural substrate on soil microbial diversity: an amplicon sequencing study. ENVIRONMENTAL MICROBIOME 2023; 18:69. [PMID: 37550709 PMCID: PMC10408225 DOI: 10.1186/s40793-023-00519-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 07/12/2023] [Indexed: 08/09/2023]
Abstract
BACKGROUND The soil microbiota has a direct impact on plant development and other metabolic systems, such as the degradation of organic matter and the availability of microelements and metabolites. In the context of agricultural soils, microbial activity is crucial for maintaining soil health and productivity. Thus, the present study aimed to identify, characterize, and quantify the microbial communities of four types of substrates with varying proportions of marine port sediment used for cultivating lemons. By investigating microbial diversity and relative abundance, the work aimed to highlight the importance of soil microbial communities in agriculture when alternative culture media was used. RESULTS The composition and structure of the sampled microbial communities were assessed through the amplification and sequencing of the V3-V4 variable regions of the 16 S rRNA gene The results revealed a diverse microbial community composition in all substrate samples, with a total of 41 phyla, 113 classes, 266 orders, 405 families, 715 genera, and 1513 species identified. Among these, Proteobacteria, Bacteroidota, Planctomycetota, Patescibacteria, Chloroflexi, Actinobacteriota, Acidobacteriota, Verrucomicrobiota, and Gemmatimonadota accounted for over 90% of the bacterial reads, indicating their dominance in the substrates. CONCLUSIONS The impact of the substrate origin on the diversity and relative abundace of the microbiota was confirmed. The higher content of beneficial bacterial communities for plant development identified in peat could explain why is considered an ideal agricultural substrate. Development of "beneficial for plants" bacterial communities in alternative agricultural substrates, regardless of the edaphic characteristics, opens the possibility of studying the forced and specific inoculation of these culture media aiming to be agriculturally ideals.
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Affiliation(s)
- Dámaris Núñez-Gómez
- Centro de Investigación e Innovación Agroalimentaria y Agroambiental (CIAGRO-UMH), Miguel Hernandez University, Ctra. Beniel, km 3.2, Orihuela, Alicante, 03312, Spain
| | - Pablo Melgarejo
- Centro de Investigación e Innovación Agroalimentaria y Agroambiental (CIAGRO-UMH), Miguel Hernandez University, Ctra. Beniel, km 3.2, Orihuela, Alicante, 03312, Spain.
| | - Juan José Martínez-Nicolás
- Centro de Investigación e Innovación Agroalimentaria y Agroambiental (CIAGRO-UMH), Miguel Hernandez University, Ctra. Beniel, km 3.2, Orihuela, Alicante, 03312, Spain
| | - Francisca Hernández
- Centro de Investigación e Innovación Agroalimentaria y Agroambiental (CIAGRO-UMH), Miguel Hernandez University, Ctra. Beniel, km 3.2, Orihuela, Alicante, 03312, Spain
| | - Rafael Martínez-Font
- Centro de Investigación e Innovación Agroalimentaria y Agroambiental (CIAGRO-UMH), Miguel Hernandez University, Ctra. Beniel, km 3.2, Orihuela, Alicante, 03312, Spain
| | - Vicente Lidón
- Centro de Investigación e Innovación Agroalimentaria y Agroambiental (CIAGRO-UMH), Miguel Hernandez University, Ctra. Beniel, km 3.2, Orihuela, Alicante, 03312, Spain
| | - Pilar Legua
- Centro de Investigación e Innovación Agroalimentaria y Agroambiental (CIAGRO-UMH), Miguel Hernandez University, Ctra. Beniel, km 3.2, Orihuela, Alicante, 03312, Spain
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119
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Weninger SN, Herman C, Meyer RK, Beauchemin ET, Kangath A, Lane AI, Martinez TM, Hasneen T, Jaramillo SA, Lindsey J, Vedantam G, Cai H, Cope EK, Caporaso JG, Duca FA. Oligofructose improves small intestinal lipid-sensing mechanisms via alterations to the small intestinal microbiota. MICROBIOME 2023; 11:169. [PMID: 37533066 PMCID: PMC10394784 DOI: 10.1186/s40168-023-01590-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 06/02/2023] [Indexed: 08/04/2023]
Abstract
BACKGROUND Upper small intestinal dietary lipids activate a gut-brain axis regulating energy homeostasis. The prebiotic, oligofructose (OFS) improves body weight and adiposity during metabolic dysregulation but the exact mechanisms remain unknown. This study examines whether alterations to the small intestinal microbiota following OFS treatment improve small intestinal lipid-sensing to regulate food intake in high fat (HF)-fed rats. RESULTS In rats fed a HF diet for 4 weeks, OFS supplementation decreased food intake and meal size within 2 days, and reduced body weight and adiposity after 6 weeks. Acute (3 day) OFS treatment restored small intestinal lipid-induced satiation during HF-feeding, and was associated with increased small intestinal CD36 expression, portal GLP-1 levels and hindbrain neuronal activation following a small intestinal lipid infusion. Transplant of the small intestinal microbiota from acute OFS treated donors into HF-fed rats also restored lipid-sensing mechanisms to lower food intake. 16S rRNA gene sequencing revealed that both long and short-term OFS altered the small intestinal microbiota, increasing Bifidobacterium relative abundance. Small intestinal administration of Bifidobacterium pseudolongum to HF-fed rats improved small intestinal lipid-sensing to decrease food intake. CONCLUSION OFS supplementation rapidly modulates the small intestinal gut microbiota, which mediates improvements in small intestinal lipid sensing mechanisms that control food intake to improve energy homeostasis. Video Abstract.
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Affiliation(s)
| | - Chloe Herman
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Rachel K Meyer
- Department of Nutritional Sciences, University of Arizona, Tucson, USA
| | - Eve T Beauchemin
- School of Animal and Comparative Biomedical Sciences, College of Agricultural and Life Sciences, University of Arizona, Tucson, USA
- Faculty of Medicine, Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Archana Kangath
- School of Animal and Comparative Biomedical Sciences, College of Agricultural and Life Sciences, University of Arizona, Tucson, USA
| | - Adelina I Lane
- Department of Physiology, University of Arizona, Tucson, USA
| | | | - Tahia Hasneen
- Department of Neuroscience, University of Arizona, Tucson, AZ, USA
| | - Sierra A Jaramillo
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jason Lindsey
- School of Animal and Comparative Biomedical Sciences, College of Agricultural and Life Sciences, University of Arizona, Tucson, USA
| | - Gayatri Vedantam
- School of Animal and Comparative Biomedical Sciences, College of Agricultural and Life Sciences, University of Arizona, Tucson, USA
- Department of Immunobiology, University of Arizona, Tucson, AZ, USA
- BIO5 Institute for Collaborative Research, University of Arizona, Tucson, USA
| | - Haijiang Cai
- Department of Neuroscience, University of Arizona, Tucson, AZ, USA
- BIO5 Institute for Collaborative Research, University of Arizona, Tucson, USA
| | - Emily K Cope
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - J Gregory Caporaso
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Frank A Duca
- School of Animal and Comparative Biomedical Sciences, College of Agricultural and Life Sciences, University of Arizona, Tucson, USA.
- BIO5 Institute for Collaborative Research, University of Arizona, Tucson, USA.
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Wu S, Cheng L, Pennhag AAL, Seifert M, Guðnadóttir U, Engstrand L, Mints M, Andersson S, Du J. The salivary microbiota is altered in cervical dysplasia patients and influenced by conization. IMETA 2023; 2:e108. [PMID: 38867925 PMCID: PMC10989756 DOI: 10.1002/imt2.108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/30/2023] [Accepted: 04/16/2023] [Indexed: 06/14/2024]
Abstract
This study supports the correlation between the salivary microbiota and cervical dysplasia and suggests that smoking influences the salivary microbiota.
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Affiliation(s)
- Shengru Wu
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome ResearchKarolinska InstituteStockholmSweden
- College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
| | - Liqin Cheng
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome ResearchKarolinska InstituteStockholmSweden
| | - Alexandra A. L. Pennhag
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome ResearchKarolinska InstituteStockholmSweden
| | - Maike Seifert
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome ResearchKarolinska InstituteStockholmSweden
| | - Unnur Guðnadóttir
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome ResearchKarolinska InstituteStockholmSweden
| | - Lars Engstrand
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome ResearchKarolinska InstituteStockholmSweden
- Science for Life LaboratoryKarolinska InstituteStockholmSweden
| | - Miriam Mints
- Department of Women's and Children's HealthKarolinska InstituteStockholmSweden
| | - Sonia Andersson
- Department of Women's and Children's HealthKarolinska InstituteStockholmSweden
| | - Juan Du
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome ResearchKarolinska InstituteStockholmSweden
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Yang C, Mai J, Cao X, Burberry A, Cominelli F, Zhang L. ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization. Bioinformatics 2023; 39:btad470. [PMID: 37527009 PMCID: PMC10425198 DOI: 10.1093/bioinformatics/btad470] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/13/2023] [Accepted: 07/30/2023] [Indexed: 08/03/2023] Open
Abstract
SUMMARY Microbiome research is now moving beyond the compositional analysis of microbial taxa in a sample. Increasing evidence from large human microbiome studies suggests that functional consequences of changes in the intestinal microbiome may provide more power for studying their impact on inflammation and immune responses. Although 16S rRNA analysis is one of the most popular and a cost-effective method to profile the microbial compositions, marker-gene sequencing cannot provide direct information about the functional genes that are present in the genomes of community members. Bioinformatic tools have been developed to predict microbiome function with 16S rRNA gene data. Among them, PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) has become one of the most popular functional profile prediction tools, which generates community-wide pathway abundances. However, no state-of-art inference tools are available to test the differences in pathway abundances between comparison groups. We have developed ggpicrust2, an R package, for analyzing functional profiles derived from 16S rRNA sequencing. This powerful tool enables researchers to conduct extensive differential abundance analyses and generate visually appealing visualizations that effectively highlight functional signals. With ggpicrust2, users can obtain publishable results and gain deeper insights into the functional composition of their microbial communities. AVAILABILITY AND IMPLEMENTATION The package is open-source under the MIT and file license and is available at CRAN and https://github.com/cafferychen777/ggpicrust2. Its shiny web is available at https://a95dps-caffery-chen.shinyapps.io/ggpicrust2_shiny/.
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Affiliation(s)
- Chen Yang
- Department of Biostatistics, Southern Medical University, Guangzhou 510515, China
| | - Jiahao Mai
- Department of Biostatistics, Southern Medical University, Guangzhou 510515, China
| | - Xuan Cao
- Department of Mathematical Sciences, University of Cincinnati, Cincinnati, OH 45221, United States
| | - Aaron Burberry
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, United States
| | - Fabio Cominelli
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, United States
- Case Digestive Health Research Institute, Case Western Reserve University, Cleveland, OH 44016, United States
| | - Liangliang Zhang
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, United States
- Case Comprehensive Cancer Center, Cleveland, OH 44106, United States
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Valečková E, Sun L, Wang H, Dube F, Ivarsson E, Kasmaei KM, Ellström P, Wall H. Intestinal colonization with Campylobacter jejuni affects broiler gut microbiota composition but is not inhibited by daily intake of Lactiplantibacillus plantarum. Front Microbiol 2023; 14:1205797. [PMID: 37577431 PMCID: PMC10416237 DOI: 10.3389/fmicb.2023.1205797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/12/2023] [Indexed: 08/15/2023] Open
Abstract
Introduction Lactobacilli may prevent broilers from colonization with Campylobacter spp. and other gram-negative zoonotic bacteria through lactic acid production and modulation of the intestinal microbiota. This study evaluated the effects of daily intake of Lactiplantibacillus plantarum 256 (LP256) on Campylobacter jejuni (C. jejuni) loads in ceca and feces of C. jejuni challenged broilers, together with the changes in the gut microbiota. Methods Two experiments were conducted using the broilers Ross 308 (R-308; Experiment 1) for 42 days and Rowan Ranger broilers (RR; Experiment 2) for 63 days. The LP256 strain was administered either via silage inoculated with LP256 or direct supplementation in the drinking water. Concurrently, haylage as a forage similar to silage but without any inoculum was tested. C. jejuni loads in fecal matter and cecal content were determined by plate counts and qPCR, respectively. The cecal microbiota, in response to treatments and the challenge, were assessed by 16S rRNA sequencing. Results and Discussion Culturing results displayed a significant reduction in C. jejuni colonization (2.01 log) in the silage treatment in comparison to the control at 1 dpi (day post-infection) in Experiment 1. However, no treatment effect on C. jejuni was observed at the end of the experiment. In Experiment 2, no treatment effects on C. jejuni colonization were found to be statistically significant. Colonization load comparison at the peak of infection (3 dpi) to that at the end of the trial (32 dpi) revealed a significant reduction in C. jejuni in all groups, regardless of treatment. Colonization dynamics of C. jejuni in the cecal samples analyzed by qPCR showed no difference between any of the treatments in Experiment 1 or 2. In both experiments, no treatment effects on the cecal microbiota were observed. However, proportional changes in the bacterial composition were observed after the C. jejuni challenge, suggesting that colonization affected the gut microbiota. Overall, the daily intake of LP256 was not effective in reducing C. jejuni colonization in either broiler type at the end of the rearing period and did not cause any significant changes in the birds' cecal microbiota composition.
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Affiliation(s)
- Eliška Valečková
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Li Sun
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Helen Wang
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Faruk Dube
- Department of Biomedical Science and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Emma Ivarsson
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Kamyar Mogodiniyai Kasmaei
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Patrik Ellström
- Department of Medical Sciences, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Helena Wall
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Xing M, Gao H, Yao L, Wang L, Zhang C, Zhu L, Cui D. Profiles and diagnostic value of intestinal microbiota in schizophrenia patients with metabolic syndrome. Front Endocrinol (Lausanne) 2023; 14:1190954. [PMID: 37576972 PMCID: PMC10415044 DOI: 10.3389/fendo.2023.1190954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/26/2023] [Indexed: 08/15/2023] Open
Abstract
Aims/hypothesis It is widely thought that the intestinal microbiota plays a significant role in the pathogenesis of metabolic disorders. However, the gut microbiota composition and characteristics of schizophrenia patients with metabolic syndrome (MetS) have been largely understudied. Herein, we investigated the association between the metabolic status of mainland Chinese schizophrenia patients with MetS and the intestinal microbiome. Methods Fecal microbiota communities from 115 male schizophrenia patients (57 with MetS and 58 without MetS) were assessed by 16S ribosomal RNA gene sequencing. We assessed the variations of gut microbiome between both groups and explored potential associations between intestinal microbiota and parameters of MetS. In addition, the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) based on the KEGG database was used to predict the function of intestinal microbiota. We also conducted Decision Tree Analysis to develop a diagnostic model for the MetS in patients with schizophrenia based on the composition of intestinal microbiota. Results The fecal microbial diversity significantly differed between groups with or without MetS (α-diversity (Shannon index and Simpson index): p=0.0155, p=0.0089; β-diversity: p=0.001). Moreover, the microbial composition was significantly different between the two groups, involving five phyla and 38 genera (p<0.05). In addition, a significant correlation was observed between the metabolic-related parameters and abundance of altered microbiota including HDL-c (r2 = 0.203, p=0.0005), GLU (r2 = 0.286, p=0.0005) and WC (r2 = 0.061, p=0.037). Furthermore, KEGG pathway analysis showed that 16 signaling pathways were significantly enriched between the two groups (p<0.05). Importantly, our diagnostic model based on five microorganisms established by decision tree analysis could effectively distinguish between patients with and without MetS (AUC = 0.94). Conclusions/interpretation Our study established the compositional and functional characteristics of intestinal microbiota in schizophrenia patients with MetS. These new findings provide novel insights into a better understanding of this disease and provide the theoretical basis for implementing new interventional therapies in clinical practice.
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Affiliation(s)
- Mengjuan Xing
- Department of General Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Hui Gao
- The First Minzheng Mental Health Center, Shanghai, China
| | - Lili Yao
- The First Minzheng Mental Health Center, Shanghai, China
| | - Li Wang
- The First Minzheng Mental Health Center, Shanghai, China
| | - Chengfang Zhang
- Shanghai Pudong New Area Mental Health Center, Tongji University School of Medicine, Shanghai, China
| | - Liping Zhu
- Department of General Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Donghong Cui
- Department of General Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
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Bittleston LS, Wolock CJ, Maeda J, Infante V, Ané JM, Pierce NE, Pringle A. Carnivorous Nepenthes Pitchers with Less Acidic Fluid House Nitrogen-Fixing Bacteria. Appl Environ Microbiol 2023; 89:e0081223. [PMID: 37338413 PMCID: PMC10370301 DOI: 10.1128/aem.00812-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 05/24/2023] [Indexed: 06/21/2023] Open
Abstract
Carnivorous pitcher plants are uniquely adapted to nitrogen limitation, using pitfall traps to acquire nutrients from insect prey. Pitcher plants in the genus Sarracenia may also use nitrogen fixed by bacteria inhabiting the aquatic microcosms of their pitchers. Here, we investigated whether species of a convergently evolved pitcher plant genus, Nepenthes, might also use bacterial nitrogen fixation as an alternative strategy for nitrogen capture. First, we constructed predicted metagenomes of pitcher organisms from three species of Singaporean Nepenthes using 16S rRNA sequence data and correlated predicted nifH abundances with metadata. Second, we used gene-specific primers to amplify and quantify the presence or absence of nifH directly from 102 environmental samples and identified potential diazotrophs with significant differential abundance in samples that also had positive nifH PCR tests. Third, we analyzed nifH in eight shotgun metagenomes from four additional Bornean Nepenthes species. Finally, we conducted an acetylene reduction assay using greenhouse-grown Nepenthes pitcher fluids to confirm nitrogen fixation is indeed possible within the pitcher habitat. Results show active acetylene reduction can occur in Nepenthes pitcher fluid. Variation in nifH from wild samples correlates with Nepenthes host species identity and pitcher fluid acidity. Nitrogen-fixing bacteria are associated with more neutral fluid pH, while endogenous Nepenthes digestive enzymes are most active at low fluid pH. We hypothesize Nepenthes species experience a trade-off in nitrogen acquisition; when fluids are acidic, nitrogen is primarily acquired via plant enzymatic degradation of insects, but when fluids are neutral, Nepenthes plants take up more nitrogen via bacterial nitrogen fixation. IMPORTANCE Plants use different strategies to obtain the nutrients that they need to grow. Some plants access their nitrogen directly from the soil, while others rely on microbes to access the nitrogen for them. Carnivorous pitcher plants generally trap and digest insect prey, using plant-derived enzymes to break down insect proteins and generate a large portion of the nitrogen that they subsequently absorb. In this study, we present results suggesting that bacteria living in the fluids formed by Nepenthes pitcher plants can fix nitrogen directly from the atmosphere, providing an alternative pathway for plants to access nitrogen. These nitrogen-fixing bacteria are only likely to be present when pitcher plant fluids are not strongly acidic. Interestingly, the plant's enzymes are known to be more active under strongly acidic conditions. We propose a potential trade-off where pitcher plants sometimes access nitrogen using their own enzymes to digest prey and at other times take advantage of bacterial nitrogen fixation.
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Affiliation(s)
- Leonora S. Bittleston
- Department of Biological Sciences, Boise State University, Boise, Idaho, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Charles J. Wolock
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Junko Maeda
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Valentina Infante
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Agronomy, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Naomi E. Pierce
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA
| | - Anne Pringle
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Botany, University of Wisconsin—Madison, Madison, Wisconsin, USA
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Sharma N, Chwastek D, Dwivedi DJ, Schlechte J, Yu IL, McDonald B, Arora J, Cani E, Eng M, Engelberts D, Kuhar E, Medeiros SK, Bourque SL, Cepinskas G, Gill SE, Jahandideh F, Macala KF, Panahi S, Pape C, Sontag D, Sunohara-Neilson J, Fergusson DA, Fox-Robichaud AE, Liaw PC, Lalu MM, Mendelson AA. Development and characterization of a fecal-induced peritonitis model of murine sepsis: results from a multi-laboratory study and iterative modification of experimental conditions. Intensive Care Med Exp 2023; 11:45. [PMID: 37460911 DOI: 10.1186/s40635-023-00533-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/04/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Preclinical sepsis models have been criticized for their inability to recapitulate human sepsis and suffer from methodological shortcomings that limit external validity and reproducibility. The National Preclinical Sepsis Platform (NPSP) is a consortium of basic science researchers, veterinarians, and stakeholders in Canada undertaking standardized multi-laboratory sepsis research to increase the efficacy and efficiency of bench-to-bedside translation. In this study, we aimed to develop and characterize a 72-h fecal-induced peritonitis (FIP) model of murine sepsis conducted in two independent laboratories. The experimental protocol was optimized by sequentially modifying dose of fecal slurry and timing of antibiotics in an iterative fashion, and then repeating the experimental series at site 1 and site 2. RESULTS Escalating doses of fecal slurry (0.5-2.5 mg/g) resulted in increased disease severity, as assessed by the modified Murine Sepsis Score (MSS). However, the MSS was poorly associated with progression to death during the experiments, and mice were found dead without elevated MSS scores. Administration of early antibiotics within 4 h of inoculation rescued the animals from sepsis compared with late administration of antibiotics after 12 h, as evidenced by 100% survival and reduced bacterial load in peritoneum and blood in the early antibiotic group. Site 1 and site 2 had statistically significant differences in mortality (60% vs 88%; p < 0.05) for the same dose of fecal slurry (0.75 mg/g) and marked differences in body temperature between groups. CONCLUSIONS We demonstrate a systematic approach to optimizing a 72-h FIP model of murine sepsis for use in multi-laboratory studies. Alterations to experimental conditions, such as dose of fecal slurry and timing of antibiotics, have clear impact on outcomes. Differences in mortality between sites despite rigorous standardization warrants further investigations to better understand inter-laboratory variation and methodological design in preclinical studies.
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Affiliation(s)
- Neha Sharma
- Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, Canada
- Department of Medical Sciences, McMaster University, Hamilton, ON, Canada
| | - Damian Chwastek
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Dhruva J Dwivedi
- Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Jared Schlechte
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Critical Care Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Ian-Ling Yu
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Critical Care Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Braedon McDonald
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Critical Care Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jaskirat Arora
- Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, Canada
- Department of Medical Sciences, McMaster University, Hamilton, ON, Canada
| | - Erblin Cani
- Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, Canada
- Department of Medical Sciences, McMaster University, Hamilton, ON, Canada
| | - Mikaela Eng
- Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, Canada
- Department of Medical Sciences, McMaster University, Hamilton, ON, Canada
| | - Doreen Engelberts
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Eva Kuhar
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Sarah K Medeiros
- Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, Canada
- Department of Medical Sciences, McMaster University, Hamilton, ON, Canada
| | - Stephane L Bourque
- Department of Anesthesiology and Pain Medicine, University of Alberta, Edmonton, AB, Canada
| | - Gediminas Cepinskas
- Centre for Critical Illness Research, Lawson Health Research Institute, London, ON, Canada
- Department of Medical Biophysics, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Sean E Gill
- Centre for Critical Illness Research, Lawson Health Research Institute, London, ON, Canada
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Forough Jahandideh
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Kimberly F Macala
- Department of Anesthesiology and Pain Medicine, University of Alberta, Edmonton, AB, Canada
- Department of Critical Care Medicine, Royal Alexandra Hospital, University of Alberta, Edmonton, AB, Canada
| | - Sareh Panahi
- Department of Anesthesiology and Pain Medicine, University of Alberta, Edmonton, AB, Canada
| | - Cynthia Pape
- Centre for Critical Illness Research, Lawson Health Research Institute, London, ON, Canada
| | - David Sontag
- Department of Medicine, Section of Critical Care Medicine, Rady Faculty of Health Sciences, University of Manitoba, Health Sciences Centre Winnipeg, Rm GF-234, 820 Sherbrook St, Winnipeg, MB, R3A 1R9, Canada
| | | | - Dean A Fergusson
- Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Clinical Epidemiology Program, Blueprint Translational Group, Ottawa Hospital Research Institute, 501 Smyth Road, P.O. Box 201B, Ottawa, ON, K1H 8L6, Canada
| | - Alison E Fox-Robichaud
- Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Patricia C Liaw
- Thrombosis and Atherosclerosis Research Institute, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Manoj M Lalu
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.
- Clinical Epidemiology Program, Blueprint Translational Group, Ottawa Hospital Research Institute, 501 Smyth Road, P.O. Box 201B, Ottawa, ON, K1H 8L6, Canada.
- Department of Anesthesiology and Pain Medicine, The Ottawa Hospital, Ottawa, ON, Canada.
| | - Asher A Mendelson
- Department of Medicine, Section of Critical Care Medicine, Rady Faculty of Health Sciences, University of Manitoba, Health Sciences Centre Winnipeg, Rm GF-234, 820 Sherbrook St, Winnipeg, MB, R3A 1R9, Canada.
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Evariste L, Lamas B, Ellero-Simatos S, Khoury L, Cartier C, Gaultier E, Chassaing B, Feltin N, Devoille L, Favre G, Audebert M, Houdeau E. A 90-day oral exposure to food-grade gold at relevant human doses impacts the gut microbiota and the local immune system in a sex-dependent manner in mice. Part Fibre Toxicol 2023; 20:27. [PMID: 37443115 DOI: 10.1186/s12989-023-00539-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/06/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Edible gold (Au) is commonly used as a food additive (E175 in EU) for confectionery and cake decorations, coatings and in beverages. Food-grade gold is most often composed of thin Au sheets or flakes exhibiting micro- and nanometric dimensions in their thickness. Concerns about the impact of mineral particles used as food additives on human health are increasing with respect to the particular physico-chemical properties of nanosized particles, which enable them to cross biological barriers and interact with various body cell compartments. In this study, male and female mice were exposed daily to E175 or an Au nanomaterial (Ref-Au) incorporated into food at relevant human dose for 90 days in order to determine the potential toxicity of edible gold. RESULTS E175 or Ref-Au exposure in mice did not induce any histomorphological damage of the liver, spleen or intestine, nor any genotoxic effects in the colon and liver despite an apparent higher intestinal absorption level of Au particles in mice exposed to Ref-Au compared to the E175 food additive. No changes in the intestinal microbiota were reported after treatment with Ref-Au, regardless of sex. In contrast, after E175 exposure, an increase in the Firmicutes/Bacteroidetes ratio and in the abundance of Proteobacteria were observed in females, while a decrease in the production of short-chain fatty acids occurred in both sexes. Moreover, increased production of IL-6, TNFα and IL-1β was observed in the colon of female mice at the end of the 90-day exposure to E175, whereas, decreased IL-6, IL-1β, IL-17 and TGFβ levels were found in the male colon. CONCLUSIONS These results revealed that a 90-day exposure to E175 added to the diet alters the gut microbiota and intestinal immune response in a sex-dependent manner in mice. Within the dose range of human exposure to E175, these alterations remained low in both sexes and mostly appeared to be nontoxic. However, at the higher dose, the observed gut dysbiosis and the intestinal low-grade inflammation in female mice could favour the occurrence of metabolic disorders supporting the establishment of toxic reference values for the safe use of gold as food additive.
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Affiliation(s)
- Lauris Evariste
- Toxalim UMR1331 (Research Centre in Food Toxicology), Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Bruno Lamas
- Toxalim UMR1331 (Research Centre in Food Toxicology), Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Sandrine Ellero-Simatos
- Toxalim UMR1331 (Research Centre in Food Toxicology), Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | | | - Christel Cartier
- Toxalim UMR1331 (Research Centre in Food Toxicology), Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Eric Gaultier
- Toxalim UMR1331 (Research Centre in Food Toxicology), Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Benoit Chassaing
- INSERM U1016, Team "Mucosal Microbiota in Chronic Inflammatory Diseases", CNRS UMR 8104, Université de Paris, Paris, France
| | | | | | | | - Marc Audebert
- Toxalim UMR1331 (Research Centre in Food Toxicology), Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
- PrediTox, Toulouse, France
| | - Eric Houdeau
- Toxalim UMR1331 (Research Centre in Food Toxicology), Toulouse University, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France.
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Turpin V, Schaffhauser M, Thabault M, Aubert A, Joffre C, Balado E, Longueville JE, Francheteau M, Burucoa C, Pichon M, Layé S, Jaber M. Mice prenatally exposed to valproic acid do not show autism-related disorders when fed with polyunsaturated fatty acid-enriched diets. Sci Rep 2023; 13:11235. [PMID: 37433863 DOI: 10.1038/s41598-023-38423-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/07/2023] [Indexed: 07/13/2023] Open
Abstract
Dietary supplementations with n-3 polyunsaturated fatty acid (PUFA) have been explored in autism spectrum disorder (ASD) but their efficiency and potential in ameliorating cardinal symptoms of the disease remain elusive. Here, we compared a n-3 long-chain (LC) PUFA dietary supplementation (n-3 supp) obtained from fatty fish with a n-3 PUFA precursor diet (n-3 bal) obtained from plant oils in the valproic acid (VPA, 450 mg/kg at E12.5) ASD mouse model starting from embryonic life, throughout lactation and until adulthood. Maternal and offspring behaviors were investigated as well as several VPA-induced ASD biological features: cerebellar Purkinje cell (PC) number, inflammatory markers, gut microbiota, and peripheral and brain PUFA composition. Developmental milestones were delayed in the n-3 supp group compared to the n-3 bal group in both sexes. Whatever the diet, VPA-exposed offspring did not show ASD characteristic alterations in social behavior, stereotypies, PC number, or gut microbiota dysbiosis while global activity, gait, peripheral and brain PUFA levels as well as cerebellar TNF-alpha levels were differentially altered by diet and treatment according to sex. The current study provides evidence of beneficial effects of n-3 PUFA based diets, including one without LCPUFAs, on preventing several behavioral and cellular symptoms related to ASD.
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Affiliation(s)
- Valentine Turpin
- Université de Poitiers, Inserm, Laboratoire de Neurosciences Expérimentales et Cliniques, Poitiers, France
| | - Maud Schaffhauser
- Université de Poitiers, Inserm, Laboratoire de Neurosciences Expérimentales et Cliniques, Poitiers, France
| | - Mathieu Thabault
- Université de Poitiers, Inserm, Laboratoire de Neurosciences Expérimentales et Cliniques, Poitiers, France
| | - Agnès Aubert
- Université de Bordeaux, INRAE, Bordeaux INP, NutriNeurO, UMR 1286, Bordeaux, France
| | - Corinne Joffre
- Université de Bordeaux, INRAE, Bordeaux INP, NutriNeurO, UMR 1286, Bordeaux, France
| | - Eric Balado
- Université de Poitiers, Inserm, Laboratoire de Neurosciences Expérimentales et Cliniques, Poitiers, France
| | - Jean-Emmanuel Longueville
- Université de Poitiers, Inserm, Laboratoire de Neurosciences Expérimentales et Cliniques, Poitiers, France
| | - Maureen Francheteau
- Université de Poitiers, Inserm, Laboratoire de Neurosciences Expérimentales et Cliniques, Poitiers, France
| | - Christophe Burucoa
- Université de Poitiers, Inserm, PHAR2, Poitiers, France
- CHU de Poitiers, Poitiers, France
| | - Maxime Pichon
- Université de Poitiers, Inserm, PHAR2, Poitiers, France
- CHU de Poitiers, Poitiers, France
| | - Sophie Layé
- Université de Bordeaux, INRAE, Bordeaux INP, NutriNeurO, UMR 1286, Bordeaux, France
| | - Mohamed Jaber
- Université de Poitiers, Inserm, Laboratoire de Neurosciences Expérimentales et Cliniques, Poitiers, France.
- CHU de Poitiers, Poitiers, France.
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Hugon AM, Golos TG. Non-human primate models for understanding the impact of the microbiome on pregnancy and the female reproductive tract†. Biol Reprod 2023; 109:1-16. [PMID: 37040316 PMCID: PMC10344604 DOI: 10.1093/biolre/ioad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 04/06/2023] [Accepted: 04/06/2023] [Indexed: 04/12/2023] Open
Abstract
The microbiome has been shown, or implicated to be involved, in multiple facets of human health and disease, including not only gastrointestinal health but also metabolism, immunity, and neurology. Although the predominant focus of microbiome research has been on the gut, other microbial communities such as the vaginal or cervical microbiome are likely involved in physiological homeostasis. Emerging studies also aim to understand the role of different microbial niches, such as the endometrial or placental microbial communities, on the physiology and pathophysiology of reproduction, including their impact on reproductive success and the etiology of adverse pregnancy outcomes (APOs). The study of the microbiome during pregnancy, specifically how changes in maternal microbial communities can lead to dysfunction and disease, can advance the understanding of reproductive health and the etiology of APOs. In this review, we will discuss the current state of non-human primate (NHP) reproductive microbiome research, highlight the progress with NHP models of reproduction, and the diagnostic potential of microbial alterations in a clinical setting to promote pregnancy health. NHP reproductive biology studies have the potential to expand the knowledge and understanding of female reproductive tract microbial communities and host-microbe or microbe-microbe interactions associated with reproductive health through sequencing and analysis. Furthermore, in this review, we aim to demonstrate that macaques are uniquely suited as high-fidelity models of human female reproductive pathology.
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Affiliation(s)
- Anna Marie Hugon
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Thaddeus G Golos
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI, USA
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, USA
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129
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Nagarajan A, Scoggin K, Gupta J, Threadgill DW, Andrews-Polymenis HL. Using the collaborative cross to identify the role of host genetics in defining the murine gut microbiome. MICROBIOME 2023; 11:149. [PMID: 37420306 PMCID: PMC10329326 DOI: 10.1186/s40168-023-01552-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/18/2023] [Indexed: 07/09/2023]
Abstract
BACKGROUND The human gut microbiota is a complex community comprised of trillions of bacteria and is critical for the digestion and absorption of nutrients. Bacterial communities of the intestinal microbiota influence the development of several conditions and diseases. We studied the effect of host genetics on gut microbial composition using Collaborative Cross (CC) mice. CC mice are a panel of mice that are genetically diverse across strains, but genetically identical within a given strain allowing repetition and deeper analysis than is possible with other collections of genetically diverse mice. RESULTS 16S rRNA from the feces of 167 mice from 28 different CC strains was sequenced and analyzed using the Qiime2 pipeline. We observed a large variance in the bacterial composition across CC strains starting at the phylum level. Using bacterial composition data, we identified 17 significant Quantitative Trait Loci (QTL) linked to 14 genera on 9 different mouse chromosomes. Genes within these intervals were analyzed for significant association with pathways and the previously known human GWAS database using Enrichr analysis and Genecards database. Multiple host genes involved in obesity, glucose homeostasis, immunity, neurological diseases, and many other protein-coding genes located in these regions may play roles in determining the composition of the gut microbiota. A subset of these CC mice was infected with Salmonella Typhimurium. Using infection outcome data, an increase in abundance of genus Lachnospiraceae and decrease in genus Parasutterella correlated with positive health outcomes after infection. Machine learning classifiers accurately predicted the CC strain and the infection outcome using pre-infection bacterial composition data from the feces. CONCLUSION Our study supports the hypothesis that multiple host genes influence the gut microbiome composition and homeostasis, and that certain organisms may influence health outcomes after S. Typhimurium infection. Video Abstract.
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Affiliation(s)
- Aravindh Nagarajan
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX USA
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, TX USA
| | - Kristin Scoggin
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX USA
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, TX USA
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX USA
| | - Jyotsana Gupta
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, TX USA
| | - David W. Threadgill
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX USA
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX USA
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX USA
- Department of Biochemistry & Biophysics and Department of Nutrition, Texas A&M University, College Station, TX USA
| | - Helene L. Andrews-Polymenis
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX USA
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, TX USA
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Song WJ, Gao J, Huang JW, Liu Y, Long Z, He LY. Is type III prostatitis also associated with bacterial infection? Front Cell Infect Microbiol 2023; 13:1189081. [PMID: 37465760 PMCID: PMC10351278 DOI: 10.3389/fcimb.2023.1189081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/16/2023] [Indexed: 07/20/2023] Open
Abstract
Objective To explore whether type III prostatitis is related to bacterial infection by detecting the composition and function of microorganisms in expressed prostatic secretion (EPS) of patients with chronic prostatitis (CP) and healthy people. Methods According to the inclusion and exclusion criteria, 57 subjects were included in our study, divided into the healthy group, type II prostatitis group, and type III prostatitis group. 16s rRNA sequencing technique was used to detect and analyze the microbial composition of EPS in each group. Additionally, the metagenomics sequencing technique was used to further explore the function of different bacteria in the type III prostatitis group. Data analysis was performed by bioinformatics software, and the results were statistically significant when P<0.05. Results Many microorganisms exist in EPS in both CP patients and healthy populations. However, the relative abundance of Pseudomonas, Haemophilus, Sneathia, Allobaculum, and Enterococcus in CP patients (including type II and III) were significantly different. Still, the relative abundance of different bacteria in type II prostatitis patients was much higher than in type III. The metagenomics sequencing results for the type III prostatitis group showed that the different bacteria had certain biological functions. Conclusion Based on our sequencing results and previous studies, we suggest that type III prostatitis may also be caused by bacterial infection.
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Affiliation(s)
- Wei-Jie Song
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Sexual Health Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jun Gao
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Sexual Health Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ji-Wei Huang
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Sexual Health Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yuan Liu
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Sexual Health Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhi Long
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Sexual Health Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Le-Ye He
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Sexual Health Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
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Fu L, Yu Y, Yu F, Xiao J, Fang H, Li W, Xie Z, Zhang F, Lin S. Profiles and spatial distributions of heavy metals, microbial communities, and metal resistance genes in sediments from an urban river. Front Microbiol 2023; 14:1188681. [PMID: 37455724 PMCID: PMC10340544 DOI: 10.3389/fmicb.2023.1188681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/29/2023] [Indexed: 07/18/2023] Open
Abstract
The occurrence and propagation of resistance genes due to exposure to heavy metals (HMs) in rivers is an emerging environmental issue. Little is known about resistance genes in microbial communities in river sediments with low HM concentrations. The profiles and spatial distributions of HMs, the microbial community, and metal resistance genes (MRGs) were analyzed in sediment samples from the Zhilong River basin in Yangjiang city, near the Pearl River Delta. Concentrations of copper (Cu), cadmium (Cd), lead (Pb), chromium (Cr), and nickel (Ni) were relatively low compared with those in other urban river sediments in China. HM chemical composition and fractions and the structure of the microbial community varied along the main channel, but the composition and abundance of MRGs were relatively homogeneous. Variations in HMs and microbial communities in mid- to upstream areas were related to the presence of tributaries, whose inputs were one of the major factors affecting HM chemical fractions and genera structure in mainstream sediments. There were no significant correlations (p < 0.05) between HM concentrations, bacterial communities, and the MRG profiles; thus, HM concentrations were not the main factor affecting MRGs in sediments. These results contribute to understanding the propagation of MRGs in urban rivers in developing cities.
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Tang K, Tao L, Wang Y, Wang Q, Fu C, Chen B, Zhang Z, Fu Y. Temporal Variations in the Gut Microbiota of the Globally Endangered Sichuan Partridge (Arborophila rufipectus): Implications for Adaptation to Seasonal Dietary Change and Conservation. Appl Environ Microbiol 2023; 89:e0074723. [PMID: 37272815 PMCID: PMC10305732 DOI: 10.1128/aem.00747-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 06/06/2023] Open
Abstract
Host-associated microbiotas are known to influence host health by aiding digestion, metabolism, nutrition, physiology, immune function, and pathogen resistance. Although an increasing number of studies have investigated the avian microbiome, there is a lack of research on the gut microbiotas of wild birds, especially endangered pheasants. Owing to the difficulty of characterizing the dynamics of dietary composition, especially in omnivores, how the gut microbiotas of birds respond to seasonal dietary changes remains poorly understood. The Sichuan partridge (Arborophila rufipectus) is an endangered pheasant species with a small population endemic to the mountains of southwest China. Here, 16S rRNA sequencing and Tax4Fun were used to characterize and compare community structure and functions of the gut microbiota in the Sichuan partridges across three critical periods of their annual life cycle (breeding, postbreeding wandering, and overwintering). We found that the microbial communities were dominated by Firmicutes, Proteobacteria, Actinobacteria, and Cyanobacteria throughout the year. Diversity of the gut microbiotas was highest during postbreeding wandering and lowest during the overwintering periods. Seasonal dietary changes and reassembly of the gut microbial community occurred consistently. Composition, diversity, and functions of the gut microbiota exhibited diet-associated variations, which might facilitate host adaptation to diverse diets in response to environmental shifts. Moreover, 28 potential pathogenic genera were detected, and their composition differed significantly between the three periods. Investigation of the wild bird gut microbiota dynamics has enhanced our understanding of diet-microbiota associations over the annual life cycle of birds, aiding in the integrative conservation of this endangered bird. IMPORTANCE Characterizing the gut microbiotas of wild birds across seasons will shed light on their annual life cycle. Due to sampling difficulties and the lack of detailed dietary information, studies on how the gut microbiota adapts to seasonal dietary changes of wild birds are scarce. Based on more detailed dietary composition, we found a seasonal reshaping pattern of the gut microbiota of Sichuan partridges corresponding to their seasonal dietary changes. The variation in diet and gut microbiota potentially facilitated the diversity of dietary niches of this endangered pheasant, revealing a seasonal diet-microbiota association across the three periods of the annual cycle. In addition, identifying a variety of potentially pathogenic bacterial genera aids in managing the health and improving survival of Sichuan partridges. Incorporation of microbiome research in the conservation of endangered species contributes to our comprehensive understanding the diet-host-microbiota relationship in wild birds and refinement of conservation practices.
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Affiliation(s)
- Keyi Tang
- Ministry of Education Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Ling Tao
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Yufeng Wang
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Qiong Wang
- Ministry of Education Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Changkun Fu
- Ministry of Education Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Benping Chen
- Laojunshan National Nature Reserve Administration, Pingshan, Sichuan, China
| | - Zhengwang Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yiqiang Fu
- Ministry of Education Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
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Kawash J, Oudemans PV, Erndwein L, Polashock JJ. Assessment and comparison of rhizosphere communities in cultivated Vaccinium spp. provide a baseline for study of causative agents in decline. FRONTIERS IN PLANT SCIENCE 2023; 14:1173023. [PMID: 37441173 PMCID: PMC10333580 DOI: 10.3389/fpls.2023.1173023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/29/2023] [Indexed: 07/15/2023]
Abstract
It has long been recognized that the community of organisms associated with plant roots is a critical component of the phytobiome and can directly or indirectly contribute to the overall health of the plant. The rhizosphere microbial community is influenced by a number of factors including the soil type, the species of plants growing in those soils, and in the case of cultivated plants, the management practices associated with crop production. Vaccinium species, such as highbush blueberry and American cranberry, are woody perennials that grow in sandy, acidic soils with low to moderate levels of organic matter and a paucity of nutrients. When properly maintained, fields planted with these crops remain productive for many years. In some cases, however, yields and fruit quality decline over time, and it is suspected that degenerating soil health and/or changes in the rhizosphere microbiome are contributing factors. Determining the assemblage of bacterial and fungal microorganisms typically associated with the rhizosphere of these crops is a critical first step toward addressing the complex issue of soil health. We hypothesized that since blueberry and cranberry are in the same genus and grow in similar soils, that their associated rhizosphere microbial communities would be similar to each other. We analyzed the eukaryotic (primarily fungal) and bacterial communities from the rhizosphere of representative blueberry and cranberry plants growing in commercial fields in New Jersey. The data presented herein show that while the bacterial communities between the crops is very similar, the fungal communities associated with each crop are quite different. These results provide a framework for examining microbial components that might contribute to the health of Vaccinium spp. crops in New Jersey and other parts of the northeastern U.S.
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Affiliation(s)
- Joseph Kawash
- USDA-ARS, Genetic Improvement of Fruits and Vegetables Laboratory, Chatsworth, NJ, United States
| | - Peter V. Oudemans
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, United States
| | - Lindsay Erndwein
- Oak Ridge Institute for Science and Education (ORISE) Postdoctoral Scholar, USDA-ARS, Genetic Improvement of Fruits and Vegetables Laboratory, Chatsworth, NJ, United States
| | - James J. Polashock
- USDA-ARS, Genetic Improvement of Fruits and Vegetables Laboratory, Chatsworth, NJ, United States
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Aguado-Norese C, Cárdenas V, Gaete A, Mandakovic D, Vasquez-Dean J, Hodar C, Pfeiffer M, Gonzalez M. Topsoil and subsoil bacterial community assemblies across different drainage conditions in a mountain environment. Biol Res 2023; 56:35. [PMID: 37355658 DOI: 10.1186/s40659-023-00445-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 06/08/2023] [Indexed: 06/26/2023] Open
Abstract
BACKGROUND High mountainous environments are of particular interest as they play an essential role for life and human societies, while being environments which are highly vulnerable to climate change and land use intensification. Despite this, our knowledge of high mountain soils in South America and their microbial community structure is strikingly scarce, which is of more concern considering the large population that depends on the ecosystem services provided by these areas. Conversely, the Central Andes, located in the Mediterranean region of Chile, has long been studied for its singular flora, whose diversity and endemism has been attributed to the particular geological history and pronounced environmental gradients in short distances. Here, we explore soil properties and microbial community structure depending on drainage class in a well-preserved Andean valley on the lower alpine vegetation belt (~2500 m a.s.l.) at 33.5˚S. This presents an opportunity to determine changes in the overall bacterial community structure across different types of soils and their distinct layers in a soil depth profile of a highly heterogeneous environment. METHODS Five sites closely located (<1.5 km) and distributed in a well preserved Andean valley on the lower alpine vegetation belt (~2500 m a.s.l.) at 33.5˚S were selected based on a pedological approach taking into account soil types, drainage classes and horizons. We analyzed 113 soil samples using high-throughput sequencing of the 16S rRNA gene to describe bacterial abundance, taxonomic composition, and co-occurrence networks. RESULTS Almost 18,427 Amplicon Sequence Variant (ASVs) affiliated to 55 phyla were detected. The bacterial community structure within the same horizons were very similar validating the pedological sampling approach. Bray-Curtis dissimilarity analysis revealed that the structure of bacterial communities in superficial horizons (topsoil) differed from those found in deep horizons (subsoil) in a site-specific manner. However, an overall closer relationship was observed between topsoil as opposed to between subsoil microbial communities. Alpha diversity of soil bacterial communities was higher in topsoil, which also showed more bacterial members interacting and with higher average connectivity compared to subsoils. Finally, abundances of specific taxa could be considered as biological markers in the transition from topsoil to subsoil horizons, like Fibrobacterota, Proteobacteria, Bacteroidota for shallower soils and Chloroflexi, Latescibacterota and Nitrospirota for deeper soils. CONCLUSIONS The results indicate the importance of the soil drainage conditions for the bacterial community composition, suggesting that information of both structure and their possible ecological relationships, might be useful in clarifying the location of the edge of the topsoil-subsoil transition in mountainous environments.
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Affiliation(s)
- Constanza Aguado-Norese
- Millennium Institute Center for Genome Regulation, Santiago, 7830490, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Macul, Chile
| | - Valentina Cárdenas
- Departamento de Ingeniería y Suelos, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
| | - Alexis Gaete
- Millennium Institute Center for Genome Regulation, Santiago, 7830490, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Macul, Chile
| | - Dinka Mandakovic
- GEMA Center for Genomics, Ecology and Environment, Universidad Mayor, Santiago, Chile
| | - Javiera Vasquez-Dean
- Millennium Institute Center for Genome Regulation, Santiago, 7830490, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Macul, Chile
| | - Christian Hodar
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Macul, Chile
- Bioinformatic and Biostatistic Laboratory for Functional Genomics, INTA-Universidad de Chile, Macul, Chile
| | - Marco Pfeiffer
- Departamento de Ingeniería y Suelos, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile.
| | - Mauricio Gonzalez
- Millennium Institute Center for Genome Regulation, Santiago, 7830490, Chile.
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Macul, Chile.
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Schul MD, Anastasious DE, Spiers LJ, Meyer JL, Frazer TK, Brown AL. Concordance of microbial and visual health indicators of white-band disease in nursery reared Caribbean coral Acropora cervicornis. PeerJ 2023; 11:e15170. [PMID: 37361046 PMCID: PMC10290447 DOI: 10.7717/peerj.15170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 03/13/2023] [Indexed: 06/28/2023] Open
Abstract
Background Coral diseases are one of the leading causes of declines in coral populations. In the Caribbean, white band disease (WBD) has led to a substantial loss of Acropora corals. Although the etiologies of this disease have not been well described, characterizing the coral microbiome during the transition from a healthy to diseased state is critical for understanding disease progression. Coral nurseries provide unique opportunities to further understand the microbial changes associated with diseased and healthy corals, because corals are monitored over time. We characterized the microbiomes before and during an outbreak of WBD in Acropora cervicornis reared in an ocean nursery in Little Cayman, CI. We asked (1) do healthy corals show the same microbiome over time (before and during a disease outbreak) and (2) are there disease signatures on both lesioned and apparently healthy tissues on diseased coral colonies? Methods Microbial mucus-tissue slurries were collected from healthy coral colonies in 2017 (before the disease) and 2019 (during the disease onset). Diseased colonies were sampled at two separate locations on an individual coral colony: at the interface of Disease and ∼10 cm away on Apparently Healthy coral tissue. We sequenced the V4 region of the 16S rRNA gene to characterize bacterial and archaeal community composition in nursery-reared A. cervicornis. We assessed alpha diversity, beta diversity, and compositional differences to determine differences in microbial assemblages across health states (2019) and healthy corals between years (2017 and 2019). Results Microbial communities from healthy A. cervicornis from 2017 (before disease) and 2019 (after disease) did not differ significantly. Additionally, microbial communities from Apparently Healthy samples on an otherwise diseased coral colony were more similar to Healthy colonies than to the diseased portion on the same colony for both alpha diversity and community composition. Microbial communities from Diseased tissues had significantly higher alpha diversity than both Healthy and Apparently Healthy tissues but showed no significant difference in beta-diversity dispersion. Our results show that at the population scale, Healthy and Apparently Healthy coral tissues are distinct from microbial communities associated with Diseased tissues. Furthermore, our results suggest stability in Little Cayman nursery coral microbiomes over time. We show healthy Caymanian nursery corals had a stable microbiome over a two-year period, an important benchmark for evaluating coral health via their microbiome.
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Affiliation(s)
- Monica D. Schul
- Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, FL, United States of America
| | - Dagny-Elise Anastasious
- Little Cayman Research Center, Central Caribbean Marine Institute, Little Cayman, Cayman Islands
| | - Lindsay J. Spiers
- School of Fisheries, University of Florida, Gainesville, FL, United States of America
- Fish & Wildlife Research Institute, Florida Fish & Wildlife Conservation Commission, Marathon, FL, United States of America
| | - Julie L. Meyer
- Department of Soil, Water, and Ecosystem Sciences, University of Florida, Gainesville, FL, United States of America
| | - Thomas K. Frazer
- College of Marine Science, University of South Florida, St. Petersburg, FL, United States of America
| | - Anya L. Brown
- School of Natural Resources and Environment, University of Florida, Gainesville, FL, United States of America
- Bodega Marine Lab, Department of Evolution and Ecology, University of California, Davis, Bodega Bay, CA, United States of America
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Gu W, Koh H, Jang H, Lee B, Kang B. MiSurv: an Integrative Web Cloud Platform for User-Friendly Microbiome Data Analysis with Survival Responses. Microbiol Spectr 2023; 11:e0505922. [PMID: 37039671 PMCID: PMC10269532 DOI: 10.1128/spectrum.05059-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 03/12/2023] [Indexed: 04/12/2023] Open
Abstract
Investigators have studied the treatment effects on human health or disease, the treatment effects on human microbiome, and the roles of the microbiome on human health or disease. Especially, in a clinical trial, investigators commonly trace disease status over a lengthy period to survey the sequential disease progression for different treatment groups (e.g., treatment versus placebo, new treatment versus old treatment). Hence, disease responses are often available in the form of survival (i.e., time-to-event) responses stratified by treatment groups. While the recent web cloud platforms have enabled user-friendly microbiome data processing and analytics, there is currently no web cloud platform to analyze microbiome data with survival responses. Therefore, we introduce here an integrative web cloud platform, called MiSurv, for comprehensive microbiome data analysis with survival responses. IMPORTANCE MiSurv consists of a data processing module and its following four data analytic modules: (i) Module 1: Comparative survival analysis between treatment groups, (ii) Module 2: Comparative analysis in microbial composition between treatment groups, (iii) Module 3: Association testing between microbial composition and survival responses, (iv) Module 4: Prediction modeling using microbial taxa on survival responses. We demonstrate its use through an example trial on the effects of antibiotic use on the survival rate against type 1 diabetes (T1D) onset and gut microbiome composition, respectively, and the effects of the gut microbiome on the survival rate against T1D onset. MiSurv is freely available on our web server (http://misurv.micloud.kr) or can alternatively run on the user's local computer (https://github.com/wg99526/MiSurvGit).
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Affiliation(s)
- Won Gu
- Department of Applied Mathematics and Statistics, The State University of New York, Korea, Incheon, South Korea
| | - Hyunwook Koh
- Department of Applied Mathematics and Statistics, The State University of New York, Korea, Incheon, South Korea
| | - Hyojung Jang
- Department of Applied Mathematics and Statistics, The State University of New York, Korea, Incheon, South Korea
| | - Byungho Lee
- Department of Applied Mathematics and Statistics, The State University of New York, Korea, Incheon, South Korea
| | - Byungkon Kang
- Department of Computer Science, The State University of New York, Korea, Incheon, South Korea
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Finlayson-Trick E, Nearing J, Fischer JAJ, Ma Y, Wang S, Krouen H, Goldfarb DM, Karakochuk CD. The Effect of Oral Iron Supplementation on Gut Microbial Composition: a Secondary Analysis of a Double-Blind, Randomized Controlled Trial among Cambodian Women of Reproductive Age. Microbiol Spectr 2023; 11:e0527322. [PMID: 37199608 PMCID: PMC10269596 DOI: 10.1128/spectrum.05273-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 04/28/2023] [Indexed: 05/19/2023] Open
Abstract
The World Health Organization recommends untargeted iron supplementation for women of reproductive age (WRA) in countries where anemia prevalence is greater than 40%, such as Cambodia. Iron supplements, however, often have poor bioavailability, so the majority remains unabsorbed in the colon. The gut houses many iron-dependent bacterial enteropathogens; thus, providing iron to individuals may be more harmful than helpful. We examined the effects of two oral iron supplements with differing bioavailability on the gut microbiomes in Cambodian WRA. This study is a secondary analysis of a double-blind, randomized controlled trial of oral iron supplementation in Cambodian WRA. For 12 weeks, participants received ferrous sulfate, ferrous bisglycinate, or placebo. Participants provided stool samples at baseline and 12 weeks. A subset of stool samples (n = 172), representing the three groups, were randomly selected for gut microbial analysis by 16S rRNA gene sequencing and targeted real-time PCR (qPCR). At baseline, 1% of women had iron-deficiency anemia. The most abundant gut phyla were Bacteroidota (45.7%) and Firmicutes (42.1%). Iron supplementation did not alter gut microbial diversity. Ferrous bisglycinate increased the relative abundance of Enterobacteriaceae, and there was a trend towards an increase in the relative abundance of Escherichia-Shigella. qPCR detected an increase in the enteropathogenic Escherichia coli (EPEC) virulence gene, bfpA, in the group that received ferrous sulfate. Thus, iron supplementation did not affect overall gut bacterial diversity in predominantly iron-replete Cambodian WRA, however, evidence does suggest an increase in relative abundance within the broad family Enterobacteriaceae associated with ferrous bisglycinate use. IMPORTANCE To the best of our knowledge, this is the first published study to characterize the effects of oral iron supplementation on the gut microbiomes of Cambodian WRA. Our study found that iron supplementation with ferrous bisglycinate increases the relative abundance of Enterobacteriaceae, which is a family of bacteria that includes many Gram-negative enteric pathogens like Salmonella, Shigella, and Escherichia coli. Using qPCR for additional analysis, we were able to detect genes associated with enteropathogenic E. coli, a type of diarrheagenic E. coli known to be present around the world, including water systems in Cambodia. The current WHO guidelines recommend blanket (untargeted) iron supplementation for Cambodian WRA despite a lack of studies in this population examining iron's effect on the gut microbiome. This study can facilitate future research that may inform evidence-based global practice and policy.
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Affiliation(s)
- Emma Finlayson-Trick
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jacob Nearing
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jordie AJ. Fischer
- Food, Nutrition and Health, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Yvonne Ma
- Food, Nutrition and Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Siyun Wang
- Food, Nutrition and Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hou Krouen
- Helen Keller International, Phnom Penh, Cambodia
| | - David M. Goldfarb
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, BC Children’s and Women’s Hospital and University of British Columbia, Vancouver, British Columbia, Canada
| | - Crystal D. Karakochuk
- Food, Nutrition and Health, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
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Su KW, Cetinbas M, Martin VM, Virkud YV, Seay H, Ndahayo R, Rosow R, Elkort M, Gupta B, Kramer E, Pronchick T, Reuter S, Sadreyev RI, Huang JL, Shreffler WG, Yuan Q. Early infancy dysbiosis in food protein-induced enterocolitis syndrome: A prospective cohort study. Allergy 2023; 78:1595-1604. [PMID: 36635218 PMCID: PMC10534226 DOI: 10.1111/all.15644] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 11/27/2022] [Accepted: 12/14/2022] [Indexed: 01/14/2023]
Abstract
BACKGROUND The microbiome associations of food protein-induced enterocolitis syndrome (FPIES) are understudied. We sought to prospectively define the clinical features of FPIES in a birth cohort, and investigate for the evidence of gut dysbiosis. METHODS We identified children diagnosed with FPIES in the Gastrointestinal Microbiome and Allergic Proctocolitis Study, a healthy infant cohort. Children were assessed and stools were collected at each well child visit. The clinical features of the children with FPIES were summarized. Stool microbiome was analyzed using 16S rRNA sequencing comparing children with and without FPIES. RESULTS Of the 874 children followed up for 3 years, 8 FPIES cases (4 male) were identified, yielding a cumulative incidence of 0.92%. The most common triggers were oat and rice (n = 3, each) followed by milk (n = 2). The children with FPIES were more likely to have family history of food allergy (50% vs. 15.9% among unaffected, p = .03). The average age of disease presentation was 6 months old. During the first 6 months of life, stool from children with FPIES contained significantly less Bifidobacterium adolescentis, but more pathobionts, including Bacteroides spp. (especially Bacteroides fragilis), Holdemania spp., Lachnobacterium spp., and Acinetobacter lwoffii. The short-chain fatty acid (SCFA)-producing Bifidobacterium shunt was expressed significantly less in the stool from FPIES children. CONCLUSIONS In this cohort, the cumulative incidence over the 3-year study period was 0.92%. During the first 6 months of life, children with FPIES had evidence of dysbiosis and SCFA production pathway was expressed less in their stool, which may play an important role in the pathogenesis of FPIES.
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Affiliation(s)
- Kuan-Wen Su
- Department of Pediatrics, Keelung Chang Gung Memorial Hospital, Keelung, Taiwan
- Department of Pediatrics, Chang Gung University, Taoyuan, Taiwan
| | - Murat Cetinbas
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Victoria M. Martin
- Harvard Medical School, Boston, Massachusetts, USA
- Food Allergy Center, Massachusetts General Hospital, Boston, Massachusetts, USA
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Yamini V. Virkud
- Department of Pediatrics, School of Medicine, University of North Carolina, North Carolina, USA
| | - Hannah Seay
- Division of Pediatric Allergy and Immunology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Renata Ndahayo
- Division of Pediatric Allergy and Immunology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Rachael Rosow
- Division of Pediatric Allergy and Immunology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Michael Elkort
- Harvard Medical School, Boston, Massachusetts, USA
- Pediatrics at Newton Wellesley, P.C., Newton, Massachusetts, USA
| | - Brinda Gupta
- Pediatrics at Newton Wellesley, P.C., Newton, Massachusetts, USA
| | - Eileen Kramer
- Pediatrics at Newton Wellesley, P.C., Newton, Massachusetts, USA
| | | | - Susan Reuter
- Pediatrics at Newton Wellesley, P.C., Newton, Massachusetts, USA
| | - Ruslan I. Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Jing-Long Huang
- Department of Pediatrics, Chang Gung University, Taoyuan, Taiwan
- Department of Pediatrics, New Taipei Municipal TuCheng Hospital, New Taipei, Taiwan
| | - Wayne G. Shreffler
- Harvard Medical School, Boston, Massachusetts, USA
- Food Allergy Center, Massachusetts General Hospital, Boston, Massachusetts, USA
- Division of Pediatric Allergy and Immunology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Qian Yuan
- Harvard Medical School, Boston, Massachusetts, USA
- Food Allergy Center, Massachusetts General Hospital, Boston, Massachusetts, USA
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Massachusetts General Hospital, Boston, Massachusetts, USA
- Pediatrics at Newton Wellesley, P.C., Newton, Massachusetts, USA
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Kraut-Cohen J, Zolti A, Rotbart N, Bar-Tal A, Laor Y, Medina S, Shawahna R, Saadi I, Raviv M, Green SJ, Yermiyahu U, Minz D. Short- and long-term effects of continuous compost amendment on soil microbiome community. Comput Struct Biotechnol J 2023; 21:3280-3292. [PMID: 38213903 PMCID: PMC10781717 DOI: 10.1016/j.csbj.2023.05.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/16/2023] [Accepted: 05/28/2023] [Indexed: 01/13/2024] Open
Abstract
Organic amendment, and especially the use of composts, is a well-accepted sustainable agricultural practice. Compost increases soil carbon and microbial biomass, changes enzymatic activity, and enriches soil carbon and nitrogen stocks. However, relatively little is known about the immediate and long-term temporal dynamics of agricultural soil microbial communities following repeated compost applications. Our study was conducted at two field sites: Newe Ya'ar (NY, Mediterranean climate) and Gilat (G, semi-arid climate), both managed organically over 4 years under either conventional fertilization (0, zero compost) or three levels of compost amendment (20, 40 and 60 m3/ha or 2, 4, 6 L/m2). Microbial community dynamics in the soils was examined by high- and low-time-resolution analyses. Annual community composition in compost-amended soils was significantly affected by compost amendment levels in G (first, second and third years) and in NY (third year). Repeated sampling at high resolution (9-10 times over 1 year) showed that at both sites, compost application initially induced a strong shift in microbial communities, lasting for up to 1 month, followed by a milder response. Compost application significantly elevated alpha diversity at both sites, but differed in the compost-dose correlation effect. We demonstrate higher abundance of taxa putatively involved in organic decomposition and characterized compost-related indicator taxa and a compost-derived core microbiome at both sites. Overall, this study describes temporal changes in the ecology of soil microbiomes in response to compost vs. conventional fertilization.
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Affiliation(s)
- Judith Kraut-Cohen
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel
| | - Avihai Zolti
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Nativ Rotbart
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel
- Shamir Research Institute, University of Haifa, Qatzrin, Israel
| | - Asher Bar-Tal
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel
| | - Yael Laor
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization - Volcani Institute, Newe Ya’ar Research Center, Ramat Yishai 30095, Israel
| | - Shlomit Medina
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization - Volcani Institute, Newe Ya’ar Research Center, Ramat Yishai 30095, Israel
| | - Raneen Shawahna
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel
| | - Ibrahim Saadi
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization - Volcani Institute, Newe Ya’ar Research Center, Ramat Yishai 30095, Israel
| | - Michael Raviv
- Institute of Plant Science, Agricultural Research Organization - Volcani Institute, Newe Ya’ar Research Center, Ramat Yishai 30095, Israel
| | - Stefan J. Green
- Genomics and Microbiome Core Facility, Rush University, Chicago, IL, USA
| | - Uri Yermiyahu
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Gilat Research Center, Israel
| | - Dror Minz
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel
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Wang Z, Peters BA, Bryant M, Hanna DB, Schwartz T, Wang T, Sollecito CC, Usyk M, Grassi E, Wiek F, Peter LS, Post WS, Landay AL, Hodis HN, Weber KM, French A, Golub ET, Lazar J, Gustafson D, Sharma A, Anastos K, Clish CB, Burk RD, Kaplan RC, Knight R, Qi Q. Gut microbiota, circulating inflammatory markers and metabolites, and carotid artery atherosclerosis in HIV infection. MICROBIOME 2023; 11:119. [PMID: 37237391 PMCID: PMC10224225 DOI: 10.1186/s40168-023-01566-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 05/05/2023] [Indexed: 05/28/2023]
Abstract
BACKGROUND Alterations in gut microbiota have been implicated in HIV infection and cardiovascular disease. However, how gut microbial alterations relate to host inflammation and metabolite profiles, and their relationships with atherosclerosis, have not been well-studied, especially in the context of HIV infection. Here, we examined associations of gut microbial species and functional components measured by shotgun metagenomics with carotid artery plaque assessed by B-mode carotid artery ultrasound in 320 women with or at high risk of HIV (65% HIV +) from the Women's Interagency HIV Study. We further integrated plaque-associated microbial features with serum proteomics (74 inflammatory markers measured by the proximity extension assay) and plasma metabolomics (378 metabolites measured by liquid chromatography tandem mass spectrometry) in relation to carotid artery plaque in up to 433 women. RESULTS Fusobacterium nucleatum, a potentially pathogenic bacteria, was positively associated with carotid artery plaque, while five microbial species (Roseburia hominis, Roseburia inulinivorans, Johnsonella ignava, Odoribacter splanchnicus, Clostridium saccharolyticum) were inversely associated with plaque. Results were consistent between women with and without HIV. Fusobacterium nucleatum was positively associated with several serum proteomic inflammatory markers (e.g., CXCL9), and the other plaque-related species were inversely associated with proteomic inflammatory markers (e.g., CX3CL1). These microbial-associated proteomic inflammatory markers were also positively associated with plaque. Associations between bacterial species (especially Fusobacterium nucleatum) and plaque were attenuated after further adjustment for proteomic inflammatory markers. Plaque-associated species were correlated with several plasma metabolites, including the microbial metabolite imidazole-propionate (ImP), which was positively associated with plaque and several pro-inflammatory markers. Further analysis identified additional bacterial species and bacterial hutH gene (encoding enzyme histidine ammonia-lyase in ImP production) associated with plasma ImP levels. A gut microbiota score based on these ImP-associated species was positively associated with plaque and several pro-inflammatory markers. CONCLUSION Among women living with or at risk of HIV, we identified several gut bacterial species and a microbial metabolite ImP associated with carotid artery atherosclerosis, which might be related to host immune activation and inflammation. Video Abstract.
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Affiliation(s)
- Zheng Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Brandilyn A Peters
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - MacKenzie Bryant
- Department of Pediatrics, University of California, La Jolla, San Diego, CA, USA
| | - David B Hanna
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Tara Schwartz
- Department of Pediatrics, University of California, La Jolla, San Diego, CA, USA
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Mykhaylo Usyk
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Evan Grassi
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Fanua Wiek
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Lauren St Peter
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Wendy S Post
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Alan L Landay
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Howard N Hodis
- Atherosclerosis Research Unit, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Audrey French
- Department of Internal Medicine, Stroger Hospital of Cook County, Chicago, IL, USA
| | - Elizabeth T Golub
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jason Lazar
- Department of Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA
| | - Deborah Gustafson
- Department of Neurology, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA
| | - Anjali Sharma
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kathryn Anastos
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Robert D Burk
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Rob Knight
- Department of Pediatrics, University of California, La Jolla, San Diego, CA, USA
- Department of Bioengineering, University of California, La Jolla, San Diego, CA, USA
- Department of Computer Science and Engineering, University of California, La Jolla, San Diego, CA, USA
- Center for Microbiome Innovation, University of California, La Jolla, San Diego, CA, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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141
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Prüter H, Gillingham MAF, Krietsch J, Kuhn S, Kempenaers B. Sexual transmission may drive pair similarity of the cloacal microbiome in a polyandrous species. J Anim Ecol 2023. [PMID: 37230950 DOI: 10.1111/1365-2656.13961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 05/05/2023] [Indexed: 05/27/2023]
Abstract
All animals host a microbial community within and on their reproductive organs, known as the reproductive microbiome. In free-living birds, studies on the sexual transmission of bacteria have typically focused on a few pathogens instead of the bacterial community as a whole, despite a potential link to reproductive function. Theory predicts higher sexual transmission of the reproductive microbiome in females via the males' ejaculates and higher rates of transmission in promiscuous systems. We studied the cloacal microbiome of breeding individuals of a socially polyandrous, sex-role-reversed shorebird, the red phalarope (Phalaropus fulicarius). We expected (i) higher microbial diversity in females compared to males; (ii) low compositional differentiation between sexes; (iii) lower variation in composition between individuals (i.e. microbiome dispersion) in females than in males; (iv) convergence in composition as the breeding season progresses as a consequence of sexual transmission and/or shared habitat use; and (v) higher similarity in microbial composition between social pair members than between two random opposite-sex individuals. We found no or small between-sex differences in cloacal microbiome diversity/richness and composition. Dispersion of predicted functional pathways was lower in females than in males. As predicted, microbiome dispersion decreased with sampling date relative to clutch initiation of the social pair. Microbiome composition was significantly more similar among social pair members than among two random opposite-sex individuals. Pair membership explained 21.5% of the variation in taxonomic composition and 10.1% of functional profiles, whereas temporal and sex effects explained only 0.6%-1.6%. Consistent with evidence of functional convergence of reproductive microbiomes within pairs, some select taxa and predicted functional pathways were less variable between social pair members than between random opposite-sex individuals. As predicted if sexual transmission of the reproductive microbiome is high, sex differences in microbiome composition were weak in a socially polyandrous system with frequent copulations. Moreover, high within-pair similarity in microbiome composition, particularly for a few taxa spanning the spectrum of the beneficial-pathogenic axis, demonstrates the link between mating behaviour and the reproductive microbiome. Our study is consistent with the hypothesis that sexual transmission plays an important role in driving reproductive microbiome ecology and evolution.
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Affiliation(s)
- Hanna Prüter
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
| | - Mark A F Gillingham
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
- Biodiversity Research Institute (CSIC, Oviedo University, Principality of Asturias), University of Oviedo, Mieres, Spain
| | - Johannes Krietsch
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
| | - Sylvia Kuhn
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
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142
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Lapidot Y, Maya M, Reshef L, Cohen D, Ornoy A, Gophna U, Muhsen K. Relationships of the gut microbiome with cognitive development among healthy school-age children. Front Pediatr 2023; 11:1198792. [PMID: 37274812 PMCID: PMC10235814 DOI: 10.3389/fped.2023.1198792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 05/05/2023] [Indexed: 06/07/2023] Open
Abstract
Background The gut microbiome might play a role in neurodevelopment, however, evidence remains elusive. We aimed to examine the relationship between the intestinal microbiome and cognitive development of school-age children. Methods This cross-sectional study included healthy Israeli Arab children from different socioeconomic status (SES). The microbiome was characterized in fecal samples by implementing 16S rRNA gene sequencing. Cognitive function was measured using Stanford-Binet test, yielding full-scale Intelligence Quotient (FSIQ) score. Sociodemographics and anthropometric and hemoglobin measurements were obtained. Multivariate models were implemented to assess adjusted associations between the gut microbiome and FSIQ score, while controlling for age, sex, SES, physical growth, and hemoglobin levels. Results Overall, 165 children (41.2% females) aged 6-9 years were enrolled. SES score was strongly related to both FSIQ score and the gut microbiome. Measures of α-diversity were significantly associated with FSIQ score, demonstrating a more diverse, even, and rich microbiome with increased FSIQ score. Significant differences in fecal bacterial composition were found; FSIQ score explained the highest variance in bacterial β-diversity, followed by SES score. Several taxonomic differences were significantly associated with FSIQ score, including Prevotella, Dialister, Sutterella, Ruminococcus callidus, and Bacteroides uniformis. Conclusions We demonstrated significant independent associations between the gut microbiome and cognitive development in school-age children.
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Affiliation(s)
- Yelena Lapidot
- Department of Epidemiology and Preventive Medicine, School of Public Health, the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Maayan Maya
- Department of Epidemiology and Preventive Medicine, School of Public Health, the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Leah Reshef
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Dani Cohen
- Department of Epidemiology and Preventive Medicine, School of Public Health, the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Asher Ornoy
- Adelson School of Medicine, Ariel University, Ariel, Israel
- Department of Medical Neurobiology, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Uri Gophna
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Khitam Muhsen
- Department of Epidemiology and Preventive Medicine, School of Public Health, the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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143
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Kouete MT, Bletz MC, LaBumbard BC, Woodhams DC, Blackburn DC. Parental care contributes to vertical transmission of microbes in a skin-feeding and direct-developing caecilian. Anim Microbiome 2023; 5:28. [PMID: 37189209 PMCID: PMC10184399 DOI: 10.1186/s42523-023-00243-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 03/20/2023] [Indexed: 05/17/2023] Open
Abstract
BACKGROUND Our current understanding of vertebrate skin and gut microbiomes, and their vertical transmission, remains incomplete as major lineages and varied forms of parental care remain unexplored. The diverse and elaborate forms of parental care exhibited by amphibians constitute an ideal system to study microbe transmission, yet investigations of vertical transmission among frogs and salamanders have been inconclusive. In this study, we assess bacteria transmission in Herpele squalostoma, an oviparous direct-developing caecilian in which females obligately attend juveniles that feed on their mother's skin (dermatophagy). RESULTS We used 16S rRNA amplicon-sequencing of the skin and gut of wild caught H. squalostoma individuals (males, females, including those attending juveniles) as well as environmental samples. Sourcetracker analyses revealed that juveniles obtain an important portion of their skin and gut bacteria communities from their mother. The contribution of a mother's skin to the skin and gut of her respective juveniles was much larger than that of any other bacteria source. In contrast to males and females not attending juveniles, only the skins of juveniles and their mothers were colonized by bacteria taxa Verrucomicrobiaceae, Nocardioidaceae, and Erysipelotrichaceae. In addition to providing indirect evidence for microbiome transmission linked to parental care among amphibians, our study also points to noticeable differences between the skin and gut communities of H. squalostoma and that of many frogs and salamanders, which warrants further investigation. CONCLUSION Our study is the first to find strong support for vertical bacteria transmission attributed to parental care in a direct-developing amphibian species. This suggests that obligate parental care may promote microbiome transmission in caecilians.
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Affiliation(s)
- Marcel T Kouete
- School of Natural Resources and Environment, University of Florida, Gainesville, FL, 32611, USA.
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.
| | - Molly C Bletz
- Department of Biology, University of Massachusetts, Boston, MA, 02125, USA
| | | | - Douglas C Woodhams
- Department of Biology, University of Massachusetts, Boston, MA, 02125, USA
| | - David C Blackburn
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
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144
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Wongsurawat T, Sutheeworapong S, Jenjaroenpun P, Charoensiddhi S, Khoiri AN, Topanurak S, Sutthikornchai C, Jintaridth P. Microbiome analysis of thai traditional fermented soybeans reveals short-chain fatty acid-associated bacterial taxa. Sci Rep 2023; 13:7573. [PMID: 37165206 PMCID: PMC10172314 DOI: 10.1038/s41598-023-34818-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 05/08/2023] [Indexed: 05/12/2023] Open
Abstract
Thua Nao is a Thai traditional fermented soybean food and low-cost protein supplement. This study aimed to evaluate the bacterial community in Thua Nao from northern Thailand and assess potentially active short-chain fatty acids (SCFAs)-related bacteria. Sixty-five Thua Nao consisting of 30 wet and 35 dried samples were collected from six provinces: Chiang Rai, Chiang Mai, Mae Hong Son, Lampang, Lamphun, and Phayao. Bacterial diversity was significantly higher in the wet samples than in the dried samples. The dominant phyla were Firmicutes (92.7%), Proteobacteria (6.7%), Actinobacteriota (0.42%), and Bacteroidota (0.26%). The genus Bacillus (67%) was the most represented in all samples. Lactobacillus, Enterococcus, and Globicatella were enriched in the wet samples. Assessment of the SCFA-microbiota relationships revealed that high butyrate and propionate concentrations were associated with an increased Clostridiales abundance, and high acetate concentrations were associated with an increased Weissella abundance. Wet products contained more SCFAs, including acetate (P = 2.8e-08), propionate (P = 0.0044), butyrate (P = 0.0021), and isovalerate (P = 0.017), than the dried products. These results provide insight into SCFA-microbiota associations in Thua Nao, which may enable the development of starter cultures for SCFA-enriched Thua Nao production.
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Affiliation(s)
- Thidathip Wongsurawat
- Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
- Siriraj Long-Read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Bangkok, 10700, Thailand.
| | - Sawannee Sutheeworapong
- Systems Biology and Bioinformatics Laboratory, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Piroon Jenjaroenpun
- Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Siriraj Long-Read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Bangkok, 10700, Thailand
| | - Suvimol Charoensiddhi
- Department of Food Science and Technology, Faculty of Agro-Industry, Kasetsart University, Bangkok, 10900, Thailand
| | - Ahmad Nuruddin Khoiri
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Supachai Topanurak
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Chantira Sutthikornchai
- Department of Protozoology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Pornrutsami Jintaridth
- Department of Tropical Nutrition and Food Science, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand.
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Nearing JT, DeClercq V, Langille MGI. Investigating the oral microbiome in retrospective and prospective cases of prostate, colon, and breast cancer. NPJ Biofilms Microbiomes 2023; 9:23. [PMID: 37127667 PMCID: PMC10151362 DOI: 10.1038/s41522-023-00391-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 04/14/2023] [Indexed: 05/03/2023] Open
Abstract
The human microbiome has been proposed as a potentially useful biomarker for several cancers. To examine this, we made use of salivary samples from the Atlantic Partnership for Tomorrow's Health (PATH) project and Alberta's Tomorrow Project (ATP). Sample selection was divided into both a retrospective and prospective case control design examining prostate, breast, and colon cancer. In total 89 retrospective and 260 prospective cancer cases were matched to non-cancer controls and saliva samples were sequenced using 16S rRNA gene sequencing. We found no significant differences in alpha diversity. All beta diversity measures were insignificant except for unweighted UniFrac profiles in retrospective breast cancer cases and weighted UniFrac, Bray-Curtis and Robust Atchinson's distances in colon cancer after testing with age and sex adjusted MiRKAT models. Differential abundance (DA) analysis showed several taxa that were associated with previous cancer in all three groupings. Only one genus (Clostridia UCG-014) in breast cancer and one ASV (Fusobacterium periodonticum) in colon cancer was identified by more than one DA tool. In prospective cases three ASVs were associated with colon cancer, one ASV with breast cancer, and one ASV with prostate cancer. Random Forest classification showed low levels of signal in both study designs in breast and prostate cancer. Contrastingly, colon cancer did show signal in our retrospective analysis (AUC: 0.737) and in one of two prospective cohorts (AUC: 0.717). Our results indicate that it is unlikely that reliable microbial oral biomarkers for breast and prostate cancer exist.. However, further research into the oral microbiome and colon cancer could be fruitful.
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Affiliation(s)
- Jacob T Nearing
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada.
| | - Vanessa DeClercq
- Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| | - Morgan G I Langille
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
- Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
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146
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Baptista LC, Zumbro EL, Graham ZA, Hernandez AR, Buchanan T, Sun Y, Yang Y, Banerjee A, Verma A, Li Q, Carter CS, Buford TW. Multiomics profiling of the impact of an angiotensin (1-7)-expressing probiotic combined with exercise training in aged male rats. J Appl Physiol (1985) 2023; 134:1135-1153. [PMID: 36892893 PMCID: PMC10125028 DOI: 10.1152/japplphysiol.00508.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 03/10/2023] Open
Abstract
Angiotensin (1-7) [Ang (1-7)] is an active heptapeptide of the noncanonical arm of the renin-angiotensin system that modulates molecular signaling pathways associated with vascular and cellular inflammation, vasoconstriction, and fibrosis. Preclinical evidence suggests that Ang (1-7) is a promising therapeutic target that may ameliorate physical and cognitive function in late life. However, treatment pharmacodynamics limits its clinical applicability. Therefore, this study explored the underlying mechanisms altered by a genetically modified probiotic (GMP) that expresses Ang (1-7) combined with and without exercise training in an aging male rat model as a potential adjunct strategy to exercise training to counteract the decline of physical and cognitive function. We evaluated cross-tissue (prefrontal cortex, hippocampus, colon, liver, and skeletal muscle) multi-omics responses. After 12 wk of intervention, the 16S mRNA microbiome analysis revealed a main effect of probiotic treatment within- and between groups. The probiotic treatment enhanced α diversity (Inverse Simpson (F[2,56] = 4.44; P = 0.02); Shannon-Wiener (F[2,56] = 4.27; P = 0.02)) and β-diversity (F[2,56] = 2.66; P = 0.01) among rats receiving our GMP. The analysis of microbes' composition revealed three genera altered by our GMP (Enterorhabdus, Muribaculaceae unclassified, and Faecalitalea). The mRNA multi-tissue data analysis showed that our combined intervention upregulated neuroremodeling pathways on prefrontal cortex (i.e., 140 genes), inflammation gene expression in the liver (i.e., 63 genes), and circadian rhythm signaling on skeletal muscle. Finally, the integrative network analysis detected different communities of tightly (|r| > 0.8 and P < 0.05) correlated metabolites, genera, and genes in these tissues.NEW & NOTEWORTHY This manuscript uses a multiomics approach (i.e., microbiome, metabolomics, and transcriptomics) to explore the underlying mechanisms driven by a genetically modified probiotic (GMP) designed to express angiotensin (1-7) combined with moderate exercise training in an aged male rat model. After 12 wk of intervention, our findings suggest that our GMP enhanced gut microbial diversity while exercise training altered the transcriptional response in relevant neuroremodeling genes, inflammation, and circadian rhythm signaling pathways in an aging animal model.
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Affiliation(s)
- Liliana C Baptista
- Division of Gerontology, Geriatrics and Palliative Care, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
- Research Center for Physical Activity, Health and Leisure, Faculty of Sport, University of Porto, Porto, Portugal
- Laboratory for Integrative and Translational Research in Population Health, University of Porto, Porto, Portugal
| | - Emily L Zumbro
- Division of Gerontology, Geriatrics and Palliative Care, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Zachary A Graham
- Research Service, Birmingham Veterans Affair Medical Center, Birmingham, Alabama, United States
- Healthspan, Resilience and Performance, Florida Institute for Human and Machine Cognition, Pensacola, Florida, United States
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Abbi R Hernandez
- Division of Gerontology, Geriatrics and Palliative Care, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Taylor Buchanan
- Division of Gerontology, Geriatrics and Palliative Care, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Yi Sun
- Division of Gerontology, Geriatrics and Palliative Care, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
- Department of Life, Health, and Physical Sciences, Gordon College, Wenham, Massachusetts, United States
| | - YouFeng Yang
- Division of Gerontology, Geriatrics and Palliative Care, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Anisha Banerjee
- Division of Gerontology, Geriatrics and Palliative Care, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Amrisha Verma
- Department of Life, Health, and Physical Sciences, Gordon College, Wenham, Massachusetts, United States
| | - Qiuhong Li
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, Florida, United States
| | - Christy S Carter
- Division of Gerontology, Geriatrics and Palliative Care, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Thomas W Buford
- Division of Gerontology, Geriatrics and Palliative Care, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
- Geriatric Research Education and Clinical Center, Birmingham VA Medical Center, Birmingham, Alabama, United States
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147
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Dragičević P, Bielen A, Žučko J, Hudina S. The mycobiome of a successful crayfish invader and its changes along the environmental gradient. Anim Microbiome 2023; 5:23. [PMID: 37041598 PMCID: PMC10088235 DOI: 10.1186/s42523-023-00245-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/26/2023] [Indexed: 04/13/2023] Open
Abstract
BACKGROUND The microbiome plays an important role in biological invasions, since it affects various interactions between host and environment. However, most studies focus on the bacteriome, insufficiently addressing other components of the microbiome such as the mycobiome. Microbial fungi are among the most damaging pathogens in freshwater crayfish populations, colonizing and infecting both native and invasive crayfish species. Invading crayfish may transmit novel fungal species to native populations, but also, dispersal process and characteristics of the novel environment may affect the invaders' mycobiome composition, directly and indirectly affecting their fitness and invasion success. This study analyzes the mycobiome of a successful invader in Europe, the signal crayfish, using the ITS rRNA amplicon sequencing approach. We explored the mycobiomes of crayfish samples (exoskeletal biofilm, hemolymph, hepatopancreas, intestine), compared them to environmental samples (water, sediment), and examined the differences in fungal diversity and abundance between upstream and downstream segments of the signal crayfish invasion range in the Korana River, Croatia. RESULTS A low number of ASVs (indicating low abundance and/or diversity of fungal taxa) was obtained in hemolymph and hepatopancreas samples. Thus, only exoskeleton, intestine, sediment and water samples were analyzed further. Significant differences were recorded between their mycobiomes, confirming their uniqueness. Generally, environmental mycobiomes showed higher diversity than crayfish-associated mycobiomes. The intestinal mycobiome showed significantly lower richness compared to other mycobiomes. Significant differences in the diversity of sediment and exoskeletal mycobiomes were recorded between different river segments (but not for water and intestinal mycobiomes). Together with the high observed portion of shared ASVs between sediment and exoskeleton, this indicates that the environment (i.e. sediment mycobiome) at least partly shapes the exoskeletal mycobiome of crayfish. CONCLUSION This study presents the first data on crayfish-associated fungal communities across different tissues, which is valuable given the lack of studies on the crayfish mycobiome. We demonstrate significant differences in the crayfish exoskeletal mycobiome along the invasion range, suggesting that different local environmental conditions may shape the exoskeletal mycobiome during range expansion, while the mycobiome of the internal organ (intestine) remained more stable. Our results provide a basis for assessing how the mycobiome contributes to the overall health of the signal crayfish and its further invasion success.
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Affiliation(s)
- Paula Dragičević
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia.
| | - Ana Bielen
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, Zagreb, Croatia
| | - Jurica Žučko
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, Zagreb, Croatia
| | - Sandra Hudina
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
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148
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Hong Q, Chen G, Tang ZZ. PhyloMed: a phylogeny-based test of mediation effect in microbiome. Genome Biol 2023; 24:72. [PMID: 37041566 PMCID: PMC10088256 DOI: 10.1186/s13059-023-02902-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 03/15/2023] [Indexed: 04/13/2023] Open
Abstract
Microbiome data from sequencing experiments contain the relative abundance of a large number of microbial taxa with their evolutionary relationships represented by a phylogenetic tree. The compositional and high-dimensional nature of the microbiome mediator challenges the validity of standard mediation analyses. We propose a phylogeny-based mediation analysis method called PhyloMed to address this challenge. Unlike existing methods that directly identify individual mediating taxa, PhyloMed discovers mediation signals by analyzing subcompositions defined on the phylogenic tree. PhyloMed produces well-calibrated mediation test p-values and yields substantially higher discovery power than existing methods.
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Affiliation(s)
- Qilin Hong
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Guanhua Chen
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Zheng-Zheng Tang
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53715, USA.
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149
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Heni AC, Fackelmann G, Eibner G, Kreinert S, Schmid J, Schwensow NI, Wiegand J, Wilhelm K, Sommer S. Wildlife gut microbiomes of sympatric generalist species respond differently to anthropogenic landscape disturbances. Anim Microbiome 2023; 5:22. [PMID: 37024947 PMCID: PMC10080760 DOI: 10.1186/s42523-023-00237-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 02/23/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND Human encroachment into nature and the accompanying environmental changes are a big concern for wildlife biodiversity and health. While changes on the macroecological scale, i.e. species community and abundance pattern, are well documented, impacts on the microecological scale, such as the host's microbial community, remain understudied. Particularly, it is unclear if impacts of anthropogenic landscape modification on wildlife gut microbiomes are species-specific. Of special interest are sympatric, generalist species, assumed to be more resilient to environmental changes and which often are well-known pathogen reservoirs and drivers of spill-over events. Here, we analyzed the gut microbiome of three such sympatric, generalist species, one rodent (Proechimys semispinosus) and two marsupials (Didelphis marsupialis and Philander opossum), captured in 28 study sites in four different landscapes in Panama characterized by different degrees of anthropogenic disturbance. RESULTS Our results show species-specific gut microbial responses to the same landscape disturbances. The gut microbiome of P. semispinosus was less diverse and more heterogeneous in landscapes with close contact with humans, where it contained bacterial taxa associated with humans, their domesticated animals, and potential pathogens. The gut microbiome of D. marsupialis showed similar patterns, but only in the most disturbed landscape. P. opossum, in contrast, showed little gut microbial changes, however, this species' absence in the most fragmented landscapes indicates its sensitivity to long-term isolation. CONCLUSION These results demonstrate that wildlife gut microbiomes even in generalist species with a large ecological plasticity are impacted by human encroachment into nature, but differ in resilience which can have critical implications on conservation efforts and One Health strategies.
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Affiliation(s)
- Alexander Christoph Heni
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, 89081, Ulm, Germany.
- Smithsonian Tropical Research Institute, Balboa, Ancón, Republic of Panama.
| | - Gloria Fackelmann
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, 89081, Ulm, Germany
| | - Georg Eibner
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, 89081, Ulm, Germany
- Institute of Virology, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Swetlana Kreinert
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, 89081, Ulm, Germany
| | - Julian Schmid
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, 89081, Ulm, Germany
- Smithsonian Tropical Research Institute, Balboa, Ancón, Republic of Panama
| | - Nina Isabell Schwensow
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, 89081, Ulm, Germany
| | - Jonas Wiegand
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, 89081, Ulm, Germany
| | - Kerstin Wilhelm
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, 89081, Ulm, Germany
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, 89081, Ulm, Germany.
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150
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Peluso AA, Lundgaard AT, Babaei P, Mousovich-Neto F, Rocha AL, Damgaard MV, Bak EG, Gnanasekaran T, Dollerup OL, Trammell SAJ, Nielsen TS, Kern T, Abild CB, Sulek K, Ma T, Gerhart-Hines Z, Gillum MP, Arumugam M, Ørskov C, McCloskey D, Jessen N, Herrgård MJ, Mori MAS, Treebak JT. Oral supplementation of nicotinamide riboside alters intestinal microbial composition in rats and mice, but not humans. NPJ AGING 2023; 9:7. [PMID: 37012386 PMCID: PMC10070358 DOI: 10.1038/s41514-023-00106-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 03/20/2023] [Indexed: 04/05/2023]
Abstract
The gut microbiota impacts systemic levels of multiple metabolites including NAD+ precursors through diverse pathways. Nicotinamide riboside (NR) is an NAD+ precursor capable of regulating mammalian cellular metabolism. Some bacterial families express the NR-specific transporter, PnuC. We hypothesized that dietary NR supplementation would modify the gut microbiota across intestinal sections. We determined the effects of 12 weeks of NR supplementation on the microbiota composition of intestinal segments of high-fat diet-fed (HFD) rats. We also explored the effects of 12 weeks of NR supplementation on the gut microbiota in humans and mice. In rats, NR reduced fat mass and tended to decrease body weight. Interestingly, NR increased fat and energy absorption but only in HFD-fed rats. Moreover, 16S rRNA gene sequencing analysis of intestinal and fecal samples revealed an increased abundance of species within Erysipelotrichaceae and Ruminococcaceae families in response to NR. PnuC-positive bacterial strains within these families showed an increased growth rate when supplemented with NR. The abundance of species within the Lachnospiraceae family decreased in response to HFD irrespective of NR. Alpha and beta diversity and bacterial composition of the human fecal microbiota were unaltered by NR, but in mice, the fecal abundance of species within Lachnospiraceae increased while abundances of Parasutterella and Bacteroides dorei species decreased in response to NR. In conclusion, oral NR altered the gut microbiota in rats and mice, but not in humans. In addition, NR attenuated body fat mass gain in rats, and increased fat and energy absorption in the HFD context.
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Affiliation(s)
- A Augusto Peluso
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Agnete T Lundgaard
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Parizad Babaei
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Felippe Mousovich-Neto
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Andréa L Rocha
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Mads V Damgaard
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Emilie G Bak
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thiyagarajan Gnanasekaran
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole L Dollerup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Samuel A J Trammell
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas S Nielsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Timo Kern
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Caroline B Abild
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Karolina Sulek
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Herlev Hospital, Herlev, Denmark
| | - Tao Ma
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Zach Gerhart-Hines
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Matthew P Gillum
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Manimozhiyan Arumugam
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Cathrine Ørskov
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Douglas McCloskey
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Niels Jessen
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Markus J Herrgård
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
- BioInnovation Institute, Copenhagen, Denmark
| | - Marcelo A S Mori
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
- Obesity and Comorbidities Research Center, University of Campinas, Campinas, SP, Brazil
- Experimental Medicine Research Cluster, University of Campinas, Campinas, SP, Brazil
| | - Jonas T Treebak
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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