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Aplakidou E, Vergoulidis N, Chasapi M, Venetsianou NK, Kokoli M, Panagiotopoulou E, Iliopoulos I, Karatzas E, Pafilis E, Georgakopoulos-Soares I, Kyrpides NC, Pavlopoulos GA, Baltoumas FA. Visualizing metagenomic and metatranscriptomic data: A comprehensive review. Comput Struct Biotechnol J 2024; 23:2011-2033. [PMID: 38765606 PMCID: PMC11101950 DOI: 10.1016/j.csbj.2024.04.060] [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: 01/27/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024] Open
Abstract
The fields of Metagenomics and Metatranscriptomics involve the examination of complete nucleotide sequences, gene identification, and analysis of potential biological functions within diverse organisms or environmental samples. Despite the vast opportunities for discovery in metagenomics, the sheer volume and complexity of sequence data often present challenges in processing analysis and visualization. This article highlights the critical role of advanced visualization tools in enabling effective exploration, querying, and analysis of these complex datasets. Emphasizing the importance of accessibility, the article categorizes various visualizers based on their intended applications and highlights their utility in empowering bioinformaticians and non-bioinformaticians to interpret and derive insights from meta-omics data effectively.
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Affiliation(s)
- Eleni Aplakidou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Nikolaos Vergoulidis
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Maria Chasapi
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Nefeli K. Venetsianou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Maria Kokoli
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Eleni Panagiotopoulou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Ioannis Iliopoulos
- Department of Basic Sciences, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Evangelos Karatzas
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Evangelos Pafilis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece
| | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Nikos C. Kyrpides
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Georgios A. Pavlopoulos
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Center of New Biotechnologies & Precision Medicine, Department of Medicine, School of Health Sciences, National and Kapodistrian University of Athens, Greece
- Hellenic Army Academy, 16673 Vari, Greece
| | - Fotis A. Baltoumas
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
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2
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Chen LA, Boyle K. The Role of the Gut Microbiome in Health and Disease in the Elderly. Curr Gastroenterol Rep 2024; 26:217-230. [PMID: 38642272 PMCID: PMC11282161 DOI: 10.1007/s11894-024-00932-w] [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] [Accepted: 04/05/2024] [Indexed: 04/22/2024]
Abstract
PURPOSE OF REVIEW Growing evidence supports the contribution of age in the composition and function of the gut microbiome, with specific findings associated with health in old age and longevity. RECENT FINDINGS Current studies have associated certain microbiota, such as Butyricimonas, Akkermansia, and Odoribacter, with healthy aging and the ability to survive into extreme old age. Furthermore, emerging clinical and pre-clinical research have shown promising mechanisms for restoring a healthy microbiome in elderly populations through various interventions such as fecal microbiota transplant (FMT), dietary interventions, and exercise programs. Despite several conceptually exciting interventional studies, the field of microbiome research in the elderly remains limited. Specifically, large longitudinal studies are needed to better understand causative relationships between the microbiome and healthy aging. Additionally, individualized approaches to microbiome interventions based on patients' co-morbidities and the underlying functional capacity of their microbiomes are needed to achieve optimal results.
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Affiliation(s)
- Lea Ann Chen
- Division of Gastroenterology and Hepatology, Department of Medicine, Rutgers, New Brunswick, NJ, USA.
| | - Kaitlyn Boyle
- Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
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3
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Li W, Zeng J, Zheng N, Ge C, Li Y, Yao H. Polyvinyl chloride microplastics in the aquatic environment enrich potential pathogenic bacteria and spread antibiotic resistance genes in the fish gut. JOURNAL OF HAZARDOUS MATERIALS 2024; 475:134817. [PMID: 38878444 DOI: 10.1016/j.jhazmat.2024.134817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/13/2024] [Accepted: 06/03/2024] [Indexed: 06/27/2024]
Abstract
Microplastics and antibiotics coexist in aquatic environments, especially in freshwater aquaculture areas. However, as the second largest production of polyvinyl chloride (PVC) in the world, the effects of co-exposure to microplastics particles and antibiotics on changes in antibiotic resistance gene (ARG) profiles and the microbial community structure of aquatic organism gut microorganisms are poorly understood. Therefore, in this study, carp (Cyprinus carpio) were exposed to single or combined PVC microplastic contamination and oxytetracycline (OTC) or sulfamethazine (SMZ) for 8 weeks. PVC microplastics can enrich potential pathogenic bacteria, such as Enterobacter and Acinetobacter, among intestinal microorganisms. The presence of PVC microplastics enhanced the selective enrichment and dissemination risk of ARGs. PVC microplastics combined with OTC (OPVC) treatment significantly increased the abundance of tetracycline resistance genes (1.40-fold) compared with that in the OTC exposure treatment, revealing an obvious co-selection effect. However, compared with those in the control group, the total abundance of ARGs and MGEs in the OPVC treatment groups were significantly lower, which was correlated with the reduced abundances of the potential host Enterobacter. Overall, our results emphasized the diffusion and spread of ARGs are more influenced by PVC microplastics than by antibiotics, which may lead to antibiotic resistance in aquaculture.
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Affiliation(s)
- Wei Li
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430073, People's Republic of China
| | - Jieyi Zeng
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, People's Republic of China
| | - Ningguo Zheng
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430073, People's Republic of China
| | - Chaorong Ge
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430073, People's Republic of China
| | - Yaying Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, People's Republic of China
| | - Huaiying Yao
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430073, People's Republic of China.
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4
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Kaczvinsky C, Levy H, Preston S, Youngflesh C, Clucas G, Lynch HJ, Hart T, Smith AL. The influence of biotic and abiotic factors on the bacterial microbiome of gentoo penguins (Pygoscelis papua) in their natural environment. Sci Rep 2024; 14:17933. [PMID: 39095393 DOI: 10.1038/s41598-024-66460-9] [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: 07/05/2023] [Accepted: 07/01/2024] [Indexed: 08/04/2024] Open
Abstract
The microbiome is a key factor in the health, well-being, and success of vertebrates, contributing to the adaptive capacity of the host. However, the impact of geographic and biotic factors that may affect the microbiome of wild birds in polar environments is not well defined. To address this, we determined the bacterial 16S rRNA gene sequence profiles in faecal samples from pygoscelid penguin populations in the Scotia Arc, focusing on gentoo penguins. This mesopredatory group breeds in defined colonies across a wide geographic range. Since diet could influence microbiome structure, we extracted dietary profiles from a eukaryotic 18S rRNA gene sequence profile. The bacterial microbiome profiles were considered in the context of a diverse set of environmental and ecological measures. Integrating wide geographic sampling with bacterial 16S and eukaryotic 18S rRNA gene sequencing of over 350 faecal samples identified associations between the microbiome profile and a suite of geographic and ecological factors. Microbiome profiles differed according to host species, colony identity, distance between colonies, and diet. Interestingly there was also a relationship between the proportion of host DNA (in relation to total 18S rRNA gene signal) and the microbiome, which may reflect gut passage time. Colony identity provided the strongest association with differences in microbiome profiles indicating that local factors play a key role in the microbiome structure of these polar seabirds. This may reflect the influence of local transfer of microbes either via faecal-oral routes, during chick feeding or other close contact events. Other factors including diet and host species also associate with variation in microbiome profile, and in at least some locations, the microbiome composition varies considerably between individuals. Given the variation in penguin microbiomes associated with diverse factors there is potential for disruption of microbiome associations at a local scale that could influence host health, productivity, and immunological competence. The microbiome represents a sensitive indicator of changing conditions, and the implications of any changes need to be considered in the wider context of environmental change and other stressors.
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Affiliation(s)
- Chloe Kaczvinsky
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Hila Levy
- Office of Science and Technology Policy, Executive Office of the President, 1650 Pennsylvania Avenue, Washington, DC, 20504, USA
| | - Stephen Preston
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Casey Youngflesh
- Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA
| | - Gemma Clucas
- Cornell Lab of Ornithology, 159 Sapsucker Woods Rd., Ithaca, NY, 14850, USA
| | - Heather J Lynch
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794, USA
- Institute for Advanced Computational Sciences, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Tom Hart
- Oxford Brookes University, Gypsy Lane, Headington, Oxford, OX3 0BP, UK.
| | - Adrian L Smith
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
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5
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Cyphert EL, Liu C, Morales AL, Nixon JC, Blackford E, Garcia M, Cevallos N, Turnbaugh PJ, Brito IL, Booth SL, Hernandez CJ. Effects of high dose aspartame-based sweetener on the gut microbiota and bone strength in young and aged mice. JBMR Plus 2024; 8:ziae082. [PMID: 39011468 PMCID: PMC11247189 DOI: 10.1093/jbmrpl/ziae082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/21/2024] [Accepted: 06/13/2024] [Indexed: 07/17/2024] Open
Abstract
In a recent study examining the effects of manipulating the gut microbiome on bone, a control group of mice in which the microbiome was altered using a non-caloric, aspartame-based sweetener resulted in whole bone strength being 40% greater than expected from geometry alone, implicating enhanced bone tissue strength. However, the study was not designed to detect changes in bone in this control group and was limited to young male mice. Here we report a replication study examining how changes in the gut microbiome caused by aspartame-based sweetener influence bone. Male and female C57Bl/6 J mice were untreated or treated with a high dose of sweetener (10 g/L) in their drinking water from either 1 to 4 mo of age (young cohort; n = 80) or 1 to 22 mo of age (aged cohort; n = 52). Sweetener did not replicate the modifications to the gut microbiome observed in the initial study and did not result in an increase in bone tissue strength in either sex at either age. Aged male mice dosed with sweetener had larger bones (+17% femur section modulus, p<.001) and greater whole bone strength (+22%, p=.006) but the increased whole bone strength was explained by the associated increase in body mass (+9%, p<.001). No differences in body mass, whole bone strength, or femoral geometry were associated with sweetener dosing in males from the young cohort or females at either age. As we were unable to replicate the gut microbiota observed in the initial experiment, it remains unclear if changes in the gut microbiome can enhance bone tissue strength. Although prior work studying gut microbiome-induced changes in bone with oral antibiotics has been highly repeatable, the current study highlights the variability of nutritional manipulations of the gut microbiota in mice.
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Affiliation(s)
- Erika L Cyphert
- Department of Orthopaedic Surgery, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, United States
- Sibley School of Mechanical & Aerospace Engineering, Cornell University, 124 Hoy Road, Ithaca, NY 14853, United States
| | - Chongshan Liu
- Sibley School of Mechanical & Aerospace Engineering, Cornell University, 124 Hoy Road, Ithaca, NY 14853, United States
| | - Angie L Morales
- Sibley School of Mechanical & Aerospace Engineering, Cornell University, 124 Hoy Road, Ithaca, NY 14853, United States
| | - Jacob C Nixon
- Sibley School of Mechanical & Aerospace Engineering, Cornell University, 124 Hoy Road, Ithaca, NY 14853, United States
| | - Emily Blackford
- Sibley School of Mechanical & Aerospace Engineering, Cornell University, 124 Hoy Road, Ithaca, NY 14853, United States
| | - Matthew Garcia
- Sibley School of Mechanical & Aerospace Engineering, Cornell University, 124 Hoy Road, Ithaca, NY 14853, United States
| | - Nicolas Cevallos
- Department of Orthopaedic Surgery, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, United States
| | - Peter J Turnbaugh
- Department of Microbiology and Immunology, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, United States
- Chan Zuckerberg Biohub, San Francisco, CA 94143, United States
| | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, 101 Weill Hall, Ithaca, NY 14853, United States
| | - Sarah L Booth
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, 711 Washington Street, Boston, MA 02111, United States
| | - Christopher J Hernandez
- Department of Orthopaedic Surgery, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, United States
- Chan Zuckerberg Biohub, San Francisco, CA 94143, United States
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, United States
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6
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Older CE, Rodrigues Hoffmann A. Considerations for performing companion animal skin microbiome studies. Vet Dermatol 2024; 35:367-374. [PMID: 38654617 DOI: 10.1111/vde.13250] [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: 11/04/2023] [Revised: 02/16/2024] [Accepted: 04/09/2024] [Indexed: 04/26/2024]
Abstract
The microbiome field has grown significantly in the past decade, and published studies have provided an overview of the microorganisms inhabiting the skin of companion animals. With the continued growth and interest in this field, concerns have been raised regarding sample collection methods, reagent contamination, data processing and environmental factors that may impair data interpretation (especially as related to low-biomass skin samples). In order to assure transparency, it is important to report all steps from sample collection to data analysis, including use of proper controls, and to make sequence data and sample metadata publicly available. Whilst interstudy variation will continue to exist, efforts to standardise methods will reduce confounding variables, and allow for reproducibility and comparability of results between studies. Companion animal microbiome studies often include clinical cases, and small sample sizes may result in lack of statistical significance within small datasets. The ability to combine results from standardised studies through meta-analyses would mitigate the limitations of these smaller studies, providing for more robust interpretation of results which could then inform clinical decisions. In this narrative review, we aim to present considerations for designing a study to evaluate the skin microbiome of companion animals, from conception to data analysis.
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Affiliation(s)
- Caitlin E Older
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Aline Rodrigues Hoffmann
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
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7
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Hu A, Zhao W, Wang J, Qi Q, Xiao X, Jing H. Microbial communities reveal niche partitioning across the slope and bottom zones of the challenger deep. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13314. [PMID: 39086173 PMCID: PMC11291871 DOI: 10.1111/1758-2229.13314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 06/25/2024] [Indexed: 08/02/2024]
Abstract
Widespread marine microbiomes exhibit compositional and functional differentiation as a result of adaptation driven by environmental characteristics. We investigated the microbial communities in both seawater and sediments on the slope (7-9 km) and the bottom (9-11 km) of the Challenger Deep of the Mariana Trench to explore community differentiation. Both metagenome-assembled genomes (MAGs) and 16S rRNA amplicon sequence variants (ASVs) showed that the microbial composition in the seawater was similar to that of sediment on the slope, while distinct from that of sediment in the bottom. This scenario suggested a potentially stronger community interaction between seawater and sediment on the slope, which was further confirmed by community assembly and population movement analyses. The metagenomic analysis also indicates a specific stronger potential of nitrate reduction and sulphate assimilation in the bottom seawater, while more versatile nitrogen and sulphur cycling pathways occur on the slope, reflecting functional differentiations among communities in conjunction with environmental features. This work implies that microbial community differentiation occurred in the different hadal niches, and was likely an outcome of microbial adaptation to the extreme hadal trench environment, especially the associated hydrological and geological conditions, which should be considered and measured in situ in future studies.
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Affiliation(s)
- Aoran Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
- International Center for Deep Life Investigation (IC‐DLI)Shanghai Jiao Tong UniversityShanghaiChina
| | - Weishu Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
- International Center for Deep Life Investigation (IC‐DLI)Shanghai Jiao Tong UniversityShanghaiChina
- School of OceanographyShanghai Jiao Tong UniversityShanghaiChina
| | - Jing Wang
- International Center for Deep Life Investigation (IC‐DLI)Shanghai Jiao Tong UniversityShanghaiChina
- School of OceanographyShanghai Jiao Tong UniversityShanghaiChina
- SJTU Yazhou Bay Institute of Deepsea Sci‐TechYongyou Industrial ParkSanyaChina
| | - Qi Qi
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
- International Center for Deep Life Investigation (IC‐DLI)Shanghai Jiao Tong UniversityShanghaiChina
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
- International Center for Deep Life Investigation (IC‐DLI)Shanghai Jiao Tong UniversityShanghaiChina
- SJTU Yazhou Bay Institute of Deepsea Sci‐TechYongyou Industrial ParkSanyaChina
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)ZhuhaiGuangdongChina
| | - Hongmei Jing
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)ZhuhaiGuangdongChina
- Institute of Deep‐Sea Science and EngineeringChinese Academy of SciencesSanyaChina
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8
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Wassel MA, Makabe-Kobayashi Y, Iqbal MM, Takatani T, Sakakura Y, Hamasaki K. The impact of tetrodotoxin (TTX) on the gut microbiome in juvenile tiger pufferfish, Takifugu rubripes. Sci Rep 2024; 14:16684. [PMID: 39085277 PMCID: PMC11291987 DOI: 10.1038/s41598-024-66112-y] [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: 03/16/2024] [Accepted: 06/27/2024] [Indexed: 08/02/2024] Open
Abstract
Tetrodotoxin (TTX) is a potent neurotoxin that accumulates in Takifugu rubripes, commonly known as pufferfish, through the ingestion of TTX-bearing organisms as part of their food chain. Although researchers believe that pufferfish use TTX to relieve stress, data are not currently available on how TTX affects the gut microbiota of pufferfish. To address this gap, our study aimed to investigate whether administering TTX to fish could alter their gut microbiota and overall health under various salinity conditions, including 30.0 ppt, 8.5 ppt, and 1.7 ppt salinity, which represent full-strength, isosmotic, and low-salinity stress, respectively. We analyzed the effect of TTX ingestion on the community structure, core microbiome, and metabolic capabilities of the gut microbiome using high-throughput sequencing technologies. The predominant bacterial taxa within the gut microbiome were Firmicutes (21-85%), Campilobacterota (2.8-67%), Spirochaetota (0.5-14%), and Proteobacteria (0.7-9.8%), with Mycoplasma, uncultured Arcobacteraceae, Brevinema, Vibrio, Rubritalea, and uncultured Pirellulaceae as core genera. Our findings indicated that the impact of TTX on high-abundance genera at 30.0 ppt and 8.5 ppt salinity levels was negligible, indicating their stability and resilience to TTX ingestion. However, at 1.7 ppt, TTX-fed fish showed a significant increase in uncultured Arcobacteraceae. Furthermore, our analysis of TTX-fed fish revealed taxonomic alterations in low-abundance taxa, which altered the predicted functions of the gut microbiota at all salinity levels. These results suggest that TTX administration could cause subtle effects on the metabolic functions of gut microbial communities. Overall, our study provides insights into the complex relationship between a TTX-accumulating animal, T. rubripes, and its gut microbiota.
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Affiliation(s)
- Mai A Wassel
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan.
- Genetics and Genetic Engineering Research Group, National Institute of Oceanography and Fisheries, NIOF, Cairo, Egypt.
| | - Yoko Makabe-Kobayashi
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
| | - Md Mehedi Iqbal
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
| | - Tomohiro Takatani
- Graduate School of Integrated Science and Technology, Nagasaki University, 1‑14 Bunkyo, Nagasaki, 852‑8521, Japan
| | - Yoshitaka Sakakura
- Graduate School of Integrated Science and Technology, Nagasaki University, 1‑14 Bunkyo, Nagasaki, 852‑8521, Japan
| | - Koji Hamasaki
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.
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9
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King WL, Grandinette EM, Trase O, Rolon ML, Salis HM, Wood H, Bell TH. Autoclaving is at least as effective as gamma irradiation for biotic clearing and intentional microbial recolonization of soil. mSphere 2024; 9:e0047624. [PMID: 38980074 PMCID: PMC11288020 DOI: 10.1128/msphere.00476-24] [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: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 07/10/2024] Open
Abstract
Sterilization is commonly used to remove or reduce the biotic constraints of a soil to allow recolonization by soil-dwelling organisms, with autoclaving and gamma irradiation being the most frequently used approaches. Many studies have characterized sterilization impacts on soil physicochemical properties, with gamma irradiation often described as the preferred approach, despite the lower cost and higher scalability of autoclaving. However, few studies have compared how sterilization techniques impact soil recolonization by microorganisms. Here, we compared how two sterilization approaches (autoclaving; gamma irradiation) and soil washing impacted microbial recolonization of soil from a diverse soil inoculum. Sterilization method had little impact on microbial alpha diversity across recolonized soils. For sterile soil regrowth microcosms, species richness and diversity were significantly reduced by autoclaving relative to gamma irradiation, particularly for fungi. There was no impact of sterilization method on bacterial composition in recolonized soils and minimal impact on fungal composition (P = 0.05). Washing soils had a greater impact on microbial composition than sterilization method, and sterile soil regrowth had negligible impacts on microbial recolonization. These data suggest that sterilization method has no clear impact on microbial recolonization, at least across the soils tested, indicating that soil autoclaving is an appropriate and economical approach for biotically clearing soils.IMPORTANCESterilized soils represent soil-like environments that act as a medium to study microbial colonization dynamics in more "natural" settings relative to artificial culturing environments. Soil sterilization is often carried out by gamma irradiation or autoclaving, which both alter soil properties, but gamma irradiation is thought to be the gentler technique. Gamma irradiation can be cost prohibitive and does not scale well for larger experiments. We sought to examine how soil sterilization technique can impact microbial colonization, and additionally looked at the impact of soil washing which is believed to remove soil toxins that inhibit soil recolonization. We found that both gamma-irradiated and autoclaved soils showed similar colonization patterns when reintroducing microorganisms. Soil washing, relative to sterilization technique, had a greater impact on which microorganisms were able to recolonize the soil. When allowing sterilized soils to regrow (i.e., persisting microorganisms), gamma irradiation performed worse, suggesting that gamma irradiation does not biotically clear soils as well as autoclaving. These data suggest that both sterilization techniques are comparable, and that autoclaving may be more effective at biotically clearing soil.
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Affiliation(s)
- William L. King
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
- School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Emily M. Grandinette
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Olivia Trase
- Department of Entomology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - M. Laura Rolon
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Howard M. Salis
- Department of Agricultural and Biological Engineering, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Harlow Wood
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Terrence H. Bell
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
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Rodríguez-Fuentes ME, Pérez-Sayáns M, Barbeito-Castiñeiras G, Molares-Vila A, Prado-Pena IB, Camolesi GCV, López-López R. Oral specimens as a tool for accurate metagenomic analysis: A pilot study. JOURNAL OF STOMATOLOGY, ORAL AND MAXILLOFACIAL SURGERY 2024:101991. [PMID: 39084558 DOI: 10.1016/j.jormas.2024.101991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Accepted: 07/27/2024] [Indexed: 08/02/2024]
Abstract
OBJECTIVES Acute oral mucosal damage, as well as other inflammatory processes seem to be related to dysbiosis of the oral microbiome. The need to study changes in the oral microbiome led us to hypothesize what type of sample would provide the most representative picture of the entire human oral microbiome. MATERIALS AND METHODS An observational, and cross-sectional study was carried out. Six healthy adult participants provided 3 different sample types each, that included saliva, oral rinse and mucosal biopsy tissue. We performed 16S rRNA sequencing of the V3-V4 region of the 18 samples using Illumina MiSeq technology. RESULTS Participants were 27 ± 6,3 years old. Bacterial alpha diversity was higher in oral rinse samples compared to whole unstimulated saliva and oral mucosa tissue (p = 0,005). However, saliva specimens showed a 56 % relative abundance of identified species followed by a 30 % in oral rinse and only 1 % in tissue samples. CONCLUSIONS This study found differences on oral microbiome composition for each type of sample. Oral rinse should be chosen when higher alpha diversity is needed, whereas whole unstimulated saliva should be more appropriate for larger amount of bacterial DNA. CLINICAL RELEVANCE The results obtained demonstrate the importance of a correct choice of the optimal type of oral sample for microbiome studies due to the differences found in its composition.
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Affiliation(s)
- Manuel Eros Rodríguez-Fuentes
- Faculty of Medicine and Dentistry, Universidade de Santiago de Compostela, c/ Entrerríos s/n, Santiago de Compostela 15782, Spain; Health Research Institute of Santiago de Compostela (IDIS, ORALRES Group), Santiago de Compostela, A Coruña 15706, Spain
| | - Mario Pérez-Sayáns
- Faculty of Medicine and Dentistry, Universidade de Santiago de Compostela, c/ Entrerríos s/n, Santiago de Compostela 15782, Spain; Health Research Institute of Santiago de Compostela (IDIS, ORALRES Group), Santiago de Compostela, A Coruña 15706, Spain.
| | - Gema Barbeito-Castiñeiras
- Microbiology Unit, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, A Coruña 15706, Spain
| | - Alberto Molares-Vila
- Health Research Institute of Santiago de Compostela (IDIS, ORALRES Group), Santiago de Compostela, A Coruña 15706, Spain; Health Research Institute of Santiago de Compostela (IDIS, RESMET Group, https://resmet.org), Santiago de Compostela, A Coruña 15706, Spain
| | - Irene B Prado-Pena
- Faculty of Medicine and Dentistry, Universidade de Santiago de Compostela, c/ Entrerríos s/n, Santiago de Compostela 15782, Spain
| | - Gisela C V Camolesi
- Faculty of Medicine and Dentistry, Universidade de Santiago de Compostela, c/ Entrerríos s/n, Santiago de Compostela 15782, Spain; Health Research Institute of Santiago de Compostela (IDIS, ORALRES Group), Santiago de Compostela, A Coruña 15706, Spain
| | - Rafael López-López
- Faculty of Medicine and Dentistry, Universidade de Santiago de Compostela, c/ Entrerríos s/n, Santiago de Compostela 15782, Spain; Medical Oncology Unit, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, A Coruña 15706, Spain
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11
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Manter DK, Reardon CL, Ashworth AJ, Ibekwe AM, Lehman RM, Maul JE, Miller DN, Creed T, Ewing PM, Park S, Ducey TF, Tyler HL, Veum KS, Weyers SL, Knaebel DB. Unveiling errors in soil microbial community sequencing: a case for reference soils and improved diagnostics for nanopore sequencing. Commun Biol 2024; 7:913. [PMID: 39069530 DOI: 10.1038/s42003-024-06594-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 07/17/2024] [Indexed: 07/30/2024] Open
Abstract
The sequencing platform and workflow strongly influence microbial community analyses through potential errors at each step. Effective diagnostics and experimental controls are needed to validate data and improve reproducibility. This cross-laboratory study evaluates sources of variability and error at three main steps of a standardized amplicon sequencing workflow (DNA extraction, polymerase chain reaction [PCR], and sequencing) using Oxford Nanopore MinION to analyze agricultural soils and a simple mock community. Variability in sequence results occurs at each step in the workflow with PCR errors and differences in library size greatly influencing diversity estimates. Common bioinformatic diagnostics and the mock community are ineffective at detecting PCR abnormalities. This work outlines several diagnostic checks and techniques to account for sequencing depth and ensure accuracy and reproducibility in soil community analyses. These diagnostics and the inclusion of a reference soil can help ensure data validity and facilitate the comparison of multiple sequencing runs within and between laboratories.
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Affiliation(s)
- Daniel K Manter
- Soil Management and Sugar Beet Research, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Fort Collins, CO, USA.
| | | | - Amanda J Ashworth
- Poultry Production and Product Safety Research Unit, USDA-ARS, Fayetteville, AR, USA
| | | | - R Michael Lehman
- North Central Agricultural Research Laboratory, USDA-ARS, Brookings, SD, USA
| | - Jude E Maul
- Sustainable Agricultural Systems Laboratory, USDA-ARS, Beltsville, MD, USA
| | - Daniel N Miller
- Agroecosystem Management Research Unit, USDA-ARS, Lincoln, NE, USA
| | - Timothy Creed
- Soil Management and Sugar Beet Research, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Fort Collins, CO, USA
| | | | - Stanley Park
- Water Efficiency and Salinity Research Unit, USDA-ARS, Riverside, CA, USA
| | - Thomas F Ducey
- Coastal Plains Soil, Water and Plant Research Center, USDA-ARS, Florence, SC, USA
| | - Heather L Tyler
- Crop Production Systems Research Unit, USDA-ARS, Stoneville, MS, USA
| | - Kristen S Veum
- Cropping Systems and Water Quality Research Unit, USDA-ARS, Columbia, MO, USA
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12
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Siegieda D, Panek J, Frąc M. Ecological processes of bacterial microbiome assembly in healthy and dysbiotic strawberry farms. BMC PLANT BIOLOGY 2024; 24:692. [PMID: 39030484 PMCID: PMC11264780 DOI: 10.1186/s12870-024-05415-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 07/12/2024] [Indexed: 07/21/2024]
Abstract
The bacterial microbiome plays crucial role in plants' resistance to diseases, nutrient uptake and productivity. We examined the microbiome characteristics of healthy and unhealthy strawberry farms, focusing on soil (bulk soil, rhizosphere soil) and plant (roots and shoots). The relative abundance of most abundant taxa were correlated with the chemical soil properties and shoot niche revealed the least amount of significant correlations between the two. While alpha and beta diversities did not show differences between health groups, we identified a number of core taxa (16-59) and marker bacterial taxa for each healthy (Unclassified Tepidisphaerales, Ohtaekwangia, Hydrocarboniphaga) and dysbiotic (Udaeobacter, Solibacter, Unclassified Chitinophagales, Unclassified Nitrosomonadaceae, Nitrospira, Nocardioides, Tardiphaga, Skermanella, Pseudomonas, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Curtobacterium) niche. We also revealed selective pressure of strawberry rhizosphere soil and roots plants in unhealthy plantations increased stochastic ecological processes of bacterial microbiome assembly in shoots. Our findings contribute to understanding sustainable agriculture and plant-microbiome interactions.
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Affiliation(s)
- Dominika Siegieda
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, Lublin, Lublin, 20-290, Poland
| | - Jacek Panek
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, Lublin, Lublin, 20-290, Poland
| | - Magdalena Frąc
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, Lublin, Lublin, 20-290, Poland.
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13
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Ioannou M, Borkent J, Andreu-Sánchez S, Wu J, Fu J, Sommer IEC, Haarman BCM. Reproducible gut microbial signatures in bipolar and schizophrenia spectrum disorders: A metagenome-wide study. Brain Behav Immun 2024; 121:165-175. [PMID: 39032544 DOI: 10.1016/j.bbi.2024.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 05/30/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024] Open
Abstract
BACKGROUND Numerous studies report gut microbiome variations in bipolar disorder (BD) and schizophrenia spectrum disorders (SSD) compared to healthy individuals, though, there is limited consensus on which specific bacteria are associated with these disorders. METHODS In this study, we performed a comprehensive metagenomic shotgun sequencing analysis in 103 Dutch patients with BD/SSD and 128 healthy controls matched for age, sex, body mass index and income, while accounting for diet quality, transit time and technical confounders. To assess the replicability of the findings, we used two validation cohorts (total n = 203), including participants from a distinct population with a different metagenomic isolation protocol. RESULTS The gut microbiome of the patients had a significantly different β-diversity, but not α-diversity nor neuroactive potential compared to healthy controls. Initially, twenty-six bacterial taxa were identified as differentially abundant in patients. Among these, the previously reported genera Lachnoclostridium and Eggerthella were replicated in the validation cohorts. Employing the CoDaCoRe learning algorithm, we identified two bacterial balances specific to BD/SSD, which demonstrated an area under the receiver operating characteristic curve (AUC) of 0.77 in the test dataset. These balances were replicated in the validation cohorts and showed a positive association with the severity of psychiatric symptoms and antipsychotic use. Last, we showed a positive association between the relative abundance of Klebsiella and Klebsiella pneumoniae with antipsychotic use and between the Anaeromassilibacillus and lithium use. CONCLUSIONS Our findings suggest that microbial balances could be a reproducible method for identifying BD/SSD-specific microbial signatures, with potential diagnostic and prognostic applications. Notably, Lachnoclostridium and Eggerthella emerge as frequently occurring bacteria in BD/SSD. Last, our study reaffirms the previously established link between Klebsiella and antipsychotic medication use and identifies a novel association between Anaeromassilibacillus and lithium use.
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Affiliation(s)
- Magdalini Ioannou
- University of Groningen and University Medical Center Groningen, Department of Psychiatry, Groningen, the Netherlands; University of Groningen and University Medical Center Groningen, Department of Biomedical Sciences, Groningen, the Netherlands.
| | - Jenny Borkent
- University of Groningen and University Medical Center Groningen, Department of Biomedical Sciences, Groningen, the Netherlands
| | - Sergio Andreu-Sánchez
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands; University of Groningen and University Medical Center Groningen, Department of Pediatrics, Groningen, the Netherlands
| | - Jiafei Wu
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Jingyuan Fu
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands; University of Groningen and University Medical Center Groningen, Department of Pediatrics, Groningen, the Netherlands
| | - Iris E C Sommer
- University of Groningen and University Medical Center Groningen, Department of Biomedical Sciences, Groningen, the Netherlands
| | - Bartholomeus C M Haarman
- University of Groningen and University Medical Center Groningen, Department of Psychiatry, Groningen, the Netherlands
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14
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Shi Z, Yao F, Chen Q, Chen Y, Zhang J, Guo J, Zhang S, Zhang C. More deterministic assembly constrains the diversity of gut microbiota in freshwater snails. Front Microbiol 2024; 15:1394463. [PMID: 39040899 PMCID: PMC11260827 DOI: 10.3389/fmicb.2024.1394463] [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: 03/01/2024] [Accepted: 06/10/2024] [Indexed: 07/24/2024] Open
Abstract
Growing evidence has suggested a strong link between gut microbiota and host fitness, yet our understanding of the assembly mechanisms governing gut microbiota remains limited. Here, we collected invasive and native freshwater snails coexisting at four independent sites in Guangdong, China. We used high-throughput sequencing to study the assembly processes of their gut microbiota. Our results revealed significant differences in the diversity and composition of gut microbiota between invasive and native snails. Specifically, the gut microbiota of invasive snails exhibited lower alpha diversity and fewer enriched bacteria, with a significant phylogenetic signal identified in the microbes that were enriched or depleted. Both the phylogenetic normalized stochasticity ratio (pNST) and the phylogenetic-bin-based null model analysis (iCAMP) showed that the assembly process of gut microbiota in invasive snails was more deterministic compared with that in native snails, primarily driven by homogeneous selection. The linear mixed-effects model revealed a significant negative correlation between deterministic processes (homogeneous selection) and alpha diversity of snail gut microbiota, especially where phylogenetic diversity explained the most variance. This indicates that homogeneous selection acts as a filter by the host for specific microbial lineages, constraining the diversity of gut microbiota in invasive freshwater snails. Overall, our study suggests that deterministic assembly-mediated lineage filtering is a potential mechanism for maintaining the diversity of gut microbiota in freshwater snails.
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Affiliation(s)
- Zhaoji Shi
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Technology Research Centre of Modern Eco-Agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China
| | - Fucheng Yao
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Technology Research Centre of Modern Eco-Agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China
| | - Qi Chen
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Technology Research Centre of Modern Eco-Agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China
| | - Yingtong Chen
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Technology Research Centre of Modern Eco-Agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China
| | - Jiaen Zhang
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Technology Research Centre of Modern Eco-Agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China
| | - Jing Guo
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan, China
| | - Shaobin Zhang
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan, China
| | - Chunxia Zhang
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Technology Research Centre of Modern Eco-Agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Eco-Circular Agriculture, South China Agricultural University, Guangzhou, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China
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15
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Montgomery TL, Wang Q, Mirza A, Dwyer D, Wu Q, Dowling CA, Martens JWS, Yang J, Krementsov DN, Mao-Draayer Y. Identification of commensal gut microbiota signatures as predictors of clinical severity and disease progression in multiple sclerosis. Sci Rep 2024; 14:15292. [PMID: 38961134 PMCID: PMC11222390 DOI: 10.1038/s41598-024-64369-x] [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: 12/21/2023] [Accepted: 06/07/2024] [Indexed: 07/05/2024] Open
Abstract
Multiple sclerosis (MS) is a chronic autoimmune disease of the central nervous system and a leading cause of neurological disability in young adults. Clinical presentation and disease course are highly heterogeneous. Typically, disease progression occurs over time and is characterized by the gradual accumulation of disability. The risk of developing MS is driven by complex interactions between genetic and environmental factors, including the gut microbiome. How the commensal gut microbiota impacts disease severity and progression over time remains unknown. In a longitudinal study, disability status and associated clinical features in 58 MS patients were tracked over 4.2 ± 0.98 years, and the baseline fecal gut microbiome was characterized via 16S amplicon sequencing. Progressor status, defined as patients with an increase in Expanded Disability Status Scale (EDSS), were correlated with features of the gut microbiome to determine candidate microbiota associated with risk of MS disease progression. We found no overt differences in microbial community diversity and overall structure between MS patients exhibiting disease progression and non-progressors. However, a total of 41 bacterial species were associated with worsening disease, including a marked depletion in Akkermansia, Lachnospiraceae, and Oscillospiraceae, with an expansion of Alloprevotella, Prevotella-9, and Rhodospirillales. Analysis of the metabolic potential of the inferred metagenome from taxa associated with progression revealed enrichment in oxidative stress-inducing aerobic respiration at the expense of microbial vitamin K2 production (linked to Akkermansia), and a depletion in SCFA metabolism (linked to Oscillospiraceae). Further, as a proof of principle, statistical modeling demonstrated that microbiota composition and clinical features were sufficient to predict disease progression. Additionally, we found that constipation, a frequent gastrointestinal comorbidity among MS patients, exhibited a divergent microbial signature compared with progressor status. These results demonstrate a proof of principle for the utility of the gut microbiome for predicting disease progression in MS in a small well-defined cohort. Further, analysis of the inferred metagenome suggested that oxidative stress, vitamin K2, and SCFAs are associated with progression, warranting future functional validation and mechanistic study.
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Affiliation(s)
- Theresa L Montgomery
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT, 05401, USA
| | - Qin Wang
- Autoimmunity Center of Excellence, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Ali Mirza
- Pharmacoepidemiology in Multiple Sclerosis Research Group, The University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Deanna Dwyer
- Autoimmunity Center of Excellence, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Qi Wu
- Autoimmunity Center of Excellence, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Catherine A Dowling
- Autoimmunity Center of Excellence, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Jacob W S Martens
- Autoimmunity Center of Excellence, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Jennifer Yang
- Autoimmunity Center of Excellence, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Dimitry N Krementsov
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT, 05401, USA.
| | - Yang Mao-Draayer
- Autoimmunity Center of Excellence, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Autoimmunity Center of Excellence, Multiple Sclerosis Center of Excellence, Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA.
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16
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Bischof PSP, Bartolomaeus TUP, Löber U, Bleidorn C. Microbiome Dynamics and Functional Composition in Coelopa frigida (Diptera, Coelopidae): Insights into Trophic Specialization of Kelp Flies. MICROBIAL ECOLOGY 2024; 87:91. [PMID: 38960913 PMCID: PMC11222186 DOI: 10.1007/s00248-024-02403-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 06/19/2024] [Indexed: 07/05/2024]
Abstract
Coelopidae (Diptera), known as kelp flies, exhibit an ecological association with beached kelp and other rotting seaweeds. This unique trophic specialization necessitates significant adaptations to overcome the limitations of an algal diet. We aimed to investigate whether the flies' microbiome could be one of these adaptive mechanisms. Our analysis focused on assessing composition and diversity of adult and larval microbiota of the kelp fly Coelopa frigida. Feeding habits of the larvae of this species have been subject of numerous studies, with debates whether they directly consume kelp or primarily feed on associated bacteria. By using a 16S rRNA metabarcoding approach, we found that the larval microbiota displayed considerably less diversity than adults, heavily dominated by only four operational taxonomic units (OTUs). Phylogenetic placement recovered the most dominant OTU of the larval microbiome, which is the source of more than half of all metabarcoding sequence reads, as an undescribed genus of Orbaceae (Gammaproteobacteria). Interestingly, this OTU is barely found among the 15 most abundant taxa of the adult microbiome, where it is responsible for less than 2% of the metabarcoding sequence reads. The other three OTUs dominating the larval microbiome have been assigned as Psychrobacter (Gammaproteobacteria), Wohlfahrtiimonas (Gammaproteobacteria), and Cetobacterium (Fusobacteriota). Moreover, we also uncovered a distinct shift in the functional composition between the larval and adult stages, where our taxonomic profiling suggests a significant decrease in functional diversity in larval samples. Our study offers insights into the microbiome dynamics and functional composition of Coelopa frigida.
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Affiliation(s)
- Paul S P Bischof
- Department for Animal Evolution and Biodiversity, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Theda U P Bartolomaeus
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Centre for Cardiovascular Research, Berlin, Germany
| | - Ulrike Löber
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Centre for Cardiovascular Research, Berlin, Germany
| | - Christoph Bleidorn
- Department for Animal Evolution and Biodiversity, Georg-August-Universität Göttingen, Göttingen, Germany.
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain.
- Biologische Anstalt Helgoland, Alfred Wegener Institute, Helgoland, Germany.
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17
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Dalsgaard NB, Gasbjerg LS, Hansen LS, Nielsen DS, Rasmussen TS, Knop FK. Two weeks of acarbose treatment shows no effect on gut microbiome composition in patients with type 2 diabetes: a randomised, placebo-controlled, double-blind, crossover study. Endocr Connect 2024; 13:e240052. [PMID: 38842918 PMCID: PMC11227053 DOI: 10.1530/ec-24-0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 06/06/2024] [Indexed: 06/07/2024]
Abstract
Aim The alpha-glucosidase inhibitor acarbose is approved for the treatment of type 2 diabetes (T2D). It acts in the lumen of the gut by reducing intestinal hydrolysis and absorption of ingested carbohydrates. This reduces postprandial blood glucose concentration and increases the content of carbohydrates in the distal parts of the intestine potentially influencing gut microbiome (GM) composition and possibly impacting the gut microbiome (GM) dysbiosis associated with T2D. Here, we investigated the effect of acarbose on GM composition in patients with T2D. Methods Faecal samples were collected in a previously conducted randomised, placebo-controlled, double-blind, crossover study in which 15 individuals with metformin-treated T2D (age 57-85 years, HbA1c 40-74 mmol/mol, BMI 23.6-34.6 kg/m2) were subjected to two 14-day treatment periods with acarbose and placebo, respectively, separated by a 6-week wash-out period. Faecal samples were collected before and by the end of each treatment period. The GM profiles were evaluated by 16S rRNA gene amplicon sequencing. Results The GM profiles after the treatment periods with acarbose or placebo remained unaffected (P > 0.7) when compared with the GM profiles before treatment. This applied to the analysis of within-sample diversity (α-diversity) and between-sample bacterial composition diversity (β-diversity). Additionally, no dominant bacterial species differentiated the treatment groups, and only minor increases in the relative abundances of Klebsiella spp. and Escherichia coli (P < 0.05) were observed after acarbose treatment. Conclusion In patients with metformin-treated T2D, 14 days of treatment with acarbose showed only minor effects on GM as seen in increased relative abundances of Klebsiella spp. and Escherichia coli.
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Affiliation(s)
- Niels B Dalsgaard
- Center for Clinical Metabolic Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - Lærke S Gasbjerg
- Center for Clinical Metabolic Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Laura S Hansen
- Center for Clinical Metabolic Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - Dennis S Nielsen
- Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Torben S Rasmussen
- Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Filip K Knop
- Center for Clinical Metabolic Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
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18
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Lavilla-Lerma ML, Aibar-Almazán A, Martínez-Amat A, Jiménez-García JD, Hita-Contreras F. Moderate-intensity continuous training and high-intensity interval training modulate the composition of the oral microbiota of elderly adults: Randomized controlled trial. Maturitas 2024; 185:107973. [PMID: 38579579 DOI: 10.1016/j.maturitas.2024.107973] [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: 10/20/2023] [Revised: 02/12/2024] [Accepted: 03/13/2024] [Indexed: 04/07/2024]
Abstract
OBJECTIVE We investigates the effects of 16-week high-intensity interval training and moderate-intensity continuous training on the composition of the oral microbiota. To the best of our knowledge, at the time of writing this paper no other scholars had described the oral metagenomic changes associated with prescribed exercise in older adults. METHODS Forty-three participants aged 60-74 years were randomized 1:1:1 to a control group, high-intensity interval training or moderate-intensity continuous training twice weekly for 16 weeks. Saliva samples were sequenced at baseline, week 8 and week 16 of intervention. RESULTS High-intensity interval training produced significant differences over time in Richness and a clear trend to decreased Simpson and Shannon diversity indices. In contrast, Simpson and Shannon indices showed an upward trend over time with moderate-intensity continuous training, which also decreased Firmicutes and increased Bacteroidetes levels. Significant differences in the abundance of pathogenic species were also observed after the participants completed the exercise interventions of either type. CONCLUSIONS Both types of exercise promoted subtle changes in the oral microbiota, confirming the modulatory effect of high-intensity interval training and moderate-intensity continuous training on the oral microbiome. Clinical trial registration NCT05220670.
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Affiliation(s)
| | - Agustín Aibar-Almazán
- Department of Health Sciences, Faculty of Heath Sciences, University of Jaén, 23071 Jaén, Spain.
| | - Antonio Martínez-Amat
- Department of Health Sciences, Faculty of Heath Sciences, University of Jaén, 23071 Jaén, Spain.
| | | | - Fidel Hita-Contreras
- Department of Health Sciences, Faculty of Heath Sciences, University of Jaén, 23071 Jaén, Spain.
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Kebede V, Ravizza T, Balosso S, Di Sapia R, Canali L, Soldi S, Galletti S, Papazlatani C, Karas PA, Vasileiadis S, Sforzini A, Pasetto L, Bonetto V, Vezzani A, Vesci L. Early treatment with rifaximin during epileptogenesis reverses gut alterations and reduces seizure duration in a mouse model of acquired epilepsy. Brain Behav Immun 2024; 119:363-380. [PMID: 38608741 DOI: 10.1016/j.bbi.2024.04.007] [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: 10/19/2023] [Revised: 04/04/2024] [Accepted: 04/09/2024] [Indexed: 04/14/2024] Open
Abstract
The gut microbiota is altered in epilepsy and is emerging as a potential target for new therapies. We studied the effects of rifaximin, a gastrointestinal tract-specific antibiotic, on seizures and neuropathology and on alterations in the gut and its microbiota in a mouse model of temporal lobe epilepsy (TLE). Epilepsy was induced by intra-amygdala kainate injection causing status epilepticus (SE) in C57Bl6 adult male mice. Sham mice were injected with vehicle. Two cohorts of SE mice were fed a rifaximin-supplemented diet for 21 days, starting either at 24 h post-SE (early disease stage) or at day 51 post-SE (chronic disease stage). Corresponding groups of SE mice (one each disease stage) were fed a standard (control) diet. Cortical ECoG recording was done at each disease stage (24/7) for 21 days in all SE mice to measure the number and duration of spontaneous seizures during either rifaximin treatment or control diet. Then, epileptic mice ± rifaximin and respective sham mice were sacrificed and brain, gut and feces collected. Biospecimens were used for: (i) quantitative histological analysis of the gut structural and cellular components; (ii) markers of gut inflammation and intestinal barrier integrity by RTqPCR; (iii) 16S rRNA metagenomics analysis in feces. Hippocampal neuronal cell loss was assessed in epileptic mice killed in the early disease phase. Rifaximin administered for 21 days post-SE (early disease stage) reduced seizure duration (p < 0.01) and prevented hilar mossy cells loss in the hippocampus compared to epileptic mice fed a control diet. Epileptic mice fed a control diet showed a reduction of both villus height and villus height/crypt depth ratio (p < 0.01) and a decreased number of goblet cells (p < 0.01) in the duodenum, as well as increased macrophage (Iba1)-immunostaining in the jejunum (p < 0.05), compared to respective sham mice. Rifaximin's effect on seizures was associated with a reversal of gut structural and cellular changes, except for goblet cells which remained reduced. Seizure duration in epileptic mice was negatively correlated with the number of mossy cells (p < 0.01) and with villus height/crypt depth ratio (p < 0.05). Rifaximin-treated epileptic mice also showed increased tight junctions (occludin and ZO-1, p < 0.01) and decreased TNF mRNA expression (p < 0.01) in the duodenum compared to epileptic mice fed a control diet. Rifaximin administered for 21 days in chronic epileptic mice (chronic disease stage) did not change the number or duration of seizures compared to epileptic mice fed a control diet. Chronic epileptic mice fed a control diet showed an increased crypt depth (p < 0.05) and reduced villus height/crypt depth ratio (p < 0.01) compared to respective sham mice. Rifaximin treatment did not affect these intestinal changes. At both disease stages, rifaximin modified α- and β-diversity in epileptic and sham mice compared to respective mice fed a control diet. The microbiota composition in epileptic mice, as well as the effects of rifaximin at the phylum, family and genus levels, depended on the stage of the disease. During the early disease phase, the abundance of specific taxa was positively correlated with seizure duration in epileptic mice. In conclusion, gut-related alterations reflecting a dysfunctional state, occur during epilepsy development in a TLE mouse model. A short-term treatment with rifaximin during the early phase of the disease, reduced seizure duration and neuropathology, and reversed some intestinal changes, strengthening the therapeutic effects of gut-based therapies in epilepsy.
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Affiliation(s)
- Valentina Kebede
- Department of Acute Brain and Cardiovascular Injury, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Teresa Ravizza
- Department of Acute Brain and Cardiovascular Injury, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Silvia Balosso
- Department of Acute Brain and Cardiovascular Injury, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Rossella Di Sapia
- Department of Acute Brain and Cardiovascular Injury, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Luca Canali
- Department of Acute Brain and Cardiovascular Injury, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Sara Soldi
- AAT Advanced Analytical Technologies Srl, Fiorenzuola d'Arda (PC), Italy
| | - Serena Galletti
- AAT Advanced Analytical Technologies Srl, Fiorenzuola d'Arda (PC), Italy
| | - Christina Papazlatani
- Dept. Biochemistry and Biotechnology University of Thessaly Biopolis, Larissa, Greece
| | - Panagiotis A Karas
- Dept. Biochemistry and Biotechnology University of Thessaly Biopolis, Larissa, Greece
| | - Sotirios Vasileiadis
- Dept. Biochemistry and Biotechnology University of Thessaly Biopolis, Larissa, Greece
| | | | - Laura Pasetto
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Valentina Bonetto
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Annamaria Vezzani
- Department of Acute Brain and Cardiovascular Injury, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy.
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20
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Suparan K, Sriwichaiin S, Thonusin C, Sripetchwandee J, Khuanjing T, Maneechote C, Nawara W, Arunsak B, Chattipakorn N, Chattipakorn SC. Donepezil ameliorates gut barrier disruption in doxorubicin-treated rats. Food Chem Toxicol 2024; 189:114741. [PMID: 38759714 DOI: 10.1016/j.fct.2024.114741] [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: 09/27/2023] [Revised: 11/03/2023] [Accepted: 05/13/2024] [Indexed: 05/19/2024]
Abstract
An impact of donepezil against doxorubicin-induced gut barrier disruption and gut dysbiosis has never been investigated. Twenty-four male Wistar rats were divided into three groups. Each group was treated with either vehicle as a control, doxorubicin, or doxorubicin-cotreated with donepezil. Heart rate variability was assessed to reflect the impact of doxorubicin and donepezil. Then, animals were euthanized, and the ileum and its contents were collected in each case to investigate the gut barrier and gut microbiota, respectively. The microbiota-derived endotoxin, trimethylamine N-oxide (TMAO), and short-chain fatty acids (SCFAs) in the serum were determined. An increase in the sympathetic tone, endotoxins, and TMAO levels with disruption of the gut barrier and a decrease in SCFAs levels were observed in doxorubicin-treated rats. Gut microbiota of doxorubicin-treated rats was significantly different from that of the control group. Donepezil treatment significantly decreased the sympathetic tone, restored the gut barrier, and reduced endotoxin and TMAO levels in doxorubicin-treated rats. Nonetheless, donepezil administration did not alter the gut microbiota profile and levels of SCFAs in doxorubicin-treated rats. Doxorubicin impaired the autonomic balance and the gut barrier, and induced gut dysbiosis, resulting in gut toxicity. Donepezil partially improved the doxorubicin-induced gut toxicity through balancing the autonomic disturbance.
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Affiliation(s)
- Kanokphong Suparan
- Immunology Unit, Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand; Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand; Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai, 50200, Thailand; Cardiac Electrophysiology Unit, Department of Physiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Sirawit Sriwichaiin
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand; Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai, 50200, Thailand; Cardiac Electrophysiology Unit, Department of Physiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Chanisa Thonusin
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand; Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai, 50200, Thailand; Cardiac Electrophysiology Unit, Department of Physiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Jirapas Sripetchwandee
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand; Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai, 50200, Thailand; Cardiac Electrophysiology Unit, Department of Physiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Thawatchai Khuanjing
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand; Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai, 50200, Thailand; Cardiac Electrophysiology Unit, Department of Physiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Chayodom Maneechote
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand; Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai, 50200, Thailand; Cardiac Electrophysiology Unit, Department of Physiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Wichwara Nawara
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand; Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Busarin Arunsak
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand; Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Nipon Chattipakorn
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand; Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai, 50200, Thailand; Cardiac Electrophysiology Unit, Department of Physiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand; The Academy of Science, The Royal Society of Thailand, Bangkok, Thailand
| | - Siriporn C Chattipakorn
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand; Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai, 50200, Thailand; Department of Oral Biology and Diagnostic Sciences, Faculty of Dentistry, Chiang Mai University, Chiang Mai, 50200, Thailand.
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21
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Chen Y, Bell TH, Gourlie S, Lei YD, Wania F. Contaminant Biomagnification in Polar Bears: Interindividual Differences, Dietary Intake Rate, and the Gut Microbiome. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:10504-10514. [PMID: 38838208 PMCID: PMC11192032 DOI: 10.1021/acs.est.4c03302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/07/2024]
Abstract
Some persistent hydrophobic pollutants biomagnify, i.e., achieve higher contaminant levels in a predator than in its prey (Cpredator/Cprey > 1). This ratio is called the biomagnification factor (BMF) and is traditionally determined using tissues from carcasses or biopsies. Using a noninvasive method that relies on equilibrium sampling in silicone-film-coated vessels and chemical analysis of paired diet and feces, we determined on three occasions the thermodynamic biomagnification limit (BMFlim) and feces-based biomagnification factor (BMFF) for three zoo-housed polar bears who experience seasonal periods of hyperphagia and hypophagia. All bears had high biomagnification capabilities (BMFlim was up to 200) owing to very efficient lipid assimilation (up to 99.5%). The bears differed up to a factor of 3 in their BMFlim. BMFlim and BMFF of a bear increased by up to a factor of 4 during the hypophagic period, when the ingestion rate was greatly reduced. Much of that variability can be explained by differences in the lipid assimilation efficiency, even though this efficiency ranged only from 98.1 to 99.5%. A high BMFlim was associated with a high abundance of Bacteroidales and Lachnospirales in the gut microbiome. Biomagnification varies to a surprisingly large extent between individuals and within the same individual over time. Future work should investigate whether this can be attributed to the influence of the gut microbiome on lipid assimilation by studying more individual bears at different key physiological stages.
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Affiliation(s)
- Yuhao Chen
- Department
of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, Canada M1C 1A4
- Department
of Chemistry, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, Canada M1C 1A4
| | - Terrence H. Bell
- Department
of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, Canada M1C 1A4
| | - Sarra Gourlie
- Nutrition
Science, Toronto Zoo, 361A Old Finch Avenue, Toronto, Ontario, Canada M1B 5K7
| | - Ying Duan Lei
- Department
of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, Canada M1C 1A4
| | - Frank Wania
- Department
of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, Canada M1C 1A4
- Department
of Chemistry, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, Canada M1C 1A4
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22
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Rodriguez CI, Isobe K, Martiny JBH. Short-term dietary fiber interventions produce consistent gut microbiome responses across studies. mSystems 2024; 9:e0013324. [PMID: 38742890 PMCID: PMC11237734 DOI: 10.1128/msystems.00133-24] [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: 01/29/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
The composition of the human gut microbiome varies tremendously among individuals, making the effects of dietary or treatment interventions difficult to detect and characterize. The consumption of fiber is important for gut health, yet the specific effects of increased fiber intake on the gut microbiome vary across studies. The variation in study outcomes might be due to inter-individual (or inter-population) variation or to the details of the interventions including the types of fiber, length of study, size of cohort, and molecular approaches. Thus, to identify generally (on average) consistent fiber-induced responses in the gut microbiome of healthy individuals, we re-analyzed 16S rRNA sequencing data from 21 dietary fiber interventions from 12 human studies, which included 2,564 fecal samples from 538 subjects across all interventions. Short-term increases in dietary fiber consumption resulted in highly consistent gut bacterial community responses across studies. Increased fiber consumption explained an average of 1.5% of compositional variation (vs 82% of variation attributed to the individual), reduced alpha-diversity, and resulted in phylogenetically conserved responses in relative abundances among bacterial taxa. Additionally, we identified bacterial clades, at approximately the genus level, that were highly consistent in their response (on average, increasing or decreasing in their relative abundance) to dietary fiber interventions across the studies. IMPORTANCE Our study is an example of the power of synthesizing and reanalyzing 16S rRNA microbiome data from many intervention studies. Despite high inter-individual variation of the composition of the human gut microbiome, dietary fiber interventions cause a consistent response both in the degree of change and the particular taxa that respond to increased fiber.
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Affiliation(s)
- Cynthia I. Rodriguez
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Kazuo Isobe
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Jennifer B. H. Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
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23
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Ferreres-Serafini L, Martín-Orúe SM, Sadurní M, Jiménez J, Moreno-Muñoz JA, Castillejos L. Supplementing infant milk formula with a multi-strain synbiotic and osteopontin enhances colonic microbial colonization and modifies jejunal gene expression in lactating piglets. Food Funct 2024; 15:6536-6552. [PMID: 38807503 DOI: 10.1039/d4fo00489b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
A total of ninety-six weaned piglets were assigned to four dietary treatments in a 2 × 2 design. The treatments included: a standard milk formula (CTR); CTR + probiotics (6.4 × 108 cfu L-1Bifidobacterium longum subsp. infantis CECT 7210 and 1.1 × 108 cfu L-1Lactobacillus rhamnosus NH001) + prebiotics (galacto-oligosaccharides 4.36 g L-1 and human-milk-oligosaccharide 0.54 g L-1) (SYN); CTR + osteopontin (0.43 g L-1) (OPN); and CTR + SYN + OPN (CON). Daily records including feed intake, body weight, and clinical signs, were maintained throughout the 15-day trial. At the end of the study samples from blood, digestive content, and gut tissues were collected to determine serum TNF-α, intestinal fermentative activity (SCFA and ammonia), colonic microbiota (16S rRNA Illumina-MiSeq), histomorphology, and jejunal gene expression (Open-Array). No statistical differences were found in weight gain; however, the animals supplemented with osteopontin exhibited higher feed intake. In terms of clinical signs, synbiotic supplementation led to a shorter duration of diarrhoea episodes. Regarding gut health, the sequenced faecal microbiota revealed better control of potentially dysbiotic bacteria with the CON diet at day 15. In the colon compartment, a significant increase in SCFA concentration, a decrease in ammonia concentration, and a significant decrease in intraepithelial lymphocyte counts were particularly observed in CON animals. The supplemented diets were also associated with modified jejunal gene expression. The synbiotic combination was characterized by the upregulation of genes related to intestinal maturation (ALPI, SI) and nutrient transport (SLC13A1, SLC15A1, SLC5A1, SLC7A8), and the downregulation of genes related to the response to pathogens (GBP1, IDO, TLR4) or the inflammatory response (IDO, IL-1β, TGF-β1). Osteopontin promoted the upregulation of a digestive function gene (GCG). Correlational analysis between the microbiota population and various intestinal environmental factors (SCFA concentration, histology, and gene expression) proposes mechanisms of communication between the gut microbiota and the host. In summary, these results suggest an improvement in the colonic colonization process and a better modulation of the immune response when milk formula is supplemented with the tested synbiotic combined with osteopontin, benefiting from a synergistic effect.
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Affiliation(s)
- Laia Ferreres-Serafini
- Animal Nutrition and Welfare Service, Department of Animal and Food Science, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Susana Mª Martín-Orúe
- Animal Nutrition and Welfare Service, Department of Animal and Food Science, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Meritxell Sadurní
- Animal Nutrition and Welfare Service, Department of Animal and Food Science, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Jesús Jiménez
- Laboratorios Ordesa S.L., Parc Científic de Barcelona, C/Baldiri Reixac 15-21, 08028 Barcelona, Spain.
| | - José Antonio Moreno-Muñoz
- Laboratorios Ordesa S.L., Parc Científic de Barcelona, C/Baldiri Reixac 15-21, 08028 Barcelona, Spain.
| | - Lorena Castillejos
- Animal Nutrition and Welfare Service, Department of Animal and Food Science, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
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24
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Siti Farah Norasyikeen SO, Ngui R, Syaza Zafirah AR, Md Zoqratt MZH, Eng WWH, Ayub Q, Amin Nordin S, Narcisse Mary Sither Joseph V, Musa S, Lim YAL. Study on intestinal parasitic infections and gut microbiota in cancer patients at a tertiary teaching hospital in Malaysia. Sci Rep 2024; 14:13650. [PMID: 38871760 DOI: 10.1038/s41598-024-59969-6] [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: 12/06/2023] [Accepted: 04/17/2024] [Indexed: 06/15/2024] Open
Abstract
Intestinal parasitic infections (IPIs) can lead to significant morbidity and mortality in cancer patients. While they are unlikely to cause severe disease and are self-limiting in healthy individuals, cancer patients are especially susceptible to opportunistic parasitic infections. The gut microbiota plays a crucial role in various aspects of health, including immune regulation and metabolic processes. Parasites occupy the same environment as bacteria in the gut. Recent research suggests intestinal parasites can disrupt the normal balance of the gut microbiota. However, there is limited understanding of this co-infection dynamic among cancer patients in Malaysia. A study was conducted to determine the prevalence and relationship between intestinal parasites and gut microbiota composition in cancer patients. Stool samples from 134 cancer patients undergoing active treatment or newly diagnosed were collected and examined for the presence of intestinal parasites and gut microbiota composition. The study also involved 17 healthy individuals for comparison and control. Sequencing with 16S RNA at the V3-V4 region was used to determine the gut microbial composition between infected and non-infected cancer patients and healthy control subjects. The overall prevalence of IPIs among cancer patients was found to be 32.8%. Microsporidia spp. Accounted for the highest percentage at 20.1%, followed by Entamoeba spp. (3.7%), Cryptosporidium spp. (3.0%), Cyclospora spp. (2.2%), and Ascaris lumbricoides (0.8%). None of the health control subjects tested positive for intestinal parasites. The sequencing data analysis revealed that the gut microbiota diversity and composition were significantly different in cancer patients than in healthy controls (p < 0.001). A significant dissimilarity was observed in the bacterial composition between parasite-infected and non-infected patients based on Bray-Curtis (p = 0.041) and Jaccard (p = 0.021) measurements. Bacteria from the genus Enterococcus were enriched in the parasite-infected groups, while Faecalibacterium prausnitzii reduced compared to non-infected and control groups. Further analysis between different IPIs and non-infected individuals demonstrated a noteworthy variation in Entamoeba-infected (unweighted UniFrac: p = 0.008), Cryptosporidium-infected (Bray-Curtis: p = 0.034) and microsporidia-infected (unweighted: p = 0.026; weighted: p = 0.019; Jaccard: p = 0.031) samples. No significant dissimilarity was observed between Cyclospora-infected groups and non-infected groups. Specifically, patients infected with Cryptosporidium and Entamoeba showed increased obligate anaerobic bacteria. Clostridiales were enriched with Entamoeba infections, whereas those from Coriobacteriales decreased. Bacteroidales and Clostridium were found in higher abundance in the gut microbiota with Cryptosporidium infection, while Bacillales decreased. Additionally, bacteria from the genus Enterococcus were enriched in microsporidia-infected patients. In contrast, bacteria from the Clostridiales order, Faecalibacterium, Parabacteroides, Collinsella, Ruminococcus, and Sporosarcina decreased compared to the non-infected groups. These findings underscore the importance of understanding and managing the interactions between intestinal parasites and gut microbiota for improved outcomes in cancer patients.
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Affiliation(s)
- Sidi Omar Siti Farah Norasyikeen
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
- Department of Paraclinical Sciences, Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Malaysia
| | - Romano Ngui
- Department of Paraclinical Sciences, Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Malaysia.
| | - Ab Rahman Syaza Zafirah
- Department of Paediatrics, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | | | - Wilhelm Wei Han Eng
- Monash University Malaysia Genomics Facility, Monash University Malaysia, 47500, Subang Jaya, Malaysia
| | - Qasim Ayub
- Monash University Malaysia Genomics Facility, Monash University Malaysia, 47500, Subang Jaya, Malaysia
| | - Syafinaz Amin Nordin
- Department of Microbiology, Faculty of Medicine & Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Malaysia
| | | | - Sabri Musa
- Department of Children's Dentistry and Orthodontics, Faculty of Dentistry, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Yvonne Ai Lian Lim
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
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25
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Robins K, O'Donnell G, Neumann A, Schmidt W, Hart A, Graham DW. Antimicrobial resistance in rural rivers: Comparative study of the Coquet (Northumberland) and Eden (Cumbria) River catchments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172348. [PMID: 38614353 DOI: 10.1016/j.scitotenv.2024.172348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/15/2024]
Abstract
Many studies have characterised resistomes in river microbial communities. However, few have compared resistomes in parallel rural catchments that have few point-source inputs of antimicrobial genes (ARGs) and organisms (i.e., AMR) - catchments where one can contrast more nebulous drivers of AMR in rural rivers. Here, we used quantitative microbial profiling (QMP) to compare resistomes and microbiomes in two rural river catchments in Northern England, the Coquet and Eden in Northumberland and Cumbria, respectively, with different hydrological and geographical conditions. The Eden has higher flow rates, higher annual surface runoff, and longer periods of soil saturation, whereas the Coquet is drier and has lower flowrates. QMP analysis showed the Eden contained significantly more abundant microbes associated with soil sources, animal faeces, and wastewater than the Coquet, which had microbiomes like less polluted rivers (Wilcoxon test, p < 0.01). The Eden also had greater ARG abundances and resistome diversity (Kruskal Wallis, p < 0.05), and higher levels of potentially clinically relevant ARGs. The Eden catchment had greater and flashier runoff and more extensive agricultural land use in its middle reach, which explains higher levels of AMR in the river. Hydrological and geographic factors drive AMR in rural rivers, which must be considered in environmental monitoring programmes.
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Affiliation(s)
- Katie Robins
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Greg O'Donnell
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Anke Neumann
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Wiebke Schmidt
- Chief Scientists Group, Environment Agency, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - Alwyn Hart
- Chief Scientists Group, Environment Agency, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
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26
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Wang B, Luan Y. Evaluation of normalization methods for predicting quantitative phenotypes in metagenomic data analysis. Front Genet 2024; 15:1369628. [PMID: 38903761 PMCID: PMC11188486 DOI: 10.3389/fgene.2024.1369628] [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: 01/12/2024] [Accepted: 05/13/2024] [Indexed: 06/22/2024] Open
Abstract
Genotype-to-phenotype mapping is an essential problem in the current genomic era. While qualitative case-control predictions have received significant attention, less emphasis has been placed on predicting quantitative phenotypes. This emerging field holds great promise in revealing intricate connections between microbial communities and host health. However, the presence of heterogeneity in microbiome datasets poses a substantial challenge to the accuracy of predictions and undermines the reproducibility of models. To tackle this challenge, we investigated 22 normalization methods that aimed at removing heterogeneity across multiple datasets, conducted a comprehensive review of them, and evaluated their effectiveness in predicting quantitative phenotypes in three simulation scenarios and 31 real datasets. The results indicate that none of these methods demonstrate significant superiority in predicting quantitative phenotypes or attain a noteworthy reduction in Root Mean Squared Error (RMSE) of the predictions. Given the frequent occurrence of batch effects and the satisfactory performance of batch correction methods in predicting datasets affected by these effects, we strongly recommend utilizing batch correction methods as the initial step in predicting quantitative phenotypes. In summary, the performance of normalization methods in predicting metagenomic data remains a dynamic and ongoing research area. Our study contributes to this field by undertaking a comprehensive evaluation of diverse methods and offering valuable insights into their effectiveness in predicting quantitative phenotypes.
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Affiliation(s)
- Beibei Wang
- Frontier Science Center for Nonlinear Expectations, Ministry of Education, Qingdao, China
- Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, China
- School of Mathematics, Shandong University, Jinan, China
| | - Yihui Luan
- Frontier Science Center for Nonlinear Expectations, Ministry of Education, Qingdao, China
- Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, China
- School of Mathematics, Shandong University, Jinan, China
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Benton LD, Lopez-Galvez N, Herman C, Caporaso JG, Cope EK, Rosales C, Gameros M, Lothrop N, Martínez FD, Wright AL, Carr TF, Beamer PI. Environmental and structural factors associated with bacterial diversity in household dust across the Arizona-Sonora border. Sci Rep 2024; 14:12803. [PMID: 38834753 PMCID: PMC11150412 DOI: 10.1038/s41598-024-63356-6] [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: 09/04/2023] [Accepted: 05/28/2024] [Indexed: 06/06/2024] Open
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, 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 Mexican homes was enriched with Alishewanella, Paracoccus, Rheinheimera genera and Intrasporangiaceae family. 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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Affiliation(s)
- Lauren D Benton
- Department of Pediatrics, Steele Children's Research Center, College of Medicine, University of Arizona Health Sciences, 1501 N. Campbell Avenue, Tucson, AZ, 85724, USA.
- Asthma and Airway Disease Research Center, University of Arizona, College of Medicine, University of Arizona Health Sciences, 1501 N. Campbell Avenue, Tucson, AZ, 85724, USA.
| | - Nicolas Lopez-Galvez
- Mel and Enid Zuckerman College of Public Health, University of Arizona, 1295 N. Martin Ave, PO 245210, Tucson, AZ, 85724, USA
- San Diego State University Research Foundation, San Diego State University, 5250 Campanile Dr, San Diego, CA, 92182, USA
| | - Chloe Herman
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, 1350 S Knoles Dr, Flagstaff, AZ, 86011, USA
- School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - J Gregory Caporaso
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, 1350 S Knoles Dr, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
- School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Emily K Cope
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, 1350 S Knoles Dr, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Cecilia Rosales
- Mel and Enid Zuckerman College of Public Health, University of Arizona, 1295 N. Martin Ave, PO 245210, Tucson, AZ, 85724, USA
| | - Mercedes Gameros
- Mel and Enid Zuckerman College of Public Health, University of Arizona, 1295 N. Martin Ave, PO 245210, Tucson, AZ, 85724, USA
| | - Nathan Lothrop
- Asthma and Airway Disease Research Center, University of Arizona, College of Medicine, University of Arizona Health Sciences, 1501 N. Campbell Avenue, Tucson, AZ, 85724, USA
- Mel and Enid Zuckerman College of Public Health, University of Arizona, 1295 N. Martin Ave, PO 245210, Tucson, AZ, 85724, USA
| | - Fernando D Martínez
- Asthma and Airway Disease Research Center, University of Arizona, College of Medicine, University of Arizona Health Sciences, 1501 N. Campbell Avenue, Tucson, AZ, 85724, USA
| | - Anne L Wright
- Asthma and Airway Disease Research Center, University of Arizona, College of Medicine, University of Arizona Health Sciences, 1501 N. Campbell Avenue, Tucson, AZ, 85724, USA
| | - Tara F Carr
- Asthma and Airway Disease Research Center, University of Arizona, College of Medicine, University of Arizona Health Sciences, 1501 N. Campbell Avenue, Tucson, AZ, 85724, USA
| | - Paloma I Beamer
- Asthma and Airway Disease Research Center, University of Arizona, College of Medicine, University of Arizona Health Sciences, 1501 N. Campbell Avenue, Tucson, AZ, 85724, USA
- Mel and Enid Zuckerman College of Public Health, University of Arizona, 1295 N. Martin Ave, PO 245210, Tucson, AZ, 85724, USA
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Pierce R, Jan NJ, Kumar P, Middleton J, Petri WA, Marie C. Persistent dysbiosis of duodenal microbiota in patients with controlled pediatric Crohn's disease after resolution of inflammation. Sci Rep 2024; 14:12668. [PMID: 38830904 PMCID: PMC11148174 DOI: 10.1038/s41598-024-63299-y] [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: 10/05/2023] [Accepted: 05/27/2024] [Indexed: 06/05/2024] Open
Abstract
Crohn's disease is an inflammatory condition of the intestine characterized by largely unknown etiology and a relapse remission cycle of disease control. While possible triggers have been identified, research is inconsistent on the precise cause of these relapses, especially in the under-researched pediatric population. We hypothesized that patients in remission would have persistent microbial and inflammatory changes in small intestinal tissue that might trigger relapse. To this end, we analyzed intestinal biopsy samples from six patients with pediatric Crohn's disease in remission and a control group of 16 pediatric patients with no evident pathogenic abnormality. We identified compositional microbiota differences, including decreases in the genera Streptococcus and Actinobacillus as well as increases in Oribacterium and Prevotella in patients with controlled Crohn's disease compared to controls. Further, a histologic analysis found that patients with controlled Crohn's disease had increased epithelial integrity, and decreased intraepithelial lymphocytes compared with controls. Additionally, we observed increased peripheral CD4+ T cells in patients with pediatric Crohn's disease. These results indicate that markers of intestinal inflammation are responsive to Crohn's disease treatment, however the interventions may not resolve the underlying dysbiosis. These findings suggest that persistent dysbiosis may increase vulnerability to relapse of pediatric Crohn's disease. This study used a nested cohort of patients from the Bangladesh Environmental Enteric Dysfunction (BEED) study (ClinicalTrials.gov ID: NCT02812615 Date of first registration: 24/06/2016).
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Affiliation(s)
- Rebecca Pierce
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Ning-Jiun Jan
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Pankaj Kumar
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Jeremy Middleton
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - William A Petri
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Chelsea Marie
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA, USA.
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Rund H, Wanzenböck J, Dobrovolny S, Kurmayer R. Relating target fish DNA concentration to community composition analysis in freshwater fish via metabarcoding. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172281. [PMID: 38588740 DOI: 10.1016/j.scitotenv.2024.172281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/04/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024]
Abstract
Metabarcoding has been widely accepted as a useful tool for biodiversity assessment based on eDNA. The method allows for the detection of entire groups of organisms in a single sample, making it particularly applicable in aquatic habitats. The high sensitivity of the molecular approaches is especially beneficial in detecting elusive and rare fish species, improving biodiversity assessments. Numerous biotic and abiotic factors that affect the persistence and availability of fish DNA in surface waters and therefore affecting species detectability, have been identified. However, little is known about the relationship between the total fish DNA concentration and the detectability of differential abundant species. In this study three controlled mock-community DNA samples (56 individual samples) were analyzed by (i) metabarcoding (MiSeq) of 12S rDNA (175 bp) and by (ii) total freshwater fish DNA quantification (via qPCR of 12S rDNA). We show that the fish DNA quantity affects the relative abundance of species-specific sequences and the detectability of rare species. In particular we found that samples with a concentration between 1000 pg/μL down to 10 pg/μL of total fish DNA revealed a stable relative frequency of DNA sequences obtained for a specific fish species, as well as a low variability between replicates. Additionally, we observed that even in complex mock-community DNA samples, a total fish DNA concentration of 23 pg/μL was sufficient to reliably detect all species in every replicate, including three rare species with proportions of ≤0.5 %. We also found that the DNA barcode similarity between species can affect detectability, if evenness is low. Our data suggest that the total DNA concentration of fish is an important factor to consider when analyzing and interpreting relative sequence abundance data. Therefore, the workflow proposed here will contribute to an ecologically and economically efficient application of metabarcoding in fish biodiversity assessment.
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Affiliation(s)
- Hans Rund
- Research Department for Limnology, Mondsee, Universität Innsbruck, Mondseestraße 9, 5310 Mondsee, Austria.
| | - Josef Wanzenböck
- Research Department for Limnology, Mondsee, Universität Innsbruck, Mondseestraße 9, 5310 Mondsee, Austria
| | - Stefanie Dobrovolny
- Department for Molecular Biology and Microbiology, Institute for Food Safety Vienna, Austrian Agency for Health and Food Safety, Spargelfeldstraße 191, 1220 Vienna, Austria
| | - Rainer Kurmayer
- Research Department for Limnology, Mondsee, Universität Innsbruck, Mondseestraße 9, 5310 Mondsee, Austria
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Leite G, Barlow GM, Rashid M, Hosseini A, Cohrs D, Parodi G, Morales W, Weitsman S, Rezaie A, Pimentel M, Mathur R. Characterization of the Small Bowel Microbiome Reveals Different Profiles in Human Subjects Who Are Overweight or Have Obesity. Am J Gastroenterol 2024; 119:1141-1153. [PMID: 38578969 PMCID: PMC11142649 DOI: 10.14309/ajg.0000000000002790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/14/2024] [Indexed: 04/07/2024]
Abstract
INTRODUCTION Gut microbiome changes are linked to obesity, but findings are based on stool data. In this article, we analyzed the duodenal microbiome and serum biomarkers in subjects with normal weight, overweight, and obesity. METHODS Duodenal aspirates and serum samples were obtained from subjects undergoing standard-of-care esophagogastroduodenoscopy without colon preparation. Aspirate DNAs were analyzed by 16S rRNA and shotgun sequencing. Predicted microbial metabolic functions and serum levels of metabolic and inflammatory biomarkers were also assessed. RESULTS Subjects with normal weight (N = 105), overweight (N = 67), and obesity (N = 42) were identified. Overweight-specific duodenal microbial features include lower relative abundance (RA) of Bifidobacterium species and Escherichia coli strain K-12 and higher Lactobacillus intestinalis , L. johnsonii , and Prevotella loescheii RA. Obesity-specific features include higher Lactobacillus gasseri RA and lower L. reuteri (subspecies rodentium ), Alloprevotella rava , and Leptotrichia spp RA. Escalation features (progressive changes from normal weight through obesity) include decreasing Bacteroides pyogenes , Staphylococcus hominis , and unknown Faecalibacterium species RA, increasing RA of unknown Lactobacillus and Mycobacterium species, and decreasing microbial potential for biogenic amines metabolism. De-escalation features (direction of change altered in normal to overweight and overweight to obesity) include Lactobacillus acidophilus , L. hominis , L. iners , and Bifidobacterium dentium . An unknown Lactobacillus species is associated with type IIa dyslipidemia and overweight, whereas Alloprevotella rava is associated with type IIb and IV dyslipidemias. DISCUSSION Direct analysis of the duodenal microbiome has identified key genera associated with overweight and obesity, including some previously identified in stool, e.g., Bifidobacterium and Lactobacillus . Specific species and strains exhibit differing associations with overweight and obesity, including escalation and de-escalation features that may represent targets for future study and therapeutics.
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Affiliation(s)
- Gabriela Leite
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, California, USA
| | - Gillian M. Barlow
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, California, USA
| | - Mohamad Rashid
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, California, USA
| | - Ava Hosseini
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, California, USA
| | - Daniel Cohrs
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, California, USA
| | - Gonzalo Parodi
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, California, USA
| | - Walter Morales
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, California, USA
| | - Stacy Weitsman
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, California, USA
| | - Ali Rezaie
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, California, USA
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai, Los Angeles, California, USA
| | - Mark Pimentel
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, California, USA
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai, Los Angeles, California, USA
| | - Ruchi Mathur
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, California, USA
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai, Los Angeles, California, USA
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Bosch J, Lebre PH, Marais E, Maggs‐Kölling G, Cowan DA. Kinetics and pathways of sub-lithic microbial community (hypolithon) development. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13290. [PMID: 38923208 PMCID: PMC11194044 DOI: 10.1111/1758-2229.13290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 05/03/2024] [Indexed: 06/28/2024]
Abstract
Type I hypolithons are microbial communities dominated by Cyanobacteria. They adhere to the underside of semi-translucent rocks in desert pavements, providing them with a refuge from the harsh abiotic stresses found on the desert soil surface. Despite their crucial role in soil nutrient cycling, our understanding of their growth rates and community development pathways remains limited. This study aimed to quantify the dynamics of hypolithon formation in the pavements of the Namib Desert. We established replicate arrays of sterile rock tiles with varying light transmission in two areas of the Namib Desert, each with different annual precipitation regimes. These were sampled annually over 7 years, and the samples were analysed using eDNA extraction and 16S rRNA gene amplicon sequencing. Our findings revealed that in the zone with higher precipitation, hypolithon formation became evident in semi-translucent rocks 3 years after the arrays were set up. This coincided with a Cyanobacterial 'bloom' in the adherent microbial community in the third year. In contrast, no visible hypolithon formation was observed at the array set up in the hyper-arid zone. This study provides the first quantitative evidence of the kinetics of hypolithon development in hot desert environments, suggesting that development rates are strongly influenced by precipitation regimes.
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Affiliation(s)
- Jason Bosch
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and MicrobiologyUniversity of PretoriaPretoriaSouth Africa
- Institute of Microbiology of the Czech Academy of SciencesCzech Academy of SciencesPrahaCzech Republic
| | - Pedro H. Lebre
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and MicrobiologyUniversity of PretoriaPretoriaSouth Africa
| | | | | | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and MicrobiologyUniversity of PretoriaPretoriaSouth Africa
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Abegaz F, Abedini D, White F, Guerrieri A, Zancarini A, Dong L, Westerhuis JA, van Eeuwijk F, Bouwmeester H, Smilde AK. A strategy for differential abundance analysis of sparse microbiome data with group-wise structured zeros. Sci Rep 2024; 14:12433. [PMID: 38816496 PMCID: PMC11139916 DOI: 10.1038/s41598-024-62437-w] [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: 08/28/2023] [Accepted: 05/16/2024] [Indexed: 06/01/2024] Open
Abstract
Comparing the abundance of microbial communities between different groups or obtained under different experimental conditions using count sequence data is a challenging task due to various issues such as inflated zero counts, overdispersion, and non-normality. Several methods and procedures based on counts, their transformation and compositionality have been proposed in the literature to detect differentially abundant species in datasets containing hundreds to thousands of microbial species. Despite efforts to address the large numbers of zeros present in microbiome datasets, even after careful data preprocessing, the performance of existing methods is impaired by the presence of inflated zero counts and group-wise structured zeros (i.e. all zero counts in a group). We propose and validate using extensive simulations an approach combining two differential abundance testing methods, namely DESeq2-ZINBWaVE and DESeq2, to address the issues of zero-inflation and group-wise structured zeros, respectively. This combined approach was subsequently successfully applied to two plant microbiome datasets that revealed a number of taxa as interesting candidates for further experimental validation.
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Affiliation(s)
- Fentaw Abegaz
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands.
- Biometris, Wageningen University & Research, 6708 PB, Wageningen, The Netherlands.
| | - Davar Abedini
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands
| | - Fred White
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands
| | - Alessandra Guerrieri
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands
| | - Anouk Zancarini
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
| | - Lemeng Dong
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands
| | - Johan A Westerhuis
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands
| | - Fred van Eeuwijk
- Biometris, Wageningen University & Research, 6708 PB, Wageningen, The Netherlands
| | - Harro Bouwmeester
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands
| | - Age K Smilde
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands
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Ayayee PA, Wong RY. Zebrafish ( Danio rerio) behavioral phenotypes not underscored by different gut microbiota. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596447. [PMID: 38853862 PMCID: PMC11160693 DOI: 10.1101/2024.05.29.596447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Different animal behavioral phenotypes maintained and selectively bred over multiple generations may be underscored by dissimilar gut microbial community compositions or not have any significant dissimilarity in community composition. Operating within the microbiota-gut-brain axis framework, we anticipated differences in gut microbiome profiles between zebrafish (Danio rerio) selectively bred to display the bold and shy personality types. This would highlight gut microbe-mediated effects on host behavior. To this end, we amplified and sequenced a fragment of the 16S rRNA gene from the guts of bold and shy zebrafish individuals (n=10) via Miseq. We uncovered no significant difference in within-group microbial diversity nor between-group microbial community composition of the two behavioral phenotypes. Interestingly, though not statistically different, we determined that the gut microbial community of the bold phenotype was dominated by Burkholderiaceae, Micropepsaceae, and Propionibacteriaceae. In contrast, the shy phenotype was dominated by Beijerinckaceae, Pirelullacaeae, Rhizobiales_Incertis_Sedis, and Rubinishaeraceae. The absence of any significant difference in gut microbiota profiles between the two phenotypes would suggest that in this species, there might exist a stable "core" gut microbiome, regardless of behavioral phenotypes, and or possibly, a limited role for the gut microbiota in modulating this selected-for host behavior. This is the first study to characterize the gut microbial community of distinct innate behavioral phenotypes of the zebrafish (that are not considered dysbiotic states) and not rely on antibiotic or probiotic treatments to induce changes in behavior. Such studies are crucial to our understanding of the modulating impacts of the gut microbiome on normative animal behavior.
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Affiliation(s)
- Paul A Ayayee
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, USA
| | - Ryan Y Wong
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, USA
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Teixeira M, Silva F, Ferreira RM, Pereira T, Figueiredo C, Oliveira HP. A review of machine learning methods for cancer characterization from microbiome data. NPJ Precis Oncol 2024; 8:123. [PMID: 38816569 PMCID: PMC11139966 DOI: 10.1038/s41698-024-00617-7] [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: 01/15/2024] [Accepted: 05/17/2024] [Indexed: 06/01/2024] Open
Abstract
Recent studies have shown that the microbiome can impact cancer development, progression, and response to therapies suggesting microbiome-based approaches for cancer characterization. As cancer-related signatures are complex and implicate many taxa, their discovery often requires Machine Learning approaches. This review discusses Machine Learning methods for cancer characterization from microbiome data. It focuses on the implications of choices undertaken during sample collection, feature selection and pre-processing. It also discusses ML model selection, guiding how to choose an ML model, and model validation. Finally, it enumerates current limitations and how these may be surpassed. Proposed methods, often based on Random Forests, show promising results, however insufficient for widespread clinical usage. Studies often report conflicting results mainly due to ML models with poor generalizability. We expect that evaluating models with expanded, hold-out datasets, removing technical artifacts, exploring representations of the microbiome other than taxonomical profiles, leveraging advances in deep learning, and developing ML models better adapted to the characteristics of microbiome data will improve the performance and generalizability of models and enable their usage in the clinic.
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Affiliation(s)
- Marco Teixeira
- Institute for Systems and Computer Engineering, Technology and Science, Porto, Portugal.
- Faculty of Engineering, University of Porto, Porto, Portugal.
| | - Francisco Silva
- Institute for Systems and Computer Engineering, Technology and Science, Porto, Portugal
- Faculty of Science, University of Porto, Porto, Portugal
| | - Rui M Ferreira
- Ipatimup - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
| | - Tania Pereira
- Institute for Systems and Computer Engineering, Technology and Science, Porto, Portugal
- Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | - Ceu Figueiredo
- Ipatimup - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - Hélder P Oliveira
- Institute for Systems and Computer Engineering, Technology and Science, Porto, Portugal
- Faculty of Science, University of Porto, Porto, Portugal
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Sierra AM, Meléndez O, Bethancourt R, Bethancourt A, Rodríguez-Castro L, López CA, Sedio BE, Saltonstall K, Villarreal A JC. Leaf Endophytes Relationship with Host Metabolome Expression in Tropical Gymnosperms. J Chem Ecol 2024:10.1007/s10886-024-01511-z. [PMID: 38809282 DOI: 10.1007/s10886-024-01511-z] [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: 12/04/2023] [Revised: 05/07/2024] [Accepted: 05/17/2024] [Indexed: 05/30/2024]
Abstract
Plant-microbe interactions play a pivotal role in shaping host fitness, especially concerning chemical defense mechanisms. In cycads, establishing direct correlations between specific endophytic microbes and the synthesis of highly toxic defensive phytochemicals has been challenging. Our research delves into the intricate relationship between plant-microbe associations and the variation of secondary metabolite production in two closely related Zamia species that grow in distinct habitats; terrestrial and epiphytic. Employing an integrated approach, we combined microbial metabarcoding, which characterize the leaf endophytic bacterial and fungal communities, with untargeted metabolomics to test if the relative abundances of specific microbial taxa in these two Zamia species were associated with different metabolome profiles. The two species studied shared approximately 90% of the metabolites spanning diverse biosynthetic pathways: alkaloids, amino acids, carbohydrates, fatty acids, polyketides, shikimates, phenylpropanoids, and terpenoids. Co-occurrence networks revealed positive associations among metabolites from different pathways, underscoring the complexity of their interactions. Our integrated analysis demonstrated to some degree that the intraspecific variation in metabolome profiles of the two host species was associated with the abundance of bacterial orders Acidobacteriales and Frankiales, as well as the fungal endophytes belonging to the orders Chaetothyriales, Glomerellales, Heliotiales, Hypocreales, and Sordariales. We further associate individual metabolic similarity with four specific fungal endophyte members of the core microbiota, but no specific bacterial taxa associations were identified. This study represents a pioneering investigation to characterize leaf endophytes and their association with metabolomes in tropical gymnosperms, laying the groundwork for deeper inquiries into this complex domain.
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Affiliation(s)
- Adriel M Sierra
- Département de Biologie, Université Laval, Québec, (QC), G1V 0A6, Canada.
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, (QC), G1V 0A6, Canada.
| | - Omayra Meléndez
- Departamento de Microbiología y Parasitología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panamá, Panamá
- Smithsonian Tropical Research Institute, Ancón, Panamá
| | - Rita Bethancourt
- Departamento de Microbiología y Parasitología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panamá, Panamá
| | - Ariadna Bethancourt
- Departamento de Microbiología y Parasitología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panamá, Panamá
| | - Lilisbeth Rodríguez-Castro
- Departamento de Microbiología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panamá, Panamá
- Smithsonian Tropical Research Institute, Ancón, Panamá
| | - Christian A López
- Smithsonian Tropical Research Institute, Ancón, Panamá
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Brian E Sedio
- Smithsonian Tropical Research Institute, Ancón, Panamá
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | | | - Juan Carlos Villarreal A
- Département de Biologie, Université Laval, Québec, (QC), G1V 0A6, Canada.
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, (QC), G1V 0A6, Canada.
- Smithsonian Tropical Research Institute, Ancón, Panamá.
- Canada Research Chair in Genomics of Tropical Symbioses, Department of Biology, Université Laval, Québec, G1V 0A6, Canadá.
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Putri RE, Vrouwenvelder JS, Farhat N. Enhancing the DNA yield intended for microbial sequencing from a low-biomass chlorinated drinking water. Front Microbiol 2024; 15:1339844. [PMID: 38855767 PMCID: PMC11157071 DOI: 10.3389/fmicb.2024.1339844] [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: 11/16/2023] [Accepted: 05/07/2024] [Indexed: 06/11/2024] Open
Abstract
DNA extraction yield from drinking water distribution systems and premise plumbing is a key metric for any downstream analysis such as 16S amplicon or metagenomics sequencing. This research aimed to optimize DNA yield from low-biomass (chlorinated) reverse osmosis-produced tap water by evaluating the impact of different factors during the DNA extraction procedure. The factors examined are (1) the impact of membrane materials and their pore sizes; (2) the impact of different cell densities; and (3) an alternative method for enhancing DNA yield via incubation (no nutrient spiking). DNA from a one-liter sampling volume of RO tap water with varying bacterial cell densities was extracted with five different filter membranes (mixed ester cellulose 0.2 μm, polycarbonate 0.2 μm, polyethersulfone 0.2 and 0.1 μm, polyvinylidene fluoride 0.1 μm) for biomass filtration. Our results show that (i) smaller membrane pore size solely did not increase the DNA yield of low-biomass RO tap water; (ii) the DNA yield was proportional to the cell density and substantially dependent on the filter membrane properties (i.e., the membrane materials and their pore sizes); (iii) by using our optimized DNA extraction protocol, we found that polycarbonate filter membrane with 0.2 μm pore size markedly outperformed in terms of quantity (DNA yield) and quality (background level of 16S gene copy number) of recovered microbial DNA; and finally, (iv) for one-liter sampling volume, incubation strategy enhanced the DNA yield and enabled accurate identification of the core members (i.e., Porphyrobacter and Blastomonas as the most abundant indicator taxa) of the bacterial community in low-biomass RO tap water. Importantly, incorporating multiple controls is crucial to distinguish between contaminant/artefactual and true taxa in amplicon sequencing studies of low-biomass RO tap water.
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Affiliation(s)
- Ratna E. Putri
- Environmental Science and Engineering, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Johannes S. Vrouwenvelder
- Environmental Science and Engineering, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Delft, Netherlands
| | - Nadia Farhat
- Environmental Science and Engineering, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Min K, Glowacki AJ, Bosma ML, McGuire JA, Tian S, McAdoo K, DelSasso A, Fourre T, Gambogi RJ, Milleman J, Milleman KR. Quantitative analysis of the effects of essential oil mouthrinses on clinical plaque microbiome: a parallel-group, randomized trial. BMC Oral Health 2024; 24:578. [PMID: 38762482 PMCID: PMC11102605 DOI: 10.1186/s12903-024-04365-9] [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: 06/19/2023] [Accepted: 05/13/2024] [Indexed: 05/20/2024] Open
Abstract
BACKGROUND The rich diversity of microorganisms in the oral cavity plays an important role in the maintenance of oral health and development of detrimental oral health conditions. Beyond commonly used qualitative microbiome metrics, such as relative proportions or diversity, both the species-level identification and quantification of bacteria are key to understanding clinical disease associations. This study reports the first-time application of an absolute quantitative microbiome analysis using spiked DNA standards and shotgun metagenome sequencing to assess the efficacy and safety of product intervention on dental plaque microbiome. METHODS In this parallel-group, randomized clinical trial, essential oil mouthrinses, including LISTERINE® Cool Mint Antiseptic (LCM), an alcohol-containing prototype mouthrinse (ACPM), and an alcohol-free prototype mouthrinse (AFPM), were compared against a hydroalcohol control rinse on clinical parameters and the oral microbiome of subjects with moderate gingivitis. To enable a sensitive and clinically meaningful measure of bacterial abundances, species were categorized according to their associations with oral conditions based on published literature and quantified using known amounts of spiked DNA standards. RESULTS Multivariate analysis showed that both LCM and ACPM shifted the dysbiotic microbiome composition of subjects with gingivitis to a healthier state after 4 weeks of twice-daily use, resembling the composition of subjects with clinically healthy oral conditions recruited for observational reference comparison at baseline. The essential oil-containing mouthrinses evaluated in this study showed statistically significant reductions in clinical gingivitis and plaque measurements when compared to the hydroalcohol control rinse after 6 weeks of use. CONCLUSIONS By establishing a novel quantitative method for microbiome analysis, this study sheds light on the mechanisms of LCM mouthrinse efficacy on oral microbial ecology, demonstrating that repeated usage non-selectively resets a gingivitis-like oral microbiome toward that of a healthy oral cavity. TRIAL REGISTRATION The trial was registered on ClinicalTrials.gov on 10/06/2021. The registration number is NCT04921371.
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Affiliation(s)
- Kyungrok Min
- Johnson & Johnson Consumer Inc, Skillman, NJ, USA.
| | | | | | | | - Sandy Tian
- Johnson & Johnson Consumer Inc, Skillman, NJ, USA
| | | | | | - Tara Fourre
- Johnson & Johnson Consumer Inc, Skillman, NJ, USA
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Cyphert EL, Nand S, Franco G, Hajkowski M, Soto L, Lee DM, Ferner M, Zabin C, Blumenthal J, Deck A, Boyer K, Burrus K, Hernandez CJ, Anand A. Combinatorial characterization of bacterial taxa-driven differences in the microbiome of oyster reefs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.594453. [PMID: 38798377 PMCID: PMC11118425 DOI: 10.1101/2024.05.15.594453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Oyster reefs are invaluable ecosystems that provide a wide array of critical ecosystem services, including water filtration, coastal protection, and habitat provision for various marine species. However, these essential habitats face escalating threats from climate change and anthropogenic stressors. To combat these challenges, numerous oyster restoration initiatives have been undertaken, representing a global effort to preserve and restore these vital ecosystems. A significant, yet poorly understood, component of oyster reefs is the microbial communities. These communities account for a substantial proportion of marine reefs and are pivotal in driving key biogeochemical processes. Particularly, the environmental microbiome plays a crucial role in supporting the health and resilience of oyster populations. In our study, we sought to shed light on the microbiome within oyster reef ecosystems by characterizing the abundance, and diversity of microorganisms in the soil, biofilm, and oysters in 4 sites using a combinatorial approach to identify differentially abundant microbes by sample type and by sampling location. Our investigation revealed distinct microbial taxa in oysters, sediment and biofilm. The maximum Shannon Index indicated a slightly increased diversity in Heron's Head (5.47), followed by Brickyard park (5.35), Dunphy Park (5.17) and Point Pinole (4.85). This is likely to be driven by significantly higher oyster mortality observed at Point Pinole during routine monitoring and restoration efforts. Interestingly Ruminococcus, Streptococcus, Staphylococcus, Prevotella, Porphyromonas, Parvimonas, Neisseria, Lactococcus, Haemophilus, Fusobacterium, Dorea, Clostridium, Campylobacter, Bacteroides, and Akkermansia were positively associated with the biofilm. Yet we have limited understanding of their beneficial and/or detrimental implications to oyster growth and survival. By unraveling the intricate relationships in microbial composition across an oyster reef, our study contributes to advancing the knowledge needed to support effective oyster reef conservation and restoration efforts.
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Affiliation(s)
| | | | | | | | | | | | - Matt Ferner
- San Francisco Bay National Estuarine Research Reserve
| | | | | | - Anna Deck
- San Francisco Bay National Estuarine Research Reserve
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Gao W, Lin W, Li Q, Chen W, Yin W, Zhu X, Gao S, Liu L, Li W, Wu D, Zhang G, Zhu R, Jiao N. Identification and validation of microbial biomarkers from cross-cohort datasets using xMarkerFinder. Nat Protoc 2024:10.1038/s41596-024-00999-9. [PMID: 38745111 DOI: 10.1038/s41596-024-00999-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/05/2024] [Indexed: 05/16/2024]
Abstract
Microbial signatures have emerged as promising biomarkers for disease diagnostics and prognostics, yet their variability across different studies calls for a standardized approach to biomarker research. Therefore, we introduce xMarkerFinder, a four-stage computational framework for microbial biomarker identification with comprehensive validations from cross-cohort datasets, including differential signature identification, model construction, model validation and biomarker interpretation. xMarkerFinder enables the identification and validation of reproducible biomarkers for cross-cohort studies, along with the establishment of classification models and potential microbiome-induced mechanisms. Originally developed for gut microbiome research, xMarkerFinder's adaptable design makes it applicable to various microbial habitats and data types. Distinct from existing biomarker research tools that typically concentrate on a singular aspect, xMarkerFinder uniquely incorporates a sophisticated feature selection process, specifically designed to address the heterogeneity between different cohorts, extensive internal and external validations, and detailed specificity assessments. Execution time varies depending on the sample size, selected algorithm and computational resource. Accessible via GitHub ( https://github.com/tjcadd2020/xMarkerFinder ), xMarkerFinder supports users with diverse expertise levels through different execution options, including step-to-step scripts with detailed tutorials and frequently asked questions, a single-command execution script, a ready-to-use Docker image and a user-friendly web server ( https://www.biosino.org/xmarkerfinder ).
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Affiliation(s)
- Wenxing Gao
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Weili Lin
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Qiang Li
- National Genomics Data Center & Bio-Med Big Data Center, Chinese Academy of Sciences Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Wanning Chen
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Wenjing Yin
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Xinyue Zhu
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Sheng Gao
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Lei Liu
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Wenjie Li
- Shanghai Southgene Technology Co., Ltd., Shanghai, P. R. China
| | - Dingfeng Wu
- National Clinical Research Center for Child Health, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P. R. China
| | - Guoqing Zhang
- National Genomics Data Center & Bio-Med Big Data Center, Chinese Academy of Sciences Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, P. R. China.
| | - Ruixin Zhu
- The Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China.
| | - Na Jiao
- National Clinical Research Center for Child Health, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P. R. China.
- State Key Laboratory of Genetic Engineering, Fudan Microbiome Center, School of Life Sciences, Fudan University, Shanghai, P. R. China.
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Fortuna R, Wang W, Mayengbam S, Tuplin EWN, Sampsell K, Sharkey KA, Hart DA, Reimer RA. Effect of prebiotic fiber on physical function and gut microbiota in adults, mostly women, with knee osteoarthritis and obesity: a randomized controlled trial. Eur J Nutr 2024:10.1007/s00394-024-03415-w. [PMID: 38713231 DOI: 10.1007/s00394-024-03415-w] [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: 11/17/2023] [Accepted: 04/18/2024] [Indexed: 05/08/2024]
Abstract
PURPOSE Obesity is a primary risk factor for knee osteoarthritis (OA). Prebiotics enhance beneficial gut microbes and can reduce body fat and inflammation. Our objective was to examine if a 6-month prebiotic intervention improved physical function in adults with knee osteoarthritis and obesity. We also measured knee pain, body composition, quality of life, gut microbiota, inflammatory markers, and serum metabolomics. METHODS Adults (n = 54, mostly women) with co-morbid obesity (BMI > 30 kg/m2) and unilateral/bilateral knee OA were randomly assigned to prebiotic (oligofructose-enriched inulin; 16 g/day; n = 31) or isocaloric placebo (maltodextrin; n = 21) for 6 months. Performance based-tests, knee pain, quality of life, serum metabolomics and inflammatory markers, and fecal microbiota and short-chain fatty acids were assessed. RESULTS Significant between group differences were detected for the change in timed-up-and-go test, 40 m fast paced walk test, and hand grip strength test from baseline that favored prebiotic over placebo. Prebiotic also reduced trunk fat mass (kg) at 6 months and trunk fat (%) at 3 months compared to placebo. There was a trend (p = 0.059) for reduced knee pain at 6 months with prebiotic versus placebo. In gut microbiota analysis, a total of 37 amplicon sequence variants differed between groups. Bifidobacterium abundance was positively correlated with distance walked in the 6-min walk test and hand grip strength. At 6 months, there was a significant separation of serum metabolites between groups with upregulation of phenylalanine and tyrosine metabolism with prebiotic. CONCLUSION Prebiotics may hold promise for conservative management of knee osteoarthritis in adults with obesity and larger trials are warranted. CLINICAL TRIAL REGISTRATION Clinicaltrials.gov/study/NCT04172688.
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Affiliation(s)
- Rafael Fortuna
- Faculty of Kinesiology, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
| | - Weilan Wang
- Faculty of Kinesiology, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
| | - Shyamchand Mayengbam
- Department of Biochemistry, Memorial University of Newfoundland, 45 Artic Ave, St. John's, NL, A1C 5S7, Canada
| | - Erin W Noye Tuplin
- Faculty of Kinesiology, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
| | - Kara Sampsell
- Faculty of Kinesiology, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
| | - Keith A Sharkey
- Department of Physiology and Pharmacology, Cumming School of Medicine, Hotchkiss Brain Institute and Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
| | - David A Hart
- Department of Surgery, and Faculty of Kinesiology, McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada
| | - Raylene A Reimer
- Faculty of Kinesiology, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada.
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada.
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Unzueta-Medina JA, González-Chávez SA, Salas-Leiva JS, Silva-Sánchez SE, Pacheco-Tena C. Differential Composition and Structure of the Microbiota from Active and Inactive Stages of HLA-B27-associated Uveitis by Paired Fecal Metagenomes. Ocul Immunol Inflamm 2024:1-9. [PMID: 38709227 DOI: 10.1080/09273948.2024.2346818] [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: 08/26/2023] [Accepted: 04/19/2024] [Indexed: 05/07/2024]
Abstract
PURPOSE To compare the diversities and abundances of bacterial taxa in the microbiome of patients with HLA B27-positive acute anterior uveitis (AAU) in the active and inactive phases. METHODS An observational descriptive prospective and comparative study was conducted in ten HLA-B27-positive AAU patients (44.6 ± 13.4 years). The microbiome of the stool samples obtained in the active and inactive stages was analyzed by sequencing the V3 region of the 16S rRNA gene. RESULTS The differences in the bacteria profile between active and inactive stages in each individual were confirmed (p < 0.0001). Ten OTUs were found exclusively in the active phase of 90% of the individuals, suggesting a proinflammatory association. Blautia OUT_4 and Faecalibacterium OUT_2 abundances showed a direct relationship between abundance and severity of ocular inflammation. Two OTUs were exclusive of the inactive stage, suggesting an anti-inflammatory role. CONCLUSION The metagenomic profile of the fecal microbiota differs in the acute phase of the AAU compared to when the inflammation subsides, despite being the same individual and a short time-lapse. AAU is a fertile field for studying the connection between subtle rapid changes in microbiota and their systemic consequences.
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Affiliation(s)
- José Antonio Unzueta-Medina
- Laboratorio PABIOM, Facultad de Medicina y Ciencias Biomédicas, Universidad Autónoma de Chihuahua, Chihuahua, México
| | - Susana Aideé González-Chávez
- Laboratorio PABIOM, Facultad de Medicina y Ciencias Biomédicas, Universidad Autónoma de Chihuahua, Chihuahua, México
| | - Joan Sebastian Salas-Leiva
- Departamento de medio ambiente y energía, CONAHCyT, Centro de Investigación en Materiales Avanzados, Chihuahua, México
| | - Sandra Estela Silva-Sánchez
- Laboratorio PABIOM, Facultad de Medicina y Ciencias Biomédicas, Universidad Autónoma de Chihuahua, Chihuahua, México
| | - César Pacheco-Tena
- Laboratorio PABIOM, Facultad de Medicina y Ciencias Biomédicas, Universidad Autónoma de Chihuahua, Chihuahua, México
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Ma ZS, Shi P. Critical complex network structures in animal gastrointestinal tract microbiomes. Anim Microbiome 2024; 6:23. [PMID: 38702785 PMCID: PMC11067214 DOI: 10.1186/s42523-024-00291-x] [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: 04/08/2023] [Accepted: 01/21/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Living things from microbes to their hosts (plants, animals and humans) interact with each other, and their relationships may be described with complex network models. The present study focuses on the critical network structures, specifically the core/periphery nodes and backbones (paths of high-salience skeletons) in animal gastrointestinal microbiomes (AGMs) networks. The core/periphery network (CPN) mirrors nearly ubiquitous nestedness in ecological communities, particularly dividing the network as densely interconnected core-species and periphery-species that only sparsely linked to the core. Complementarily, the high-salience skeleton network (HSN) mirrors the pervasive asymmetrical species interactions (strictly microbial species correlations), particularly forming heterogenous pathways in AGM networks with both "backbones" and "rural roads" (regular or weak links). While the cores and backbones can act as critical functional structures, the periphery nodes and weak links may stabilize network functionalities through redundancy. RESULTS Here, we build and analyze 36 pairs of CPN/HSN for the AGMs based on 4903 gastrointestinal-microbiome samples containing 473,359 microbial species collected from 318 animal species covering all vertebrate and four major invertebrate classes. The network analyses were performed at host species, order, class, phylum, kingdom scales and diet types with selected and comparative taxon pairs. Besides diet types, the influence of host phylogeny, measured with phylogenetic (evolutionary) timeline or "age", were integrated into the analyses. For example, it was found that the evolutionary trends of three primary microbial phyla (Bacteroidetes/Firmicutes/Proteobacteria) and their pairwise abundance-ratios in animals do not mirror the patterns in modern humans phylogenetically, although they are consistent in terms of diet types. CONCLUSIONS Overall, the critical network structures of AGMs are qualitatively and structurally similar to those of the human gut microbiomes. Nevertheless, it appears that the critical composition (the three phyla of Bacteroidetes, Firmicutes, and Proteobacteria) in human gut microbiomes has broken the evolutionary trend from animals to humans, possibly attributable to the Anthropocene epoch and reflecting the far-reaching influences of agriculture and industrial revolution on the human gut microbiomes. The influences may have led to the deviations between modern humans and our hunter-gather ancestors and animals.
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Affiliation(s)
- Zhanshan Sam Ma
- Computational Biology and Medical Ecology Lab, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
- Faculty of Arts and Science, Harvard Forest, Harvard University, Cambridge, MA, 02138, USA.
| | - Peng Shi
- Evolutionary and Functional Genomics Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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Trecarten S, Fongang B, Liss M. Current Trends and Challenges of Microbiome Research in Prostate Cancer. Curr Oncol Rep 2024; 26:477-487. [PMID: 38573440 DOI: 10.1007/s11912-024-01520-x] [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] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
Abstract
PURPOSE OF REVIEW The role of the gut microbiome in prostate cancer is an emerging area of research interest. However, no single causative organism has yet been identified. The goal of this paper is to examine the role of the microbiome in prostate cancer and summarize the challenges relating to methodology in specimen collection, sequencing technology, and interpretation of results. RECENT FINDINGS Significant heterogeneity still exists in methodology for stool sampling/storage, preservative options, DNA extraction, and sequencing database selection/in silico processing. Debate persists over primer choice in amplicon sequencing as well as optimal methods for data normalization. Statistical methods for longitudinal microbiome analysis continue to undergo refinement. While standardization of methodology may help yield more consistent results for organism identification in prostate cancer, this is a difficult task due to considerable procedural variation at each step in the process. Further reproducibility and methodology research is required.
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Affiliation(s)
- Shaun Trecarten
- Department of Urology, UT Health San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229, USA
| | - Bernard Fongang
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX, USA
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA
- Department of Population Health Sciences, UT Health San Antonio, San Antonio, TX, USA
| | - Michael Liss
- Department of Urology, UT Health San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229, USA.
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Shtossel O, Finkelstein S, Louzoun Y. mi-Mic: a novel multi-layer statistical test for microbiota-disease associations. Genome Biol 2024; 25:113. [PMID: 38693546 PMCID: PMC11064322 DOI: 10.1186/s13059-024-03256-0] [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: 12/06/2023] [Accepted: 04/22/2024] [Indexed: 05/03/2024] Open
Abstract
mi-Mic, a novel approach for microbiome differential abundance analysis, tackles the key challenges of such statistical tests: a large number of tests, sparsity, varying abundance scales, and taxonomic relationships. mi-Mic first converts microbial counts to a cladogram of means. It then applies a priori tests on the upper levels of the cladogram to detect overall relationships. Finally, it performs a Mann-Whitney test on paths that are consistently significant along the cladogram or on the leaves. mi-Mic has much higher true to false positives ratios than existing tests, as measured by a new real-to-shuffle positive score.
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Affiliation(s)
- Oshrit Shtossel
- Department of Mathematics, Bar-Ilan University, Ramat Gan, 52900, Israel
| | - Shani Finkelstein
- Department of Mathematics, Bar-Ilan University, Ramat Gan, 52900, Israel
| | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan, 52900, Israel.
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Bunbury-Blanchette AL, Fan L, Kernaghan G. Yeast communities of a North American hybrid wine grape differ between organic and conventional vineyards. J Appl Microbiol 2024; 135:lxae092. [PMID: 38621715 DOI: 10.1093/jambio/lxae092] [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: 12/08/2023] [Revised: 03/20/2024] [Accepted: 04/13/2024] [Indexed: 04/17/2024]
Abstract
AIMS To compare the species diversity and composition of indigenous yeast communities of hybrid grapes from conventionally and organically cultivated vineyards of an emerging cool-climate wine producing region. METHODS AND RESULTS Illumina MiSeq sequences from L'Acadie blanc grape musts were processed and filtered to characterize indigenous yeast communities in organic and conventional vineyards of the Annapolis Valley wine region in Nova Scotia, Canada. While cultivation practice was not associated with yeast diversity or species richness, there was a strong effect on yeast community composition, with conventional vineyards characterized by higher proportions of Sporidiobolales and Filobasidium magnum, and organic vineyards supporting Filobasidium species other than F. magnum and higher proportions of Symmetrospora. There was also variation in yeast community composition among individual vineyards, and from year to year. CONCLUSIONS This is the first comprehensive assessment of yeasts associated with hybrid grapes grown using different cultivation practices in a North American cool climate wine region. Communities were dominated by basidiomycete yeasts and species composition of these yeasts differed significantly between vineyards employing organic and conventional cultivation practices. The role of basidiomycete yeasts in winemaking is not well understood, but some species may influence wine characteristics.
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Affiliation(s)
- Adele L Bunbury-Blanchette
- Saint Mary's University, Faculty of Graduate Studies and Research, 923 Robie St, Atrium Building, Suite 210, Halifax, Nova Scotia B3H 1G3, Canada
| | - Lihua Fan
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, 32 Main St, Kentville, Nova Scotia B4N 1J5, Canada
| | - Gavin Kernaghan
- Mount Saint Vincent University, Department of Biology, 166 Bedford Highway, Halifax, Nova Scotia, B3M 1J9, Canada
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Marques TC, Monteiro HF, Melo DB, Coelho WM, Salman S, Marques LR, Leão KM, Machado VS, Menta P, Dubey D, Sun F, Lima FS. Effect of rumen-protected choline on dairy cow metabolism, immunity, lactation performance, and vaginal discharge microbiome. J Dairy Sci 2024; 107:2864-2882. [PMID: 38101729 DOI: 10.3168/jds.2023-23850] [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: 06/09/2023] [Accepted: 11/12/2023] [Indexed: 12/17/2023]
Abstract
Rumen-protected choline (RPC) promotes benefits in milk production, immunity, and health in dairy cows by optimizing lipid metabolism during transition period management and early lactation. However, the RPC success in dairy cows depends on choline bioavailability, which is affected by the type of protection used in rumen-protected choline. Therefore, our objectives were to determine the effects of a novel RPC on dry matter intake (DMI), identify markers of metabolism and immunity, and evaluate lactation performance. Dry Holstein (n = 48) cows at 245 ± 3 d of gestation were blocked by parity and assigned to control or RPC treatment within each block. Cows enrolled in the RPC treatment received 15 g/d of CholiGEM (Kemin Industries, Cavriago RE, Italy) from 21 d prepartum and 30 g/d of CholiGEM from calving to 21 d postpartum. During the transition period, DMI was measured daily, and blood was sampled weekly for energy-related metabolites such as β-hydroxybutyrate (BHB), glucose, and nonesterified fatty acids (NEFA), as well as immune function markers such as haptoglobin (Hp) and lipopolysaccharide-binding protein (LPB). Vaginal discharge samples were collected at the calving and 7 d postpartum and stored in microcentrifuge tubes at -80°C until 16S rRNA sequencing. The main responses of body condition score, body weight, DMI, milk yield, milk components, and immune function markers were analyzed using the GLIMMIX procedure of SAS with the effects of treatment, time, parity, and relevant covariates added to the models. The relative abundance of microbiome α-diversity was evaluated by 3 indexes (Chao1, Shannon, and Simpson) and β-diversity by principal coordinate analysis and permutational multivariate ANOVA. We found no differences in DMI in the pre- and postpartum periods. Cows fed RPC increased the yields of energy- and 3.5% fat-corrected milk and fat yield in primiparous and multiparous cows, with an interaction between treatment and parity for these lactation variables. However, we found no differences in milk protein and lactose up to 150 DIM between treatments. Glucose, NEFA, and BHB had no differences between the treatments. However, RPC decreased BHB numerically (control = 1.07 ± 0.13 vs. RPC = 0.63 ± 0.13) in multiparous on the third week postpartum and tended to reduce the incidence of subclinical ketosis (12.7% vs. 4.2%). No effects for Hp and LPB were found in cows fed RPC. Chao1, Shannon, and Simpson indexes were lower at calving in the RPC treatment than in the Control. However, no differences were found 7 d later for Chao1, Shannon, and Simpson indexes. The vaginal discharge microbiome was altered in cows fed RPC at 7 d postpartum. Fusobacterium, a common pathogen associated with metritis, was reduced in cows fed RPC. Rumen-protected choline enhanced lactation performance and health and altered the vaginal discharge microbiome which is a potential proxy for uterine healthy in dairy cows. The current study's findings corroborate that RPC is a tool to support adaptation to lactation and shed light on opportunities for further research in reproductive health.
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Affiliation(s)
- T C Marques
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA 95616; Department of Animal Science, Instituto Federal Goiano, Rio Verde, Goias 75901-970, Brazil
| | - H F Monteiro
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA 95616
| | - D B Melo
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA 95616
| | - W M Coelho
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA 95616
| | - S Salman
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA 95616
| | - L R Marques
- Department of Animal Science, Instituto Federal Goiano, Rio Verde, Goias 75901-970, Brazil
| | - K M Leão
- Department of Animal Science, Instituto Federal Goiano, Rio Verde, Goias 75901-970, Brazil
| | - V S Machado
- Department of Veterinary Sciences, College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX 79409
| | - P Menta
- Department of Veterinary Sciences, College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX 79409
| | - D Dubey
- Kemin Europa NV, Herentals 2640, Belgium
| | - F Sun
- Kemin Industries Inc., Des Moines, IA 50317
| | - F S Lima
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA 95616.
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Li J, Chen C, Ji L, Wen S, Peng J, Yang L, He G. Urbanization-driven forest soil greenhouse gas emissions: Insights from the role of soil bacteria in carbon and nitrogen cycling using a metagenomic approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171364. [PMID: 38438026 DOI: 10.1016/j.scitotenv.2024.171364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/07/2024] [Accepted: 02/27/2024] [Indexed: 03/06/2024]
Abstract
Increasing population densities and urban sprawl have induced greenhouse gas (GHG) emissions from the soil, and the soil microbiota of urban forests play a critical role in the production and consumption of GHGs, supporting green development. However, the function and potential mechanism of soil bacteria in GHG emissions from forests during urbanization processes need to be better understood. Here, we measured the fluxes of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) in Cinnamomum camphora forest soils along an urbanization gradient. 16S amplicon and metagenomic sequencing approaches were employed to examine the structure and potential functions of the soil bacterial community involved in carbon (C) and nitrogen (N) cycling. In this study, the CH4 and CO2 emissions from urban forest soils (sites U and G) were significantly greater than those from suburban soils (sites S and M). The N2O emissions in the urban center (site U) were 24.0 % (G), 13.8 % (S), and 13.5 % (M) greater than those at the other three sites. These results were related to the increasing bacterial alpha diversity, interactions, and C and N cycling gene abundances (especially those involved in denitrification) in urban forest soils. Additionally, the soil pH and metal contents (K, Ca, Mg) affected key bacterial populations (such as Methylomirabilota, Acidobacteriota, and Proteobacteria) and indicators (napA, nosZ, nrfA, nifH) involved in reducing N2O emissions. The soil heavy metal contents (Fe, Cr, Pb) were the main contributors to CH4 emissions, possibly by affecting methanogens (Desulfobacterota) and methanotrophic bacteria (Proteobacteria, Actinobacteriota, and Patescibacteria). Our study provides new insights into the benefits of conservation-minded urban planning and close-to-nature urban forest management and construction, which are conducive to mitigating GHG emissions and supporting urban sustainable development by mediating the core bacterial population.
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Affiliation(s)
- Jing Li
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China
| | - Chuxiang Chen
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China
| | - Li Ji
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China.
| | - Shizhi Wen
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China
| | - Jun Peng
- Hunan Geological Experiment and Testing Center, Changsha, 290 Middle Chengnan Road, 410007, PR China
| | - Lili Yang
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China
| | - Gongxiu He
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China.
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Andriienko V, Buczek M, Meier R, Srivathsan A, Łukasik P, Kolasa MR. Implementing high-throughput insect barcoding in microbiome studies: impact of non-destructive DNA extraction on microbiome reconstruction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.30.591865. [PMID: 38746196 PMCID: PMC11092579 DOI: 10.1101/2024.04.30.591865] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Background Symbiotic relationships with diverse microorganisms are crucial for many aspects of insect biology. However, while our understanding of insect taxonomic diversity and the distribution of insect species in natural communities is limited, we know much less about their microbiota. In the era of rapid biodiversity declines, as researchers increasingly turn towards DNA-based monitoring, developing and broadly implementing approaches for high-throughput and cost-effective characterization of both insect and insect-associated microbial diversity is essential. We need to verify whether approaches such as high-throughput barcoding, a powerful tool for identifying wild insects, would permit subsequent microbiota reconstruction in these specimens. Methods High-throughput barcoding ("megabarcoding") methods often rely on non-destructive approaches for obtaining template DNA for PCR amplification by leaching DNA out of insect specimens using alkaline buffers such as HotSHOT. This study investigated the impact of HotSHOT on microbial abundance estimates and the reconstructed bacterial community profiles. We addressed this question by comparing quantitative 16S rRNA amplicon sequencing data for HotSHOT-treated or untreated specimens of 16 insect species representing six orders and selected based on the expectation of limited variation among individuals. Results We find that in 13 species, the treatment significantly reduced microbial abundance estimates, corresponding to an estimated 15-fold decrease in amplifiable 16S rRNA template on average. On the other hand, HotSHOT pre-treatment had a limited effect on microbial community composition. The reconstructed presence of abundant bacteria with known significant effects was not affected. On the other hand, we observed changes in the presence of low-abundance microbes, those close to the reliable detection threshold. Alpha and beta diversity analyses showed compositional differences in only a few species. Conclusion Our results indicate that HotSHOT pre-treated specimens remain suitable for microbial community composition reconstruction, even if abundance may be hard to estimate. These results indicate that we can cost-effectively combine barcoding with the study of microbiota across wild insect communities. Thus, the voucher specimens obtained using megabarcoding studies targeted at characterizing insect communities can be used for microbiome characterizations. This can substantially aid in speeding up the accumulation of knowledge on the microbiomes of abundant and hyperdiverse insect species.
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Affiliation(s)
- Veronika Andriienko
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Institute of Zoology and Biomedical Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
| | - Mateusz Buczek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | | | | | - Piotr Łukasik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Michał R Kolasa
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
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49
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Gregori J, Ibañez-Lligoña M, Colomer-Castell S, Campos C, Quer J. Virus Quasispecies Rarefaction: Subsampling with or without Replacement? Viruses 2024; 16:710. [PMID: 38793592 PMCID: PMC11126021 DOI: 10.3390/v16050710] [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: 04/18/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
In quasispecies diversity studies, the comparison of two samples of varying sizes is a common necessity. However, the sensitivity of certain diversity indices to sample size variations poses a challenge. To address this issue, rarefaction emerges as a crucial tool, serving to normalize and create fairly comparable samples. This study emphasizes the imperative nature of sample size normalization in quasispecies diversity studies using next-generation sequencing (NGS) data. We present a thorough examination of resampling schemes using various simple hypothetical cases of quasispecies showing different quasispecies structures in the sense of haplotype genomic composition, offering a comprehensive understanding of their implications in general cases. Despite the big numbers implied in this sort of study, often involving coverages exceeding 100,000 reads per sample and amplicon, the rarefaction process for normalization should be performed with repeated resampling without replacement, especially when rare haplotypes constitute a significant fraction of interest. However, it is noteworthy that different diversity indices exhibit distinct sensitivities to sample size. Consequently, some diversity indicators may be compared directly without normalization, or instead may be resampled safely with replacement.
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Affiliation(s)
- Josep Gregori
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.I.-L.); (S.C.-C.); (C.C.)
| | - Marta Ibañez-Lligoña
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.I.-L.); (S.C.-C.); (C.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Sergi Colomer-Castell
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.I.-L.); (S.C.-C.); (C.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Carolina Campos
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.I.-L.); (S.C.-C.); (C.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Josep Quer
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (M.I.-L.); (S.C.-C.); (C.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
- Medicine Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
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50
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Ahammad I, Bhattacharjee A, Chowdhury ZM, Rahman A, Hossain MU, Dewan G, Talukder S, Das KC, Keya CA, Salimullah M. Gut microbiome composition reveals the distinctiveness between the Bengali people and the Indigenous ethnicities in Bangladesh. Commun Biol 2024; 7:500. [PMID: 38664512 PMCID: PMC11045797 DOI: 10.1038/s42003-024-06191-9] [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: 09/30/2022] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Ethnicity has a significant role in shaping the composition of the gut microbiome, which has implications in human physiology. This study intends to investigate the gut microbiome of Bengali people as well as several indigenous ethnicities (Chakma, Marma, Khyang, and Tripura) residing in the Chittagong Hill Tracts areas of Bangladesh. Following fecal sample collection from each population, part of the bacterial 16 s rRNA gene was amplified and sequenced using Illumina NovaSeq platform. Our findings indicated that Bangladeshi gut microbiota have a distinct diversity profile when compared to other countries. We also found out that Bangladeshi indigenous communities had a higher Firmicutes to Bacteroidetes ratio than the Bengali population. The investigation revealed an unclassified bacterium that was differentially abundant in Bengali samples while the genus Alistipes was found to be prevalent in Chakma samples. Further research on these bacteria might help understand diseases associated with these populations. Also, the current small sample-sized pilot study hindered the comprehensive understanding of the gut microbial diversity of the Bangladeshi population and its potential health implications. However, our study will help establish a basic understanding of the gut microbiome of the Bangladeshi population.
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Affiliation(s)
- Ishtiaque Ahammad
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Arittra Bhattacharjee
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Zeshan Mahmud Chowdhury
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Anisur Rahman
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Mohammad Uzzal Hossain
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Gourab Dewan
- Rangamati Medical College, Hospital Road, Rangamati-4500, Rangamati, Bangladesh
| | - Shiny Talukder
- Rangamati Medical College, Hospital Road, Rangamati-4500, Rangamati, Bangladesh
| | - Keshob Chandra Das
- Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Chaman Ara Keya
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka, 1229, Bangladesh
| | - Md Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh.
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