201
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Li J, Bates KA, Hoang KL, Hector TE, Knowles SCL, King KC. Experimental temperatures shape host microbiome diversity and composition. GLOBAL CHANGE BIOLOGY 2023; 29:41-56. [PMID: 36251487 PMCID: PMC10092218 DOI: 10.1111/gcb.16429] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/20/2022] [Indexed: 05/10/2023]
Abstract
Global climate change has led to more extreme thermal events. Plants and animals harbour diverse microbial communities, which may be vital for their physiological performance and help them survive stressful climatic conditions. The extent to which microbiome communities change in response to warming or cooling may be important for predicting host performance under global change. Using a meta-analysis of 1377 microbiomes from 43 terrestrial and aquatic species, we found a decrease in the amplicon sequence variant-level microbiome phylogenetic diversity and alteration of microbiome composition under both experimental warming and cooling. Microbiome beta dispersion was not affected by temperature changes. We showed that the host habitat and experimental factors affected microbiome diversity and composition more than host biological traits. In particular, aquatic organisms-especially in marine habitats-experienced a greater depletion in microbiome diversity under cold conditions, compared to terrestrial hosts. Exposure involving a sudden long and static temperature shift was associated with microbiome diversity loss, but this reduction was attenuated by prior-experimental lab acclimation or when a ramped regime (i.e., warming) was used. Microbial differential abundance and co-occurrence network analyses revealed several potential indicator bacterial classes for hosts in heated environments and on different biome levels. Overall, our findings improve our understanding on the impact of global temperature changes on animal and plant microbiome structures across a diverse range of habitats. The next step is to link these changes to measures of host fitness, as well as microbial community functions, to determine whether microbiomes can buffer some species against a more thermally variable and extreme world.
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Affiliation(s)
- Jingdi Li
- Department of BiologyUniversity of OxfordOxfordUK
| | | | - Kim L. Hoang
- Department of BiologyUniversity of OxfordOxfordUK
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202
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Dong H, Chen X, Zhao X, Zhao C, Mehmood K, Kulyar MFEA, Bhutta ZA, Zeng J, Nawaz S, Wu Q, Li K. Intestine microbiota and SCFAs response in naturally Cryptosporidium-infected plateau yaks. Front Cell Infect Microbiol 2023; 13:1105126. [PMID: 36936759 PMCID: PMC10014559 DOI: 10.3389/fcimb.2023.1105126] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/16/2023] [Indexed: 03/06/2023] Open
Abstract
Diarrhea is a severe bovine disease, globally prevalent in farm animals with a decrease in milk production and a low fertility rate. Cryptosporidium spp. are important zoonotic agents of bovine diarrhea. However, little is known about microbiota and short-chain fatty acids (SCFAs) changes in yaks infected with Cryptosporidium spp. Therefore, we performed 16S rRNA sequencing and detected the concentrations of SCFAs in Cryptosporidium-infected yaks. Results showed that over 80,000 raw and 70,000 filtered sequences were prevalent in yak samples. Shannon (p<0.01) and Simpson (p<0.01) were both significantly higher in Cryptosporidium-infected yaks. A total of 1072 amplicon sequence variants were shared in healthy and infected yaks. There were 11 phyla and 58 genera that differ significantly between the two yak groups. A total of 235 enzymes with a significant difference in abundance (p<0.001) were found between healthy and infected yaks. KEGG L3 analysis discovered that the abundance of 43 pathways was significantly higher, while 49 pathways were significantly lower in Cryptosporidium-infected yaks. The concentration of acetic acid (p<0.05), propionic acid (p<0.05), isobutyric acid (p<0.05), butyric acid (p<0.05), and isovaleric acid was noticeably lower in infected yaks, respectively. The findings of the study revealed that Cryptosporidium infection causes gut dysbiosis and results in a significant drop in the SCFAs concentrations in yaks with severe diarrhea, which may give new insights regarding the prevention and treatment of diarrhea in livestock.
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Affiliation(s)
- Hailong Dong
- Key Laboratory of Clinical Veterinary Medicine in Tibet, Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, China
| | - Xiushuang Chen
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xiaoxiao Zhao
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Chenxi Zhao
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Khalid Mehmood
- Department of Clinical Medicine and Surgery, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | | | - Zeeshan Ahmad Bhutta
- Laboratory of Biochemistry and Immunology, College of Veterinary Medicine, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Jiangyong Zeng
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Shah Nawaz
- Department of Anatomy, Faculty of Veterinary Science, University of Agriculture, Faisalabad, Pakistan
| | - Qingxia Wu
- Key Laboratory of Clinical Veterinary Medicine in Tibet, Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, China
- *Correspondence: Qingxia Wu, ; Kun Li,
| | - Kun Li
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Qingxia Wu, ; Kun Li,
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203
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McKay I, van Dorst J, Katz T, Doumit M, Prentice B, Owens L, Belessis Y, Chuang S, Jaffe A, Thomas T, Coffey M, Ooi CY. Diet and the gut-lung axis in cystic fibrosis - direct & indirect links. Gut Microbes 2023; 15:2156254. [PMID: 36573804 PMCID: PMC9809969 DOI: 10.1080/19490976.2022.2156254] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 12/02/2022] [Indexed: 12/28/2022] Open
Abstract
Cystic fibrosis (CF) is a multisystem, autosomal, recessive disease primarily affecting the lungs, pancreas, gastrointestinal tract, and liver. Whilst there is increasing evidence of a microbial 'gut-lung axis' in chronic respiratory conditions, there has been limited analysis of such a concept in CF. We performed a comprehensive dietary and microbiota analysis to explore the interactions between diet, gastrointestinal microbiota, respiratory microbiota, and clinical outcomes in children with CF. Our results demonstrate significant alterations in intestinal inflammation and respiratory and gastrointestinal microbiota when compared to age and gender matched children without CF. We identified correlations between the gastrointestinal and respiratory microbiota, lung function, CF pulmonary exacerbations and anthropometrics, supporting the concept of an altered gut-lung axis in children with CF. We also identified significant differences in dietary quality with CF children consuming greater relative proportions of total, saturated and trans fats, and less relative proportions of carbohydrates, wholegrains, fiber, insoluble fiber, starch, and resistant starch. Our findings position the CF diet as a potential modulator in gastrointestinal inflammation and the proposed gut-lung axial relationship in CF. The dietary intake of wholegrains, fiber and resistant starch may be protective against intestinal inflammation and should be explored as potential therapeutic adjuvants for children with CF.
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Affiliation(s)
- Isabelle McKay
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
| | - Josie van Dorst
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
| | - Tamarah Katz
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
- Department of Nutrition and Dietetics, Sydney Children’s Hospital Randwick, Randwick, Australia
| | - Michael Doumit
- Department of Physiotherapy, Sydney Children’s Hospital Randwick, Randwick, Australia
| | - Bernadette Prentice
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
- Molecular and Integrative Cystic Fibrosis (miCF) Research Centre, University of New South Wales, Randwick, Australia
- Department of Respiratory Medicine, Sydney Childrens Hospital, Randwick, Australia
| | - Louisa Owens
- Department of Respiratory Medicine, Sydney Childrens Hospital, Randwick, Australia
| | - Yvonne Belessis
- Department of Respiratory Medicine, Sydney Childrens Hospital, Randwick, Australia
| | - Sandra Chuang
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
- Department of Respiratory Medicine, Sydney Childrens Hospital, Randwick, Australia
| | - Adam Jaffe
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
- Molecular and Integrative Cystic Fibrosis (miCF) Research Centre, University of New South Wales, Randwick, Australia
- Department of Respiratory Medicine, Sydney Childrens Hospital, Randwick, Australia
| | - Torsten Thomas
- Biological, Earth and Environmental Sciences, University of New South Wales, Randwick, Australia
- University of New South Wales, Centre for Marine Science and Innovation, Randwick, Australia
| | - Michael Coffey
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
- Department of Gastroenterology, Sydney Children’s Hospital, Randwick, Australia
| | - Chee Y. Ooi
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, UNSW Medicine and Health, Univeristy of New South Wales, Randwick, Australia
- Molecular and Integrative Cystic Fibrosis (miCF) Research Centre, University of New South Wales, Randwick, Australia
- Department of Gastroenterology, Sydney Children’s Hospital, Randwick, Australia
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204
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Shaffer M, Thurimella K, Sterrett JD, Lozupone CA. SCNIC: Sparse correlation network investigation for compositional data. Mol Ecol Resour 2023; 23:312-325. [PMID: 36001047 PMCID: PMC9744196 DOI: 10.1111/1755-0998.13704] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 12/14/2022]
Abstract
Microbiome studies are often limited by a lack of statistical power due to small sample sizes and a large number of features. This problem is exacerbated in correlative studies of multi-omic datasets. Statistical power can be increased by finding and summarizing modules of correlated observations, which is one dimensionality reduction method. Additionally, modules provide biological insight as correlated groups of microbes can have relationships among themselves. To address these challenges, we developed SCNIC: Sparse Cooccurrence Network Investigation for compositional data. SCNIC is open-source software that can generate correlation networks and detect and summarize modules of highly correlated features. Modules can be formed using either the Louvain Modularity Maximization (LMM) algorithm or a Shared Minimum Distance algorithm (SMD) that we newly describe here and relate to LMM using simulated data. We applied SCNIC to two published datasets and we achieved increased statistical power and identified microbes that not only differed across groups, but also correlated strongly with each other, suggesting shared environmental drivers or cooperative relationships among them. SCNIC provides an easy way to generate correlation networks, identify modules of correlated features and summarize them for downstream statistical analysis. Although SCNIC was designed considering properties of microbiome data, such as compositionality and sparsity, it can be applied to a variety of data types including metabolomics data and used to integrate multiple data types. SCNIC allows for the identification of functional microbial relationships at scale while increasing statistical power through feature reduction.
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Affiliation(s)
- Michael Shaffer
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kumar Thurimella
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA,Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - John D. Sterrett
- Department of Integrative Physiology, University of Colorado, Boulder, Colorado, USA
| | - Catherine A. Lozupone
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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205
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Association between ustekinumab therapy and changes in specific anti-microbial response, serum biomarkers, and microbiota composition in patients with IBD: A pilot study. PLoS One 2022; 17:e0277576. [PMID: 36584073 PMCID: PMC9803183 DOI: 10.1371/journal.pone.0277576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/29/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Ustekinumab, is a new therapy for patients with IBD, especially for patients suffering from Crohn's disease (CD) who did not respond to anti-TNF treatment. To shed light on the longitudinal effect of ustekinumab on the immune system, we investigated the effect on skin and gut microbiota composition, specific immune response to commensals, and various serum biomarkers. METHODOLOGY/PRINCIPAL FINDINGS We recruited 11 patients with IBD who were monitored over 40 weeks of ustekinumab therapy and 39 healthy controls (HC). We found differences in the concentrations of serum levels of osteoprotegerin, TGF-β1, IL-33, and serum IgM antibodies against Lactobacillus plantarum between patients with IBD and HC. The levels of these biomarkers did not change in response to ustekinumab treatment or with disease improvement during the 40 weeks of observation. Additionally, we identified differences in stool abundance of uncultured Subdoligranulum, Faecalibacterium, and Bacteroides between patients with IBD and HC. CONCLUSION/SIGNIFICANCE In this preliminary study, we provide a unique overview of the longitudinal monitoring of fecal and skin microbial profiles as well as various serum biomarkers and humoral and cellular response to gut commensals in a small cohort of patients with IBD on ustekinumab therapy.
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206
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Ueyama J, Hayashi M, Hirayama M, Nishiwaki H, Ito M, Saito I, Tsuboi Y, Isobe T, Ohno K. Effects of Pesticide Intake on Gut Microbiota and Metabolites in Healthy Adults. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 20:ijerph20010213. [PMID: 36612532 PMCID: PMC9819155 DOI: 10.3390/ijerph20010213] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 06/03/2023]
Abstract
Animal experiments have indicated that pesticides may affect gut microbiota, which is responsible for the production of short-chain fatty acids (SCFAs) and polyamines. Here, we present a preliminary observation of the relationship between pesticide exposure and fecal SCFAs and polyamines in Japanese adults. In total, 38 healthy adults aged 69 ± 10 years (mean ± SD) were recruited and subjected to stool and spot urine tests. Urinary dialkylphosphates (DAP), 3-phenoxybenzoic acid, and glyphosate were assayed as pesticide exposure markers of organophosphorus insecticide (OP), a pyrethroid insecticide, and glyphosate, respectively. Significant negative correlations (p < 0.05, Spearman’s rank correlation coefficient) were found between urinary DAP, fecal acetate (r = −0.345), and lactate (r = −0.391). Multiple regression analyses revealed that urinary DAP was a significant explanatory variable of fecal acetate concentration (p < 0.001, β = −24.0, SE = 4.9, t = −4.9) with some vegetable intake (adjusted R-square = 0.751). These findings suggest that OP exposure is independently associated with lower fecal acetate levels, which may contribute to human health in middle-aged and older adult groups. Given that the human gut environment has long-term effects on the host, studies on wide-range age groups, including children, are necessary.
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Affiliation(s)
- Jun Ueyama
- Department of Pathophysiological Laboratory Sciences, Field of Radiological and Medical Laboratory Sciences, Nagoya University Graduate School of Medicine, 1-1-20 Daiko-minami, Higashi-ku, Nagoya 461-8673, Japan
| | - Mai Hayashi
- Department of Pathophysiological Laboratory Sciences, Field of Radiological and Medical Laboratory Sciences, Nagoya University Graduate School of Medicine, 1-1-20 Daiko-minami, Higashi-ku, Nagoya 461-8673, Japan
| | - Masaaki Hirayama
- Department of Pathophysiological Laboratory Sciences, Field of Radiological and Medical Laboratory Sciences, Nagoya University Graduate School of Medicine, 1-1-20 Daiko-minami, Higashi-ku, Nagoya 461-8673, Japan
| | - Hiroshi Nishiwaki
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Mikako Ito
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Isao Saito
- Department of Pathophysiological Laboratory Sciences, Field of Radiological and Medical Laboratory Sciences, Nagoya University Graduate School of Medicine, 1-1-20 Daiko-minami, Higashi-ku, Nagoya 461-8673, Japan
| | - Yoshio Tsuboi
- Department of Neurology, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Tomohiko Isobe
- Health and Environmental Risk Division, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba 305-8506, Japan
| | - Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
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207
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Lo LSH, Xu Z, Lee SS, Lau WK, Qiu JW, Liu H, Qian PY, Cheng J. How elevated nitrogen load affects bacterial community structure and nitrogen cycling services in coastal water. Front Microbiol 2022; 13:1062029. [PMID: 36620064 PMCID: PMC9815024 DOI: 10.3389/fmicb.2022.1062029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
Nutrient pollution in the coastal environment has been accelerated by progressively intensifying aquaculture activities. Excessive nutrients can lead to coastal eutrophication with serious economic and ecological consequences. In this study, we studied coastal planktonic microbial community over a year to understand the aquaculture impact on coastal water quality and function. We observed increased total inorganic nitrogen concentrations in active fish farms to favor the diverse Alpha- and Gammaproteobacteria. Bacterial community alpha diversity in fish farms was positively correlated with total inorganic nitrogen, and active fish farming co-influenced the bacterial structural composition and regional beta diversity. By analyzing the nitrogen cycle-related functional compositions and pathways using PICRUSt2 prediction on inferred genomes, we identified the contribution of over 600 bacterial species to four major pathways. Enhanced nitrogen load in active fish farms was positively correlated with elevated dissimilatory nitrate reduction and denitrification pathway abundances. Fallowed fish farms were characterized by a predicted high abundance of nirA and narB genes contributing to assimilatory nitrate reduction pathway due to the prevalence of Cyanobacteria. Overall, these results suggested active operation and short hiatus in coastal aquaculture practices could rapidly impact planktonic bacterial communities and further influence nitrogen cycling and associated processes. These findings will improve the understanding of the responses and interactions between microbiome and aquaculture activities. In a world of increasing aquaculture demands, this work has important implications for sustainable water resource management and development.
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Affiliation(s)
- Linus Shing Him Lo
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China,The Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhimeng Xu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China,The Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Sangwook Scott Lee
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China,The Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Wing Keung Lau
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Jian-Wen Qiu
- The Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China,Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Hongbin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China,The Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China,*Correspondence: Hongbin Liu,
| | - Pei-Yuan Qian
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China,The Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China,Pei-Yuan Qian,
| | - Jinping Cheng
- The Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China,Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, Hong Kong SAR, China,Jinping Cheng,
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208
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Chmiel JA, Carr C, Stuivenberg GA, Venema R, Chanyi RM, Al KF, Giguere D, Say H, Akouris PP, Domínguez Romero SA, Kwong A, Tai V, Koval SF, Razvi H, Bjazevic J, Burton JP. New perspectives on an old grouping: The genomic and phenotypic variability of Oxalobacter formigenes and the implications for calcium oxalate stone prevention. Front Microbiol 2022; 13:1011102. [PMID: 36620050 PMCID: PMC9812493 DOI: 10.3389/fmicb.2022.1011102] [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: 08/03/2022] [Accepted: 10/28/2022] [Indexed: 12/24/2022] Open
Abstract
Oxalobacter formigenes is a unique bacterium with the ability to metabolize oxalate as a primary carbon source. Most kidney stones in humans are composed of calcium and oxalate. Therefore, supplementation with an oxalate-degrading bacterium may reduce stone burden in patients suffering from recurrent calcium oxalate-based urolithiasis. Strains of O. formigenes are divided into two groups: group I and group II. However, the differences between strains from each group remain unclear and elucidating these distinctions will provide a better understanding of their physiology and potential clinical applications. Here, genomes from multiple O. formigenes strains underwent whole genome sequencing followed by phylogenetic and functional analyses. Genetic differences suggest that the O. formigenes taxon should be divided into an additional three species: Oxalobacter aliiformigenes sp. nov, Oxalobacter paeniformigenes sp. nov, and Oxalobacter paraformigenes sp. nov. Despite the similarities in the oxalyl-CoA gene (oxc), which is essential for oxalate degradation, these strains have multiple unique genetic features that may be potential exploited for clinical use. Further investigation into the growth of these strains in a simulated fecal environment revealed that O. aliiformigenes strains are capable of thriving within the human gut microbiota. O. aliiformigenes may be a better therapeutic candidate than current group I strains (retaining the name O. formigenes), which have been previously tested and shown to be ineffective as an oral supplement to mitigate stone disease. By performing genomic analyses and identifying these novel characteristics, Oxalobacter strains better suited to mitigation of calcium oxalate-based urolithiasis may be identified in the future.
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Affiliation(s)
- John A. Chmiel
- Department of Microbiology and Immunology, Western University, London, ON, Canada,Canadian Centre for Human Microbiome and Probiotics Research, London, ON, Canada
| | - Charles Carr
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Gerrit A. Stuivenberg
- Department of Microbiology and Immunology, Western University, London, ON, Canada,Canadian Centre for Human Microbiome and Probiotics Research, London, ON, Canada
| | - Robertson Venema
- Department of Medicine, The University of British Columbia, Vancouver, BC, Canada
| | - Ryan M. Chanyi
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Kait F. Al
- Department of Microbiology and Immunology, Western University, London, ON, Canada,Canadian Centre for Human Microbiome and Probiotics Research, London, ON, Canada
| | - Daniel Giguere
- Department of Biology, Western University, London, ON, Canada
| | - Henry Say
- Department of Biology, Western University, London, ON, Canada
| | - Polycronis P. Akouris
- Department of Microbiology and Immunology, Western University, London, ON, Canada,Canadian Centre for Human Microbiome and Probiotics Research, London, ON, Canada
| | | | - Aaron Kwong
- Department of Medicine, Western University, London, ON, Canada
| | - Vera Tai
- Department of Biology, Western University, London, ON, Canada
| | - Susan F. Koval
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Hassan Razvi
- Division of Urology, Department of Surgery, Western University, London, ON, Canada
| | - Jennifer Bjazevic
- Division of Urology, Department of Surgery, Western University, London, ON, Canada
| | - Jeremy P. Burton
- Department of Microbiology and Immunology, Western University, London, ON, Canada,Canadian Centre for Human Microbiome and Probiotics Research, London, ON, Canada,Division of Urology, Department of Surgery, Western University, London, ON, Canada,*Correspondence: Jeremy P. Burton,
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209
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synDNA-a Synthetic DNA Spike-in Method for Absolute Quantification of Shotgun Metagenomic Sequencing. mSystems 2022; 7:e0044722. [PMID: 36317886 PMCID: PMC9765022 DOI: 10.1128/msystems.00447-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Microbiome studies have the common goal of determining which microbial taxa are present, respond to specific conditions, or promote phenotypic changes in the host. Most of these studies rely on relative abundance measurements to drive conclusions. Inherent limitations of relative values are the inability to determine whether an individual taxon is more or less abundant and the magnitude of this change between the two samples. These limitations can be overcome by using absolute abundance quantifications, which can allow for a more complete understanding of community dynamics by measuring variations in total microbial loads. Obtaining absolute abundance measurements is still technically challenging. Here, we developed synthetic DNA (synDNA) spike-ins that enable precise and cost-effective absolute quantification of microbiome data by adding defined amounts of synDNAs to the samples. We designed 10 synDNAs with the following features: 2,000-bp length, variable GC content (26, 36, 46, 56, or 66% GC), and negligible identity to sequences found in the NCBI database. Dilution pools were generated by mixing the 10 synDNAs at different concentrations. Shotgun metagenomic sequencing showed that the pools of synDNAs with different percentages of GC efficiently reproduced the serial dilution, showing high correlation (r = 0.96; R2 ≥ 0.94) and significance (P < 0.01). Furthermore, we demonstrated that the synDNAs can be used as DNA spike-ins to generate linear models and predict with high accuracy the absolute number of bacterial cells in complex microbial communities. IMPORTANCE The synDNAs designed in this study enable accurate and reproducible measurements of absolute amount and fold changes of bacterial species in complex microbial communities. The method proposed here is versatile and promising as it can be applied to bacterial communities or genomic features like genes and operons, in addition to being easily adaptable by other research groups at a low cost. We also made the synDNAs' sequences and the plasmids available to encourage future application of the proposed method in the study of microbial communities.
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210
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Fulham M, Power M, Gray R. Gut microbiota of endangered Australian sea lion pups is unchanged by topical ivermectin treatment for endemic hookworm infection. Front Microbiol 2022; 13:1048013. [PMID: 36601397 PMCID: PMC9806137 DOI: 10.3389/fmicb.2022.1048013] [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: 09/19/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022] Open
Abstract
The gut microbiota is essential for the development and maintenance of the hosts' immune system. Disturbances to the gut microbiota in early life stages can result in long-lasting impacts on host health. This study aimed to determine if topical ivermectin treatment for endemic hookworm (Uncinaria sanguinis) infection in endangered Australian sea lion (Neophoca cinerea) pups resulted in gut microbial changes. The gut microbiota was characterised for untreated (control) (n = 23) and treated (n = 23) Australian sea lion pups sampled during the 2019 and 2020/21 breeding seasons at Seal Bay, Kangaroo Island. Samples were collected pre- and post-treatment on up to four occasions over a four-to-five-month period. The gut microbiota of untreated (control) and treated pups in both seasons was dominated by five bacterial phyla, Fusobacteria, Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes. A significant difference in alpha diversity between treatment groups was seen in pups sampled during the 2020/21 breeding season (p = 0.008), with higher richness and diversity in treated pups. Modelling the impact of individual pup identification (ID), capture, pup weight (kg), standard length (cm), age and sex on beta diversity revealed that pup ID accounted for most of the variation (35% in 2019 and 42% in 2020/21), with pup ID, capture, and age being the only significant contributors to microbial variation (p < 0.05). There were no statistically significant differences in the composition of the microbiota between treatment groups in both the 2019 and 2020/21 breeding seasons, indicating that topical ivermectin treatment did not alter the composition of the gut microbiota. To our knowledge, this is the first study to characterise the gut microbiota of free-ranging Australian pinniped pups, compare the composition across multiple time points, and to consider the impact of parasitic treatment on overall diversity and microbial composition of the gut microbiota. Importantly, the lack of compositional changes in the gut microbiota with treatment support the utility of topical ivermectin as a safe and minimally invasive management strategy to enhance pup survival in this endangered species.
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Affiliation(s)
- Mariel Fulham
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camperdown, NSW, Australia
| | - Michelle Power
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, North Ryde, NSW, Australia
| | - Rachael Gray
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camperdown, NSW, Australia,*Correspondence: Rachael Gray,
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211
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Chen K, Ponnusamy L, Mouhamadou CS, Fodjo BK, Sadia GC, Affoue FPK, Deguenon JM, Roe RM. Internal and external microbiota of home-caught Anopheles coluzzii (Diptera: Culicidae) from Côte d'Ivoire, Africa: Mosquitoes are filthy. PLoS One 2022; 17:e0278912. [PMID: 36520830 PMCID: PMC9754230 DOI: 10.1371/journal.pone.0278912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 11/23/2022] [Indexed: 12/23/2022] Open
Abstract
Over the past 10 years, studies using high-throughput 16S rRNA gene sequencing have shown that mosquitoes harbor diverse bacterial communities in their digestive system. However, no previous research has examined the total bacteria community inside versus outside of mosquitoes and whether bacteria found on the outside could represent a potential health threat through mechanical transfer. We examined the bacterial community of the external surface and internal body of female Anopheles coluzzii adults collected from homes in Côte d'Ivoire, Africa, by Illumina sequencing of the V3 to V4 region of 16S rRNA gene. Anopheles coluzzii is in the Anopheles gambiae sensu lato (s.l.) species complex and important in the transmission of malaria. The total 16S rRNA reads were assigned to 34 phyla, 73 orders, 325 families, and 700 genera. At the genus level, the most abundant genera inside and outside combined were Bacillus, Staphylococcus, Enterobacter, Corynebacterium, Kocuria, Providencia, and Sphingomonas. Mosquitoes had a greater diversity of bacterial taxa internally compared to the outside. The internal bacterial communities were similar between homes, while the external body samples were significantly different between homes. The bacteria on the external body were associated with plants, human and animal skin, and human and animal infections. Internally, Rickettsia bellii and Rickettsia typhi were found, potentially of importance, since this genus is associated with human diseases. Based on these findings, further research is warranted to assess the potential mechanical transmission of bacteria by mosquitoes moving into homes and the importance of the internal mosquito microbiota in human health.
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Affiliation(s)
- Kaiying Chen
- Department of Entomology and Plant Pathology, College of Agriculture and Life Sciences, North Carolina State University, Raleigh, NC, United States of America
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Loganathan Ponnusamy
- Department of Entomology and Plant Pathology, College of Agriculture and Life Sciences, North Carolina State University, Raleigh, NC, United States of America
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States of America
- * E-mail: (LP); (RMR)
| | - Chouaïbou S. Mouhamadou
- Department of Entomology and Plant Pathology, College of Agriculture and Life Sciences, North Carolina State University, Raleigh, NC, United States of America
| | - Behi Kouadio Fodjo
- Centre Suisse de Recherches Scientifiques, Abidjan, Cote d’Ivoire, Africa
| | | | | | - Jean M. Deguenon
- Department of Entomology and Plant Pathology, College of Agriculture and Life Sciences, North Carolina State University, Raleigh, NC, United States of America
| | - R. Michael Roe
- Department of Entomology and Plant Pathology, College of Agriculture and Life Sciences, North Carolina State University, Raleigh, NC, United States of America
- Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States of America
- * E-mail: (LP); (RMR)
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212
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Jurburg SD, Buscot F, Chatzinotas A, Chaudhari NM, Clark AT, Garbowski M, Grenié M, Hom EFY, Karakoç C, Marr S, Neumann S, Tarkka M, van Dam NM, Weinhold A, Heintz-Buschart A. The community ecology perspective of omics data. MICROBIOME 2022; 10:225. [PMID: 36510248 PMCID: PMC9746134 DOI: 10.1186/s40168-022-01423-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
The measurement of uncharacterized pools of biological molecules through techniques such as metabarcoding, metagenomics, metatranscriptomics, metabolomics, and metaproteomics produces large, multivariate datasets. Analyses of these datasets have successfully been borrowed from community ecology to characterize the molecular diversity of samples (ɑ-diversity) and to assess how these profiles change in response to experimental treatments or across gradients (β-diversity). However, sample preparation and data collection methods generate biases and noise which confound molecular diversity estimates and require special attention. Here, we examine how technical biases and noise that are introduced into multivariate molecular data affect the estimation of the components of diversity (i.e., total number of different molecular species, or entities; total number of molecules; and the abundance distribution of molecular entities). We then explore under which conditions these biases affect the measurement of ɑ- and β-diversity and highlight how novel methods commonly used in community ecology can be adopted to improve the interpretation and integration of multivariate molecular data. Video Abstract.
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Affiliation(s)
- Stephanie D Jurburg
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
- Institute of Biology, Leipzig University, Leipzig, Germany.
| | - François Buscot
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Soil Ecology, Helmholtz Centre for Environmental Research- UFZ, Halle, Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Narendrakumar M Chaudhari
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Adam T Clark
- Institute of Biology, University of Graz, Graz, Austria
| | - Magda Garbowski
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Botany, University of Wyoming, Wyoming, USA
| | - Matthias Grenié
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Erik F Y Hom
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Biology and Center for Biodiversity and Conservation Research, University of Mississippi, Oxford, Mississippi, USA
| | - Canan Karakoç
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Biology, Indiana University, Indiana, USA
| | - Susanne Marr
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Geobotany and Botanical Garden, Martin Luther University Halle Wittenberg, Halle, Germany
- Leibniz Institute of Plant Biochemistry, Bioinformatics and Scientific Data, Halle, Germany
| | - Steffen Neumann
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Leibniz Institute of Plant Biochemistry, Bioinformatics and Scientific Data, Halle, Germany
| | - Mika Tarkka
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Soil Ecology, Helmholtz Centre for Environmental Research- UFZ, Halle, Germany
| | - Nicole M van Dam
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Großbeeren, Germany
| | - Alexander Weinhold
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Anna Heintz-Buschart
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
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213
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Martínez-Ugalde E, Ávila-Akerberg V, González Martínez TM, Vázquez Trejo M, Zavala Hernández D, Anaya-Morales SL, Rebollar EA. The skin microbiota of the axolotl Ambystoma altamirani is highly influenced by metamorphosis and seasonality but not by pathogen infection. Anim Microbiome 2022; 4:63. [PMID: 36503640 PMCID: PMC9743558 DOI: 10.1186/s42523-022-00215-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/16/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Microbiomes have been increasingly recognized as major contributors to host health and survival. In amphibians, bacterial members of the skin microbiota protect their hosts by inhibiting the growth of the fungal pathogen Batrachochytrium dendrobatidis (Bd). Even though several studies describe the influence of biotic and abiotic factors over the skin microbiota, it remains unclear how these symbiotic bacterial communities vary across time and development. This is particularly relevant for species that undergo metamorphosis as it has been shown that host physiology and ecology drastically influence diversity of the skin microbiome. RESULTS We found that the skin bacterial communities of the axolotl A. altamirani are largely influenced by the metamorphic status of the host and by seasonal variation of abiotic factors such as temperature, pH, dissolved oxygen and conductivity. Despite high Bd prevalence in these samples, the bacterial diversity of the skin microbiota did not differ between infected and non-infected axolotls, although relative abundance of particular bacteria were correlated with Bd infection intensity. CONCLUSIONS Our work shows that metamorphosis is a crucial process that shapes skin bacterial communities and that axolotls under different developmental stages respond differently to environmental seasonal variations. Moreover, this study greatly contributes to a better understanding of the factors that shape amphibian skin microbiota, especially in a largely underexplored group like axolotls (Mexican Ambystoma species).
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Affiliation(s)
| | - Víctor Ávila-Akerberg
- Instituto de Ciencias Agropecuarias y Rurales, Universidad Autónoma del Estado de México, Toluca, Mexico
| | | | | | | | - Sara Lucia Anaya-Morales
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
- Department of Biology, University of Mississippi, Oxford, MS, USA
| | - Eria A Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.
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214
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Abstract
Gut microbiota and fecal bile acids were analyzed in 278 patients with α-synucleinopathies, which were comprised of 28 patients with dementia with Lewy bodies (DLB), 224 patients with Parkinson's disease (PD), and 26 patients with idiopathic rapid eye movement sleep behavior disorder (iRBD). Similarly to PD, short-chain fatty acids-producing genera were decreased in DLB. Additionally, Ruminococcus torques and Collinsella were increased in DLB, which were not changed in PD. Random forest models to differentiate DLB and PD showed that high Ruminococcus torques and high Collinsella, which presumably increase intestinal permeability, as well as low Bifidobacterium, which are also observed in Alzheimer's disease, were predictive of DLB. As Ruminococcus torques and Collinsella are also major secondary bile acids-producing bacteria, we quantified fecal bile acids and found that the production of ursodeoxycholic acid (UDCA) was high in DLB. Increased UDCA in DLB may mitigate neuroinflammation at the substantia nigra, whereas neuroinflammation may not be critical at the neocortex. Theraeutic intervention to increase Bifidobacteirum and its metabolites may retard the development and progression of DLB.
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215
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Román-Camacho JJ, García-García I, Santos-Dueñas IM, Ehrenreich A, Liebl W, García-Martínez T, Mauricio JC. Combining omics tools for the characterization of the microbiota of diverse vinegars obtained by submerged culture: 16S rRNA amplicon sequencing and MALDI-TOF MS. Front Microbiol 2022; 13:1055010. [PMID: 36569054 PMCID: PMC9767973 DOI: 10.3389/fmicb.2022.1055010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
Vinegars elaborated in southern Spain are highly valued all over the world because of their exceptional organoleptic properties and high quality. Among the factors which influence the characteristics of the final industrial products, the composition of the microbiota responsible for the process and the raw material used as acetification substrate have a crucial role. The current state of knowledge shows that few microbial groups are usually present throughout acetification, mainly acetic acid bacteria (AAB), although other microorganisms, present in smaller proportions, may also affect the overall activity and behavior of the microbial community. In the present work, the composition of a starter microbiota propagated on and subsequently developing three acetification profiles on different raw materials, an alcohol wine medium and two other natural substrates (a craft beer and fine wine), was characterized and compared. For this purpose, two different "omics" tools were combined for the first time to study submerged vinegar production: 16S rRNA amplicon sequencing, a culture-independent technique, and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), a culture-dependent method. Analysis of the metagenome revealed numerous taxa from 30 different phyla and highlighted the importance of the AAB genus Komagataeibacter, which was much more frequent than the other taxa, and Acetobacter; interestingly, also archaea from the Nitrososphaeraceae family were detected by 16S rRNA amplicon sequencing. MALDI-TOF MS confirmed the presence of Komagataeibacter by the identification of K. intermedius. These tools allowed for identifying some taxonomic groups such as the bacteria genera Cetobacterium and Rhodobacter, the bacteria species Lysinibacillus fusiformis, and even archaea, never to date found in this medium. Definitely, the effect of the combination of these techniques has allowed first, to confirm the composition of the predominant microbiota obtained in our previous metaproteomics approaches; second, to identify the microbial community and discriminate specific species that can be cultivated under laboratory conditions; and third, to obtain new insights on the characterization of the acetification raw materials used. These first findings may contribute to improving the understanding of the microbial communities' role in the vinegar-making industry.
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Affiliation(s)
- Juan J. Román-Camacho
- Department of Agricultural Chemistry, Edaphology and Microbiology, Agrifood Campus of International Excellence ceiA3, University of Córdoba, Córdoba, Spain
| | - Isidoro García-García
- Department of Inorganic Chemistry and Chemical Engineering, Agrifood Campus of International Excellence ceiA3, Nano Chemistry Institute (IUNAN), University of Córdoba, Córdoba, Spain,*Correspondence: Isidoro García-García,
| | - Inés M. Santos-Dueñas
- Department of Inorganic Chemistry and Chemical Engineering, Agrifood Campus of International Excellence ceiA3, Nano Chemistry Institute (IUNAN), University of Córdoba, Córdoba, Spain
| | - Armin Ehrenreich
- Department of Microbiology, School of Life Sciences, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Wolfgang Liebl
- Department of Microbiology, School of Life Sciences, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Teresa García-Martínez
- Department of Agricultural Chemistry, Edaphology and Microbiology, Agrifood Campus of International Excellence ceiA3, University of Córdoba, Córdoba, Spain
| | - Juan C. Mauricio
- Department of Agricultural Chemistry, Edaphology and Microbiology, Agrifood Campus of International Excellence ceiA3, University of Córdoba, Córdoba, Spain
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216
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Singer J, Tunbridge M, Perkins GB, Salehi T, Ying T, Wu H, Coates PT, Chadban SJ. Rapamycin and inulin for third-dose vaccine response stimulation (RIVASTIM): Inulin - study protocol for a pilot, multicentre, randomised, double-blinded, controlled trial of dietary inulin to improve SARS-CoV-2 vaccine response in kidney transplant recipients. BMJ Open 2022; 12:e062747. [PMID: 36456021 PMCID: PMC9716412 DOI: 10.1136/bmjopen-2022-062747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
INTRODUCTION Kidney transplant recipients (KTRs) are at an increased risk of hospitalisation and death from COVID-19. Vaccination against SARS-CoV-2 is our primary risk mitigation strategy, yet vaccine effectiveness in KTRs is suboptimal. Strategies to enhance vaccine efficacy are therefore required. Current evidence supports the role of the gut microbiota in shaping the immune response to vaccination. Gut dysbiosis is common in KTRs and is a potential contributor to impaired COVID-19 vaccine responses. We hypothesise that dietary fibre supplementation will attenuate gut dysbiosis and promote vaccine responsiveness in KTRs. METHODS AND ANALYSIS Rapamycin and inulin for third-dose vaccine response stimulation-inulin is a multicentre, randomised, prospective, double-blinded, placebo-controlled pilot trial examining the effect of dietary inulin supplementation prior to a third dose of COVID-19 vaccine in KTRs who have failed to develop protective immunity following a 2-dose COVID-19 vaccine schedule. Participants will be randomised 1:1 to inulin (active) or maltodextrin (placebo control), administered as 20 g/day of powdered supplement dissolved in water, for 4 weeks prior to and following vaccination. The primary outcome is the proportion of participants in each trial arm that achieve in vitro neutralisation of live SARS-CoV-2 virus at 4 weeks following a third dose of COVID-19 vaccine. Secondary outcomes include the safety and tolerability of dietary inulin, the diversity and differential abundance of gut microbiota, and vaccine-specific immune cell populations and responses. ETHICS AND DISSEMINATION Ethics approval was obtained from the Central Adelaide Local Health Network (CALHN) Human Research Ethics Committee (HREC) (approval number: 2021/HRE00354) and the Sydney Local Health District (SHLD) HREC (approval numbers: X21-0411 and 2021/STE04280). Results of this trial will be published following peer-review and presented at scientific meetings and congresses. TRIAL REGISTRATION NUMBER ACTRN12621001465842.
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Affiliation(s)
- Julian Singer
- Kidney Node, Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Department of Renal Medicine, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Matthew Tunbridge
- Central and Northern Adelaide Renal and Transplantation Service (CNARTS), Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Griffith B Perkins
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Immunology, SA Pathology, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - Tania Salehi
- Central and Northern Adelaide Renal and Transplantation Service (CNARTS), Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Tracey Ying
- Kidney Node, Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Department of Renal Medicine, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Huiling Wu
- Kidney Node, Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Department of Renal Medicine, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - P Toby Coates
- Central and Northern Adelaide Renal and Transplantation Service (CNARTS), Royal Adelaide Hospital, Adelaide, South Australia, Australia
- Discipline of Medicine, Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Steven J Chadban
- Kidney Node, Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Department of Renal Medicine, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
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217
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Vega L, Bohórquez L, Ramírez JD, Muñoz M. Do we need to change our perspective about gut biomarkers? A public data mining approach to identify differentially abundant bacteria in intestinal inflammatory diseases. Front Cell Infect Microbiol 2022; 12:918237. [PMID: 36478676 PMCID: PMC9719923 DOI: 10.3389/fcimb.2022.918237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/31/2022] [Indexed: 11/22/2022] Open
Abstract
Introduction The gut microbiome is involved in multiple processes that influence host physiology, and therefore, disruptions in microbiome homeostasis have been linked to diseases or secondary infections. Given the importance of the microbiome and the communities of microorganisms that compose it (microbiota), the term biomarkers were coined, which are bacteria correlated with disease states, diets, and the lifestyle of the host. However, a large field in the study of intestinal biomarkers remains unexplored because the bacterial communities associated with a given disease state have not been exactly defined yet. Methods Here, we analyzed public data of studies focused on describing the intestinal microbiota of patients with some intestinal inflammatory diseases together with their respective controls. With these analyses, we aimed to identify differentially abundant bacteria between the subjects with the disease and their controls. Results We found that frequently reported bacteria such as Fusobacterium, Streptococcus, and Escherichia/Shigella were differentially abundant between the groups, with a higher abundance mostly in patients with the disease in contrast with their controls. On the other hand, we also identified potentially beneficial bacteria such as Faecalibacterium and Phascolarctobacterium, with a higher abundance in control patients. Discussion Our results of the differentially abundant bacteria contrast with what was already reported in previous studies on certain inflammatory diseases, but we highlight the importance of considering more comprehensive approaches to redefine or expand the definition of biomarkers. For instance, the intra-taxa diversity within a bacterial community must be considered, as well as environmental and genetic factors of the host, and even consider a functional validation of these biomarkers through in vivo and in vitro approaches. With the above, these key bacterial communities in the intestinal microbiota may have potential as next-generation probiotics or may be functional for the design of specific therapies in certain intestinal diseases.
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Affiliation(s)
- Laura Vega
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Laura Bohórquez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia,Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia,*Correspondence: Marina Muñoz,
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218
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Airway Bacterial Biodiversity in Exhaled Breath Condensates of Asthmatic Children-Does It Differ from the Healthy Ones? J Clin Med 2022; 11:jcm11226774. [PMID: 36431251 PMCID: PMC9698396 DOI: 10.3390/jcm11226774] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/09/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022] Open
Abstract
Asthma etiopathology is still not fully determined. One of its possible causes can be found in airway microbiome dysbiosis. The study's purpose was to determine whether there are any significant differences in the bacterial microbiome diversity of lower airways microbiota of asthmatic children, since knowledge of this topic is very scarce. To the authors' knowledge, this is the first research using exhaled breath condensates in children's lower airways for bacterial assessment. Exhaled breath condensates (EBC) and oropharyngeal swabs were obtained from pediatric asthmatic patients and a healthy group (n = 38, 19 vs. 19). The microbial assessment was conducted through genetic material PCR amplification, followed by bacterial 16S rRNA amplicon sequencing. Collected data were analyzed, in terms of taxonomy and alpha and beta diversity between assessed groups. Swab samples are characterized by higher species richness compared to exhaled breath condensates (Shannon diversity index (mean 4.11 vs. 2.867, p = 9.108 × 10-8), observed features (mean 77.4 vs. 17.3, p = 5.572 × 10-11), and Faith's phylogenetic diversity (mean 7.686 vs. 3.280 p = 1.296 × 10-10)). Asthmatic children had a higher abundance of bacterial species (Shannon diversity index, mean 3.029 vs. 2.642, p = 0.026) but more even distribution (Pielou's evenness, mean 0.742 vs. 0.648, p = 0.002) in EBC than healthy ones; the same results were observed within pediatric patients born naturally within EBC samples. In children with a positive family history of allergic diseases, alpha diversity of lower airway material was increased (Shannon's diversity index p = 0.026, Faith's phylogenetic diversity p = 0.011, observed features p = 0.003). Class Gammaproteobacteria and Bacilli were less abundant among asthmatics in the exhaled breath samples. The most dominant bacteria on a phylum level in both sample types were Firmicutes, followed by Proteobacteria and Actinobacteriota. The obtained outcome of higher bacterial diversity of lower airways among asthmatic patients indicates a further need for future studies of microbiota connection with disease pathogenesis.
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219
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Nakatsu CH, Pavlovic NB, Byappanahalli MN. Bacteria common to rhizosphere communities of Asiatic bittersweet across a post-glacial landscape. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.999099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Invasive plants such as Asiatic bittersweet (Celastrus orbiculatus Thunb.) are a significant problem for land managers as they impact plant species composition, disrupt nutrient dynamics and structure of native ecosystems, and are difficult to eradicate. As a result of the increasing abundance of Asiatic bittersweet across the eastern U.S., we have been investigating underlying factors potentially contributing to the success of this plant. Recently, ecologists have been investigating the role of plant-soil-microbe interactions contributing to plant invasion. This work has led to question: are there certain microbes (e.g., bacteria, fungi) contributing to the success of some invasive plants? We hypothesize that despite differences in geologic age of soils where Asiatic bittersweet has established in the Indiana Dunes National Park there are sufficient common factors that led to common bacterial taxa in their rhizosphere. The objectives were to determine differences and commonalities in the soil chemistry, plant community and bacterial communities of Asiatic bittersweet plants. To achieve these objectives, bittersweet plants were collected at thirteen locations in the national park from soils ranging in geologic age from 150 to over 14,500 years. Surrounding soil chemistry, plant cover and the 16S rRNA gene amplicon sequences of rhizosphere soil bacterial communities of these Asiatic bittersweet were compared. Asiatic bittersweet coverage of sampling sites ranged from 2 to 77% averaging 52 ± 2%. There were statistically significant differences (p < 0.05) in alpha diversity (Shannon, Faith’s PD and Pielou’s evenness) and beta diversity (Bray Curtis, Jaccard, unweighted Unifrac, weighted Unifrac) among the samples when grouped by soil age or habitat. Despite these differences in the bacterial communities from different soil ages and habitats, some bacterial taxa (e.g., Bacillus, Streptomyces, Sphingomonas and Rhizobiales) previously found in other studies to be beneficial to plant growth were found in every rhizosphere community sampled. These microbes provide insight into a possible contributing factor to the success of this invasive plant at the Indiana Dunes National Park, and a strategy for future work to reduce the impact of Asiatic bittersweet establishment and offer some new strategies to manage this nuisance species.
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Yang X, Bao L, Zhang Y, Long J, Li Y, Wang H, Cui Y, Yan D. Novel weight loss diet attenuates dietary-induced obesity in mice and might correlate with altered gut microbiota and metabolite profiles. Front Nutr 2022; 9:987955. [DOI: 10.3389/fnut.2022.987955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/27/2022] [Indexed: 11/13/2022] Open
Abstract
Although many dietary patterns have been studied for weight loss, various limitations still exist. Therefore, we designed a novel weight loss diet (NWLD) with carbohydrate, protein, and fat (energy) contents of 45%, 20%, and 35%, respectively. The saturated fatty acids: monounsaturated fatty acids:polyunsaturated fatty acids ratio was 1:2:1, and the insoluble: soluble dietary fiber ratio was 2:1. We aimed to observe the effect of NWLD on weight loss and understand the underlying metabolic mechanisms. Twenty-nine male C57BL/6J mice were selected. Nine mice were fed ordinary feed in a blank control group, and the rest were fed a high-fat diet (HFD) to establish obese mouse models. Twelve weeks later, obesity models were established, and 10 obese mice were switched to NWLD feeding. Six weeks after switching the diet, the serum, intestinal feces, and kidneys of mice were collected. Obesity-related indicators, gut microbial composition, and fecal metabolite profiles of all the mice were determined, and the correlations among these indicators were analyzed. Kidney function indicators were also assessed. The results showed that the NWLD attenuated HFD-induced weight gain, serum triglycerides (TG), and inflammatory factors, optimized the body composition without kidney function impairment. Amino acid metabolism pathways and metabolites might play key roles in this process. The findings of this research imply that NWLD could be an effective nutritional remedy for managing dietary-induced obesity.
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Graber LC, Ramalho MO, Powell S, Moreau CS. Identifying the Role of Elevation, Geography, and Species Identity in Structuring Turtle Ant (Cephalotes Latreille, 1802) Bacterial Communities. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02128-z. [PMID: 36352137 DOI: 10.1007/s00248-022-02128-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Bacterial communities in animals are often necessary for hosts to survive, particularly for hosts with nutrient-limited diets. The composition, abundance, and richness of these bacterial communities may be shaped by host identity and external ecological factors. The turtle ants (genus Cephalotes) are predominantly herbivorous and known to rely on bacterial communities to enrich their diet. Cephalotes have a broad Neotropical distribution, with high diversity in the South American Cerrado, a geologically and biologically diverse savanna. Using 16S rRNA amplicon sequencing, we examined the bacterial communities of forty-one Cephalotes samples of sixteen different species collected from multiple locations across two sites in the Cerrado (MG, Brazil) and compared the bacterial communities according to elevation, locality, species, and species group, defined by host phylogeny. Beta diversity of bacterial communities differed with respect to all categories but particularly strongly when compared by geographic location, species, and species group. Differences seen in species and species groups can be partially explained by the high abundance of Mesorhizobium in Cephalotes pusillus and Cephalotes depressus species groups, when compared to other clades via the Analysis of Composition of Microbiome (ANCOM). Though the Cephalotes bacterial community is highly conserved, results from this study indicate that multiple external factors can affect and change bacterial community composition and abundance.
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Affiliation(s)
- Leland C Graber
- Department of Entomology, Cornell University, 129 Garden Ave, Ithaca, NY, 14853, USA.
| | - Manuela O Ramalho
- Department of Entomology, Cornell University, 129 Garden Ave, Ithaca, NY, 14853, USA
- Department of Biology, West Chester University, West Chester, PA, USA
| | - Scott Powell
- Department of Biological Sciences, George Washington University, Washington, D.C., USA
| | - Corrie S Moreau
- Department of Entomology, Cornell University, 129 Garden Ave, Ithaca, NY, 14853, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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Bringhurst B, Allert M, Greenwold M, Kellner K, Seal JN. Environments and Hosts Structure the Bacterial Microbiomes of Fungus-Gardening Ants and their Symbiotic Fungus Gardens. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02138-x. [PMID: 36344828 DOI: 10.1007/s00248-022-02138-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
The fungus gardening-ant system is considered a complex, multi-tiered symbiosis, as it is composed of ants, their fungus, and microorganisms associated with either ants or fungus. We examine the bacterial microbiome of Trachymyrmex septentrionalis and Mycetomoellerius turrifex ants and their symbiotic fungus gardens, using 16S rRNA Illumina sequencing, over a region spanning approximately 350 km (east and central Texas). Typically, microorganisms can be acquired from a parent colony (vertical transmission) or from the environment (horizontal transmission). Because the symbiosis is characterized by co-dispersal of the ants and fungus, elements of both ant and fungus garden microbiome could be characterized by vertical transmission. The goals of this study were to explore how both the ant and fungus garden bacterial microbiome are acquired. The main findings were that different mechanisms appear to explain the structure the microbiomes of ants and their symbiotic fungus gardens. Ant associated microbiomes had a strong host ant signature, which could be indicative of vertical inheritance of the ant associated bacterial microbiome or an unknown mechanism of active uptake or screening. On the other hand, the bacterial microbiome of the fungus garden was more complex in that some bacterial taxa appear to be structured by the ant host species, whereas others by fungal lineage or the environment (geographic region). Thus bacteria in fungus gardens appear to be acquired both horizontally and vertically.
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Affiliation(s)
- Blake Bringhurst
- Department of Biology, University of Texas at Tyler, 3900 University Blvd, Tyler, TX, 75799, USA
| | - Mattea Allert
- Department of Biology, University of Texas at Tyler, 3900 University Blvd, Tyler, TX, 75799, USA
| | - Matthew Greenwold
- Department of Biology, University of Texas at Tyler, 3900 University Blvd, Tyler, TX, 75799, USA
| | - Katrin Kellner
- Department of Biology, University of Texas at Tyler, 3900 University Blvd, Tyler, TX, 75799, USA
| | - Jon N Seal
- Department of Biology, University of Texas at Tyler, 3900 University Blvd, Tyler, TX, 75799, USA.
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Serrano M, Srivastava A, Buck G, Zhu B, Edupuganti L, Adegbulugbe E, Shankaranarayanan D, Kopp JB, Raj DS. Dietary Protein and Fiber Affect Gut Microbiome and Treg/Th17 Commitment in Chronic Kidney Disease Mice. Am J Nephrol 2022; 53:646-651. [PMID: 36349783 PMCID: PMC10367184 DOI: 10.1159/000526957] [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: 07/01/2022] [Accepted: 08/19/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND Patients with chronic kidney disease (CKD) have dysbiosis, dysmetabolism, and immune dysregulation. Gut microbiome plays an important role shaping the immune system which is an important modulator of CKD progression. METHODS We compared the effect of a diet low in protein and high in fiber (LP-HF; n = 7) to that of diet rich in protein, but low in fiber (HP-LF; n = 7) on gut microbiome and T-cell commitment in male CKD (Alb/TGF-β1) mice. The gut microbiomes of these mice were subjected to 16S rRNA taxonomic profiling at baseline, 6 weeks and 12 weeks of the study. RESULTS The LP-HF diet was associated with an increase in Butyricicoccus pullicaecorum BT, a taxon whose functions include those closely related to butyric acid synthesis (Kendall's W statistic = 180 in analysis of microbiome composition). HP-LF diet was associated with increased abundance of two predominantly proteolytic bacterial strains related to Parabacteroides distasonis (W statistic = 173), Mucispirillum schaedleri, and Bacteroides dorei (W statistic = 192). Pathway analysis suggested that the LP-HF diet induced carbohydrate, lipid, and butyrate metabolism. As compared with HP-LF mice, LP-HF mice had 1.7-fold increase in CD4+Foxp3+Treg cells in spleen and 2.4-fold increase of these cells in peripheral blood. There was an 87% decrease in percentage of CD4+ Th17 + cells in spleen and an 85% decrease in peripheral blood, respectively, in LP-HF mice compared to the HP-LF mice. CONCLUSION The LP-HF diet promotes the proliferation of saccharolytic bacteria and favors T-cell commitment toward Treg cells in a CKD mouse of model. Clinical significance of the finding needs to be further investigated.
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Affiliation(s)
- Myrna Serrano
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Anvesha Srivastava
- Division of Kidney Diseases and Hypertension, George Washington University School of Medicine, Washington, District of Columbia, USA,
| | - Gregory Buck
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Bin Zhu
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Laahirie Edupuganti
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Esther Adegbulugbe
- Division of Kidney Diseases and Hypertension, George Washington University School of Medicine, Washington, District of Columbia, USA
| | - Divya Shankaranarayanan
- Division of Kidney Diseases and Hypertension, George Washington University School of Medicine, Washington, District of Columbia, USA
| | - Jeffrey B Kopp
- Kidney Disease Section, NIDDK, NIH, Bethesda, Maryland, USA
| | - Dominic S Raj
- Division of Kidney Diseases and Hypertension, George Washington University School of Medicine, Washington, District of Columbia, USA
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Rosso AD, Aguilera P, Quesada S, Mascardi F, Mascuka SN, Cimolai MC, Cerezo J, Spiazzi R, Conlon C, Milano C, Iraola GM, Penas-Steinhardt A, Belforte FS. Comprehensive Phenotyping in Inflammatory Bowel Disease: Search for Biomarker Algorithms in the Transkingdom Interactions Context. Microorganisms 2022; 10:2190. [PMID: 36363782 PMCID: PMC9698371 DOI: 10.3390/microorganisms10112190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/27/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Inflammatory bowel disease (IBD) is the most common form of intestinal inflammation associated with a dysregulated immune system response to the commensal microbiota in a genetically susceptible host. IBD includes ulcerative colitis (UC) and Crohn's disease (CD), both of which are remarkably heterogeneous in their clinical presentation and response to treatment. This translates into a notable diagnostic challenge, especially in underdeveloped countries where IBD is on the rise and access to diagnosis or treatment is not always accessible for chronic diseases. The present work characterized, for the first time in our region, epigenetic biomarkers and gut microbial profiles associated with UC and CD patients in the Buenos Aires Metropolitan area and revealed differences between non-IBD controls and IBD patients. General metabolic functions associated with the gut microbiota, as well as core microorganisms within groups, were also analyzed. Additionally, the gut microbiota analysis was integrated with relevant clinical, biochemical and epigenetic markers considered in the follow-up of patients with IBD, with the aim of generating more powerful diagnostic tools to discriminate phenotypes. Overall, our study provides new insights into data analysis algorithms to promote comprehensive phenotyping tools using quantitative and qualitative analysis in a transkingdom interactions network context.
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Affiliation(s)
- Ayelén D. Rosso
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
- Instituto de Ecología y Desarrollo Sustentable (INEDES-CONICET-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
| | - Pablo Aguilera
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
| | - Sofía Quesada
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
| | - Florencia Mascardi
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET, Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano de Buenos Aires (HIBA), Ciudad Autónoma de Buenos Aires C1199, Argentina
| | - Sebastian N. Mascuka
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
| | - María C. Cimolai
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
| | - Jimena Cerezo
- Servicio de Gastroenterología, Hospital Nacional Prof. Alejandro Posadas, Ciudad Autónoma de Buenos Aires 1704, Argentina
| | - Renata Spiazzi
- Servicio de Gastroenterología, Hospital Nacional Prof. Alejandro Posadas, Ciudad Autónoma de Buenos Aires 1704, Argentina
| | - Carolina Conlon
- Servicio de Gastroenterología, Hospital Nacional Prof. Alejandro Posadas, Ciudad Autónoma de Buenos Aires 1704, Argentina
| | - Claudia Milano
- Servicio de Gastroenterología, Hospital Nacional Prof. Alejandro Posadas, Ciudad Autónoma de Buenos Aires 1704, Argentina
| | - Gregorio M. Iraola
- Laboratorio de Genómica Microbiana, Institut Pasteur Montevideo, Montevideo 11400, Uruguay
- Centro de Biología Integrativa, Universidad Mayor, Santiago 7510041, Chile
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridgeshire CB10 1SA, UK
| | - Alberto Penas-Steinhardt
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
- Instituto Universitario de Ciencias de la Salud, Fundación H.A. Barceló, Ciudad Autónoma de Buenos Aires 1127, Argentina
| | - Fiorella S. Belforte
- Laboratorio de Genómica Computacional (GeC-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Programa del Estudio de Comunicación y Señalización Interreino (PECSI-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1425FQB, Argentina
- Instituto de Ecología y Desarrollo Sustentable (INEDES-CONICET-UNLu), Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján 6700, Argentina
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Zhang J, Wu Y, Liu J, Yang Y, Li H, Wu X, Zheng X, Liang Y, Tu C, Chen M, Tan C, Chang B, Huang Y, Wang Z, Tian G, Ding T. Differential Oral Microbial Input Determines Two Microbiota Pneumo-Types Associated with Health Status. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2203115. [PMID: 36031410 PMCID: PMC9661847 DOI: 10.1002/advs.202203115] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/02/2022] [Indexed: 05/09/2023]
Abstract
The oral and upper respiratory tracts are closely linked anatomically and physiologically with the lower respiratory tract and lungs, and the influence of oral and upper respiratory microbes on the lung microbiota is increasingly being recognized. However, the ecological process and individual heterogeneity of the oral and upper respiratory tract microbes shaping the lung microbiota remain unclear owing to the lack of controlled analyses with sufficient sample sizes. Here, the microbiomes of saliva, nasal cavity, oropharyngeal area, and bronchoalveolar lavage samples are profiled and the shaping process of multisource microbes on the lung microbiota is measured. It is found that oral and nasal microbial inputs jointly shape the lung microbiota by occupying different ecological niches. It is also observed that the spread of oral microbes to the lungs is heterogeneous, with more oral microbes entering the lungs being associated with decreased lung function and increased lung proinflammatory cytokines. These results depict the external shaping process of lung microbiota and indicate the great value of oral samples, such as saliva, in monitoring and assessing lung microbiota status in clinical settings.
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Affiliation(s)
- Jingxiang Zhang
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
| | - Yiping Wu
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
| | - Jing Liu
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Yongqiang Yang
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
| | - Hui Li
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
| | - Xiaorong Wu
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
| | - Xiaobin Zheng
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Yingjian Liang
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Changli Tu
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Meizhu Chen
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Cuiyan Tan
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Bozhen Chang
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
| | - Yiying Huang
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Zhengguo Wang
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Guo‐Bao Tian
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
- School of MedicineXizang Minzu UniversityXianyangShaanxi712082China
| | - Tao Ding
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
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Fuerniss LK, Davis HE, Belk AD, Metcalf JL, Engle TE, Scanga JA, Garry FB, Bryant TC, Martin JN. Liver abscess microbiota of feedlot steers finished in natural and traditional management programs. J Anim Sci 2022; 100:skac252. [PMID: 35938914 PMCID: PMC9645556 DOI: 10.1093/jas/skac252] [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: 03/23/2022] [Accepted: 08/04/2022] [Indexed: 11/14/2022] Open
Abstract
Liver abscess etiology in feedlot steers involves the escape of bacteria from the digestive tract to form a polymicrobial abscess within or on the external surface of the liver. However, little is known about the effects of feedlot finishing systems on the microbial composition of the liver abscess purulent material. Liver abscesses were collected at the time of harvest from steers originating from a single feedlot managed in either a traditional program (which included tylosin phosphate supplementation) or a natural program (without tylosin phosphate supplementation). The purulent material of liver abscesses from traditionally managed steers (N = 53 abscesses) and that of naturally managed steers (N = 62 abscesses) was characterized using the V4 region of the 16S rRNA gene. Two phyla and three genera were found in greater than 1% relative abundance across all abscesses. The genus Fusobacterium was identified in all liver abscess samples and accounted for 64% of sequencing reads. Bacteroides and Porphyromonas genera accounted for 33% and 1% of reads, respectively. Trueperella was more likely to be found in the liver abscesses of naturally managed steers than traditionally managed steers (P = 0.022). Over 99% of the genus-level bacterial sequences observed across all liver abscesses belonged to Gram-negative genera. Bacteria known to colonize both the rumen and hindgut were identified within liver abscesses. No differences in alpha diversity or beta diversity were detected between liver abscess communities (between the two management programs or individual pens) when tested as richness, Shannon Diversity Index, or weighted UniFrac distances (P > 0.05). These results were consistent with previous identification of Fusobacterium necrophorum as the primary bacteriologic agent within liver abscesses and emphasized the relationship between the gastrointestinal microbiota and liver abscess formation. Though the microbiota of the liver abscess purulent material was similar between steers fed an antibiotic-free diet and those fed an antibiotic-containing diet from the same feedlot, divergence was detected in liver abscess communities with some being dominated by Fusobacterium and others being dominated by Bacteroides.
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Affiliation(s)
- Luke K Fuerniss
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Haley E Davis
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Aeriel D Belk
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Jessica L Metcalf
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Terry E Engle
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - John A Scanga
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Franklyn B Garry
- Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Tony C Bryant
- Five Rivers Cattle Feeding, LLC, Johnstown, Colorado, USA
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Elias L, Hearn AJM, Blazier JC, Rogovska YV, Wang J, Li S, Liu S, Nebogatkin IV, Rogovskyy AS. The Microbiota of Ixodes ricinus and Dermacentor reticulatus Ticks Collected from a Highly Populated City of Eastern Europe. MICROBIAL ECOLOGY 2022; 84:1072-1086. [PMID: 34767049 DOI: 10.1007/s00248-021-01921-6] [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: 08/17/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
Recent investigations have examined, through sequencing the V6 region of 16S rRNA gene, the microbiota of questing Ixodes ricinus and Dermacentor reticulatus ticks collected from rural areas of Central (Dnipropetrovs'k (region D) and Poltava (region P)) and Northeastern (Kharkiv (region K)) Ukraine. In addition to defining the bacterial microbiota of both tick species, the previous investigations also revealed a high degree of inter-sex and inter-regional variations in the tick microbiota. As a continuation of the two studies, the present investigation has analyzed individual microbiota of questing I. ricinus (n = 50) and D. reticulatus (n = 50) ticks originating from Kyiv, the largest city of Ukraine. The Kyiv tick microbiota were compared between males and females for each tick species. Additionally, a cross-regional analysis was performed to compare the microbiota of Kyiv ticks to those from regions D, K, and P. Numerous statistically significant inter-sex and inter-regional variations were detected when alpha diversity, beta diversity, the bacterial relative and differential abundances were assessed. The overall results demonstrated that the microbiota of Kyiv ticks were statistically different compared to the ticks of the other three regions. Besides existing climatic and geographical differences between the four regions, the authors hypothesize that various anthropogenic factors of the megapolis (e.g., animal species translocation, land management, ecology) could have contributed to the distinct microbiota of Kyiv ticks observed in this study.
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Affiliation(s)
- Leta Elias
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, 4467 TAMU, Texas A&M University, College Station, TX, 77843, USA
| | - Aimee-Joy M Hearn
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, 4467 TAMU, Texas A&M University, College Station, TX, 77843, USA
| | - John C Blazier
- Texas A&M Institute for Genomics Sciences and Society, Texas A&M University, College Station, TX, 77843, USA
| | - Yuliya V Rogovska
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, 4467 TAMU, Texas A&M University, College Station, TX, 77843, USA
| | - Jiangli Wang
- Department of Statistics and Finance, School of Management, University of Science and Technology of China (USTC), Hefei, 230026, Anhui, China
| | - Sijia Li
- Statistical Collaboration Center, Department of Statistics, College of Science, Texas A&M University, College Station, TX, 77843, USA
| | - Shuling Liu
- Statistical Collaboration Center, Department of Statistics, College of Science, Texas A&M University, College Station, TX, 77843, USA
| | - Igor V Nebogatkin
- I.I. Schmalhausen Institute of Zoology of National Academy of Sciences of Ukraine, Kyiv, 01601, Ukraine
| | - Artem S Rogovskyy
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, 4467 TAMU, Texas A&M University, College Station, TX, 77843, USA.
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228
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Li Z, Yu X, Guo H, Lee T, Hu J. A maximum-type microbial differential abundance test with application to high-dimensional microbiome data analyses. Front Cell Infect Microbiol 2022; 12:988717. [PMID: 36389165 PMCID: PMC9650337 DOI: 10.3389/fcimb.2022.988717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 10/04/2022] [Indexed: 12/03/2022] Open
Abstract
Background High-throughput metagenomic sequencing technologies have shown prominent advantages over traditional pathogen detection methods, bringing great potential in clinical pathogen diagnosis and treatment of infectious diseases. Nevertheless, how to accurately detect the difference in microbiome profiles between treatment or disease conditions remains computationally challenging. Results In this study, we propose a novel test for identifying the difference between two high-dimensional microbiome abundance data matrices based on the centered log-ratio transformation of the microbiome compositions. The test p-value can be calculated directly with a closed-form solution from the derived asymptotic null distribution. We also investigate the asymptotic statistical power against sparse alternatives that are typically encountered in microbiome studies. The proposed test is maximum-type equal-covariance-assumption-free (MECAF), making it widely applicable to studies that compare microbiome compositions between conditions. Our simulation studies demonstrated that the proposed MECAF test achieves more desirable power than competing methods while having the type I error rate well controlled under various scenarios. The usefulness of the proposed test is further illustrated with two real microbiome data analyses. The source code of the proposed method is freely available at https://github.com/Jiyuan-NYU-Langone/MECAF. Conclusions MECAF is a flexible differential abundance test and achieves statistical efficiency in analyzing high-throughput microbiome data. The proposed new method will allow us to efficiently discover shifts in microbiome abundances between disease and treatment conditions, broadening our understanding of the disease and ultimately improving clinical diagnosis and treatment.
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Affiliation(s)
- Zhengbang Li
- School of Mathematics and Statistics, Central China Normal University, Wuhan, China
| | - Xiaochen Yu
- School of Mathematics and Statistics, Central China Normal University, Wuhan, China
| | - Hongping Guo
- School of Mathematics and Statistics, Hubei Normal University, Huangshi, China
| | - TingFang Lee
- Division of Biostatistics, Department of Population Health, New York University (NYU) Grossman School of Medicine, New York, NY, United States
| | - Jiyuan Hu
- Division of Biostatistics, Department of Population Health, New York University (NYU) Grossman School of Medicine, New York, NY, United States
- *Correspondence: Jiyuan Hu,
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A Pilot Study: the Development of a Facility-Associated Microbiome and Its Association with the Presence of Listeria Spp. in One Small Meat Processing Facility. Microbiol Spectr 2022; 10:e0204522. [PMID: 35980043 PMCID: PMC9603805 DOI: 10.1128/spectrum.02045-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Microbial communities which persist in food processing facilities may have a detrimental impact on food safety and spoilage. In meat processing, Listeria monocytogenes is an organism of concern due to its ability to cause significant human illnesses and persist in refrigerated environments. The microbial ecology of Listeria spp. in small meat processing facilities has not been well characterized. Therefore, we collected samples from a newly constructed meat processing facility as an opportunity to investigate several research objectives: (i) to determine whether a stable, consistent microbiome develops in a small meat processing facility during the first 18 months of operation, (ii) to evaluate the environmental factors that drive microbial community formation, and (iii) to elucidate the relationship between microbial communities and the presence of Listeria species. We evaluated microbiomes using 16S rRNA gene sequencing and Listeria presence using quantitative PCR. We demonstrated that microbial communities differentiate by the functional room type, which is representative of several environmental differences such as temperature, sources of microbes, and activity. Temperature was an especially important factor; in rooms with low temperatures, communities were dominated by psychotrophs, especially Pseudomonas, while warmer rooms supported greater diversity. A stable core community formed in facility drains, indicating that mechanisms which cause persistence are present in the communities. The overall presence of Listeria in the facility was low but could be tied to specific organisms within a room, and the species of Listeria could be stratified by room function. IMPORTANCE This study provides critical knowledge to improve meat safety and quality from small meat processing facilities. Principally, it demonstrates the importance of facility design and room condition to the development of important microbial communities; temperature, sanitation regimen, and physical barriers all influence the ability of microorganisms to join the stable core community. It also demonstrates a relationship between the microbial community and Listeria presence in the facility, showing the importance of managing facility sanitation plans for not only pathogens, but also the general facility microbiome.
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230
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Love CJ, Gubert C, Kodikara S, Kong G, Lê Cao KA, Hannan AJ. Microbiota DNA isolation, 16S rRNA amplicon sequencing, and bioinformatic analysis for bacterial microbiome profiling of rodent fecal samples. STAR Protoc 2022; 3:101772. [PMID: 36313541 PMCID: PMC9597187 DOI: 10.1016/j.xpro.2022.101772] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Fecal samples are frequently used to characterize bacterial populations of the gastrointestinal tract. A protocol is provided to profile gut bacterial populations using rodent fecal samples. We describe the optimal procedures for collecting rodent fecal samples, isolating genomic DNA, 16S rRNA gene V4 region sequencing, and bioinformatic analyses. This protocol includes detailed instructions and example outputs to ensure accurate, reproducible results and data visualization. Comprehensive troubleshooting and limitation sections address technical and statistical issues that may arise when profiling microbiota. For complete details on the use and execution of this protocol, please refer to Gubert et al. (2022).
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Affiliation(s)
- Chloe J. Love
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC 3010, Australia
| | - Carolina Gubert
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC 3010, Australia,Corresponding author
| | - Saritha Kodikara
- Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC 3010, Australia,Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne, Parkville VIC, 3010, Australia
| | - Geraldine Kong
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC 3010, Australia
| | - Kim-Anh Lê Cao
- Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Anthony J. Hannan
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC 3010, Australia,Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC 3010, Australia,Corresponding author
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231
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Weinroth MD, Oakley B, Ramírez GA, Reyes A, Harris CE, Buhr RJ. 16S rRNA gene-based assessment of common broiler chicken sampling methods: Evaluating intra-flock sample size, cecal pair similarity, and cloacal swab similarity to other alimentary tract locations. Front Physiol 2022; 13:996654. [PMID: 36338471 PMCID: PMC9627029 DOI: 10.3389/fphys.2022.996654] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/03/2022] [Indexed: 08/25/2024] Open
Abstract
16S rRNA gene sequencing for characterization of microbiomes has become more common in poultry research and can be used to both answer specific research questions and help inform experimental design choices. The objective of this study was to use 16S rRNA gene sequencing to examine common sampling practices in broiler chicken studies such as: the required number of birds selected from a flock to adequately capture microbiome diversity, the differences between cecal pairs within the same bird, and whether cloacal swabs are representative of other alimentary tract (AT) locations. To do this, nine market age broilers were euthanized and immediately sampled in ten AT locations: crop, gizzard, proventriculus, duodenum, jejunum, ileum, cecal samples from each pouch, colon, and cloacal swab. DNA was extracted and subjected to 16S rRNA gene amplification and sequencing. Each location within the broiler AT hosts distinct microbial communities. When each sampling location was considered, it was found that sampling after 2.8 birds (range 2-4) resulted in less than 10% new amplicon sequencing variants (ASV) being added while sampling after 7.6 birds (range 6-10) increases new observed ASVs by less than 1%. Additionally, when cecal pairs from the same bird were evaluated, it was found that cecal pair mates are an adequate replication if interested in the total cecal microbiome but may be less useful if a rare lineage is of interest. Furthermore, when compared to other AT locations, the cecal microbiome was enriched in Firmicutes and Bacteroides while several lineages, most notably Lactobacillus, were under-represented. Finally, when cloacal swabs were compared to other AT locations, community similarity exhibited a direct distance relationship, i.e., the more aborad samples were the more similar they were to the swab. These findings indicate that while cloacal swabs can approximate overall changes in microbiome composition, they are not adequate for inferring changes to specific taxa in other parts of the AT tract-even those that are highly abundant within the microbial community. These data provide new insights guiding appropriate sample size selection within flocks and add to the consensus data regarding cecal pair similarity and destructive versus non-destructive sampling methods.
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Affiliation(s)
| | - Brian Oakley
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA, United States
| | - Gustavo A. Ramírez
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA, United States
- Department of Biological Sciences, California State University, Los Angeles, CA, United States
| | - Arquimides Reyes
- Department of Animal and Food Science, University of Wisconsin-River Falls, River Falls, WI, United States
| | - Caitlin E. Harris
- PMSPRU, USNPRC, USDA-ARS, Athens, GA, United States
- Department of Poultry Science, The University of Georgia, Athens, GA, United States
| | - R. Jeff Buhr
- PMSPRU, USNPRC, USDA-ARS, Athens, GA, United States
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232
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Knudsen KS, Lehmann S, Nielsen R, Tangedal S, Paytuvi-Gallart A, Sanseverino W, Martinsen EMH, Hiemstra PS, Eagan TM. The lower airways microbiota and antimicrobial peptides indicate dysbiosis in sarcoidosis. MICROBIOME 2022; 10:175. [PMID: 36258251 PMCID: PMC9580159 DOI: 10.1186/s40168-022-01362-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/30/2022] [Indexed: 05/14/2023]
Abstract
BACKGROUND The role of the pulmonary microbiome in sarcoidosis is unknown. The objectives of this study were the following: (1) examine whether the pulmonary fungal and bacterial microbiota differed in patients with sarcoidosis compared with controls; (2) examine whether there was an association between the microbiota and levels of the antimicrobial peptides (AMPs) in protected bronchoalveolar lavage (PBAL). METHODS Thirty-five sarcoidosis patients and 35 healthy controls underwent bronchoscopy and were sampled with oral wash (OW), protected BAL (PBAL), and left protected sterile brushes (LPSB). The fungal ITS1 region and the V3V4 region of the bacterial 16S rRNA gene were sequenced. Bioinformatic analyses were performed with QIIME 2. The AMPs secretory leucocyte protease inhibitor (SLPI) and human beta defensins 1 and 2 (hBD-1 and hBD-2), were measured in PBAL by enzyme-linked immunosorbent assay (ELISA). RESULTS Aspergillus dominated the PBAL samples in sarcoidosis. Differences in bacterial taxonomy were minor. There was no significant difference in fungal alpha diversity between sarcoidosis and controls, but the bacterial alpha diversity in sarcoidosis was significantly lower in OW (p = 0.047) and PBAL (p = 0.03) compared with controls. The beta diversity for sarcoidosis compared with controls differed for both fungi and bacteria. AMP levels were significantly lower in sarcoidosis compared to controls (SLPI and hBD-1: p < 0.01). No significant correlations were found between alpha diversity and AMPs. CONCLUSIONS The pulmonary fungal and bacterial microbiota in sarcoidosis differed from in controls. Lower antimicrobial peptides levels were seen in sarcoidosis, indicating an interaction between the microbiota and the innate immune system. Whether this dysbiosis represents a pathogenic mechanism in sarcoidosis needs to be confirmed in experimental studies. Video Abstract.
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Affiliation(s)
| | - Sverre Lehmann
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Rune Nielsen
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Solveig Tangedal
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | | | | | | | - Pieter S. Hiemstra
- Department of Pulmonology, Leiden University Medical Center, Leiden, Netherlands
| | - Tomas M. Eagan
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
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233
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Boertien JM, Murtomäki K, Pereira PAB, van der Zee S, Mertsalmi TH, Levo R, Nojonen T, Mäkinen E, Jaakkola E, Laine P, Paulin L, Pekkonen E, Kaasinen V, Auvinen P, Scheperjans F, van Laar T. Fecal microbiome alterations in treatment-naive de novo Parkinson's disease. NPJ Parkinsons Dis 2022; 8:129. [PMID: 36216843 PMCID: PMC9551094 DOI: 10.1038/s41531-022-00395-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 09/14/2022] [Indexed: 11/09/2022] Open
Abstract
Gut microbiota alterations in Parkinson's disease (PD) have been found in several studies and are suggested to contribute to the pathogenesis of PD. However, previous results could not be adequately adjusted for a potential confounding effect of PD medication and disease duration, as almost all PD participants were already using dopaminergic medication and were included several years after diagnosis. Here, the gut microbiome composition of treatment-naive de novo PD subjects was assessed compared to healthy controls (HC) in two large independent case-control cohorts (n = 136 and 56 PD, n = 85 and 87 HC), using 16S-sequencing of fecal samples. Relevant variables such as technical batches, diet and constipation were assessed for their potential effects. Overall gut microbiome composition differed between PD and HC in both cohorts, suggesting gut microbiome alterations are already present in de novo PD subjects at the time of diagnosis, without the possible confounding effect of dopaminergic medication. Although no differentially abundant taxon could be replicated in both cohorts, multiple short chain fatty acids (SCFA) producing taxa were decreased in PD in both cohorts. In particular, several taxa belonging to the family Lachnospiraceae were decreased in abundance. Fewer taxonomic differences were found compared to previous studies, indicating smaller effect sizes in de novo PD.
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Affiliation(s)
- Jeffrey M. Boertien
- grid.4494.d0000 0000 9558 4598Department of Neurology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Kirsi Murtomäki
- grid.7737.40000 0004 0410 2071Department of Neurology, Helsinki University Hospital and Clinicum, University of Helsinki, Helsinki, Finland
| | - Pedro A. B. Pereira
- grid.7737.40000 0004 0410 2071Department of Neurology, Helsinki University Hospital and Clinicum, University of Helsinki, Helsinki, Finland ,grid.7737.40000 0004 0410 2071Institute of Biotechnology, DNA Sequencing and Genomics Laboratory, University of Helsinki, Helsinki, Finland
| | - Sygrid van der Zee
- grid.4494.d0000 0000 9558 4598Department of Neurology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Tuomas H. Mertsalmi
- grid.7737.40000 0004 0410 2071Department of Neurology, Helsinki University Hospital and Clinicum, University of Helsinki, Helsinki, Finland
| | - Reeta Levo
- grid.7737.40000 0004 0410 2071Department of Neurology, Helsinki University Hospital and Clinicum, University of Helsinki, Helsinki, Finland
| | - Tanja Nojonen
- grid.7737.40000 0004 0410 2071Department of Neurology, Helsinki University Hospital and Clinicum, University of Helsinki, Helsinki, Finland
| | - Elina Mäkinen
- grid.7737.40000 0004 0410 2071Department of Neurology, Helsinki University Hospital and Clinicum, University of Helsinki, Helsinki, Finland ,grid.410552.70000 0004 0628 215XClinical Neurosciences, University of Turku and Neurocenter, Turku University Hospital, Turku, Finland
| | - Elina Jaakkola
- grid.410552.70000 0004 0628 215XClinical Neurosciences, University of Turku and Neurocenter, Turku University Hospital, Turku, Finland
| | - Pia Laine
- grid.7737.40000 0004 0410 2071Institute of Biotechnology, DNA Sequencing and Genomics Laboratory, University of Helsinki, Helsinki, Finland
| | - Lars Paulin
- grid.7737.40000 0004 0410 2071Institute of Biotechnology, DNA Sequencing and Genomics Laboratory, University of Helsinki, Helsinki, Finland
| | - Eero Pekkonen
- grid.7737.40000 0004 0410 2071Department of Neurology, Helsinki University Hospital and Clinicum, University of Helsinki, Helsinki, Finland
| | - Valtteri Kaasinen
- grid.410552.70000 0004 0628 215XClinical Neurosciences, University of Turku and Neurocenter, Turku University Hospital, Turku, Finland
| | - Petri Auvinen
- grid.7737.40000 0004 0410 2071Institute of Biotechnology, DNA Sequencing and Genomics Laboratory, University of Helsinki, Helsinki, Finland
| | - Filip Scheperjans
- grid.7737.40000 0004 0410 2071Department of Neurology, Helsinki University Hospital and Clinicum, University of Helsinki, Helsinki, Finland
| | - Teus van Laar
- grid.4494.d0000 0000 9558 4598Department of Neurology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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234
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Shulman RJ, Chichlowski M, Orozco FG, Harris CL, Wampler JL, Bokulich NA, Berseth CL. Infant behavioral state and stool microbiome in infants receiving Lactocaseibacillus rhamnosus GG in formula: randomized controlled trial. BMC Pediatr 2022; 22:580. [PMID: 36207675 PMCID: PMC9541012 DOI: 10.1186/s12887-022-03647-x] [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: 06/21/2022] [Accepted: 09/26/2022] [Indexed: 11/29/2022] Open
Abstract
Background Our aim was to evaluate infant behavioral state, stool microbiome profile and calprotectin in infants with infantile colic receiving a partially hydrolyzed protein formula with or without added Lacticaseibacillus (formerly Lactobacillus) rhamnosus GG (LGG). Methods In this single-center, double-blind, controlled, parallel, prospective study, term infants (14–28 days of age) identified with colic (using modified Wessel’s criteria: cried and/or fussed ≥ 3 h/day for ≥ 3 days/week, in a one-week period) were randomized to receive one of two formulas over a three-week feeding period: marketed partially hydrolyzed cow’s milk-based infant formula (PHF, n = 35) or a similar formula with added LGG (PHF-LGG, n = 36). Parent-reported infant behavior was recorded at three time points (Study Days 2–4, 10–12, and 18–20). Duration (hours/day) of crying/fussing (averaged over each three-day period) was the primary outcome. Stool samples were collected at Baseline and Study End (Days 19–21) to determine stool LGG colonization (by qPCR) and microbial abundance (using 16S rRNA gene sequencing) and calprotectin (μg/g). Results Duration of crying/fussing (mean ± SE) decreased and awake/content behavior increased over time with no significant group differences over the course of the study. There were no group differences in the percentage of infants who experienced colic by study end. Colic decreased by Study End vs Baseline in both groups. Change in fecal calprotectin also was similar between groups. Comparing Study End vs Baseline, LGG abundance was greater in the PHF-LGG group (P < 0.001) whereas alpha diversity was greater in the PHF group (P = 0.022). Beta diversity was significantly different between PHF and PHF-LGG at Study End (P = 0.05). By study end, relative abundance of L. rhamnosus was higher in the PHF-LGG vs PHF group and vs Baseline. Conclusions In this pilot study of infants with colic, both study formulas were well tolerated. Crying/fussing decreased and awake/content behavior increased in both study groups over the course of the study. Study results demonstrate a successful introduction of the probiotic to the microbiome. The partially hydrolyzed protein formula with added LGG was associated with significant changes in the gut microbiome. Trial registration ClinicalTrials.gov, ClinicalTrials.gov Identifier: NCT02340143. Registered 16/01/2015. Supplementary Information The online version contains supplementary material available at 10.1186/s12887-022-03647-x.
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Affiliation(s)
- Robert J Shulman
- Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Center for Pediatric Abdominal Pain Research, Baylor College of Medicine, Houston, TX, 77030, USA. .,Texas Children's Hospital, 6621 Fannin St., Houston, TX, 77030, USA. .,USDA/ARS Children's Nutrition Research Center, 1100 Bates St., Room 8072, Houston, TX, 77030, USA.
| | - Maciej Chichlowski
- Medical and Scientific Affairs, Reckitt
- Mead Johnson Nutrition Institute, Evansville, IN, 47721, USA
| | - Fabiola Gutierrez Orozco
- Medical and Scientific Affairs, Reckitt
- Mead Johnson Nutrition Institute, Evansville, IN, 47721, USA
| | - Cheryl L Harris
- Medical and Scientific Affairs, Reckitt
- Mead Johnson Nutrition Institute, Evansville, IN, 47721, USA
| | - Jennifer L Wampler
- Medical and Scientific Affairs, Reckitt
- Mead Johnson Nutrition Institute, Evansville, IN, 47721, USA
| | - Nicholas A Bokulich
- Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition, and Health, ETH Zurich, Zurich, Switzerland
| | - Carol Lynn Berseth
- Medical and Scientific Affairs, Reckitt
- Mead Johnson Nutrition Institute, Evansville, IN, 47721, USA
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235
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Pin Viso ND, Rizzo PF, Young BJ, Gabioud E, Bres P, Riera NI, Merino L, Farber MD, Crespo DC. The Use of Raw Poultry Waste as Soil Amendment Under Field Conditions Caused a Loss of Bacterial Genetic Diversity Together with an Increment of Eutrophic Risk and Phytotoxic Effects. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02119-0. [PMID: 36197502 DOI: 10.1007/s00248-022-02119-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Poultry waste has been used as fertilizer to avoid soil degradation caused by the long-term application of chemical fertilizer. However, few studies have evaluated field conditions where livestock wastes have been used for extended periods of time. In this study, physicochemical parameters, metabarcoding of the 16S rRNA gene, and ecotoxicity indexes were used for the characterization of chicken manure and poultry litter to examine the effect of their application to agricultural soils for 10 years. Poultry wastes showed high concentrations of nutrients and increased electrical conductivity leading to phytotoxic effects on seeds. The bacterial communities were dominated by typical members of the gastrointestinal tract, noting the presence of pathogenic bacteria. Soils subjected to poultry manure applications showed statistically higher values of total and extractable phosphorous, increasing the risk of eutrophication. Moreover, while the soil bacterial community remained dominated by the ones related to the biogeochemical cycles of nutrients and plant growth promotion, losses of alpha diversity were observed on treated soils. Altogether, our work would contribute to understand the effects of common local agricultural practices and support the adoption of the waste treatment process in compliance with environmental sustainability guidelines.
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Affiliation(s)
- Natalia D Pin Viso
- Instituto de Agrobiotecnología y Biología Molecular, IABiMo, INTA-CONICET, Calle Las Cabañas y Los Reseros s/n, Casilla de Correo 25, 1712, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz 2290, 1425, Ciudad Autónoma de Buenos Aires, Argentina
- Universidad Nacional de Hurlingham, Tte. Origone 151, 1688, Hurlingham, Buenos Aires, Argentina
| | - Pedro F Rizzo
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola (IMyZA), Calle Las Cabañas y Los Reseros S/N, Casilla de Correo 25, 1712, Hurlingham, Buenos Aires, Argentina
| | - Brian J Young
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola (IMyZA), Calle Las Cabañas y Los Reseros S/N, Casilla de Correo 25, 1712, Hurlingham, Buenos Aires, Argentina
| | - Emmanuel Gabioud
- Instituto Nacional de Tecnología Agropecuaria (INTA), Estación Experimental Agropecuaria Paraná, Ruta 11 Km 12.5, 3101, Oro Verde, Entre Ríos, Argentina
| | - Patricia Bres
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola (IMyZA), Calle Las Cabañas y Los Reseros S/N, Casilla de Correo 25, 1712, Hurlingham, Buenos Aires, Argentina
| | - Nicolás I Riera
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola (IMyZA), Calle Las Cabañas y Los Reseros S/N, Casilla de Correo 25, 1712, Hurlingham, Buenos Aires, Argentina
| | - Lina Merino
- Universidad Nacional de Hurlingham, Tte. Origone 151, 1688, Hurlingham, Buenos Aires, Argentina
| | - Marisa D Farber
- Instituto de Agrobiotecnología y Biología Molecular, IABiMo, INTA-CONICET, Calle Las Cabañas y Los Reseros s/n, Casilla de Correo 25, 1712, Hurlingham, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz 2290, 1425, Ciudad Autónoma de Buenos Aires, Argentina.
- Universidad Nacional de Hurlingham, Tte. Origone 151, 1688, Hurlingham, Buenos Aires, Argentina.
| | - Diana C Crespo
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz 2290, 1425, Ciudad Autónoma de Buenos Aires, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola (IMyZA), Calle Las Cabañas y Los Reseros S/N, Casilla de Correo 25, 1712, Hurlingham, Buenos Aires, Argentina
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236
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Yang H, Heirbaut S, Jing X, De Neve N, Vandaele L, Jeyanathan J, Fievez V. Susceptibility of dairy cows to subacute ruminal acidosis is reflected in both prepartum and postpartum bacteria as well as odd- and branched-chain fatty acids in feces. J Anim Sci Biotechnol 2022; 13:87. [PMID: 36195941 PMCID: PMC9533591 DOI: 10.1186/s40104-022-00738-8] [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: 01/09/2022] [Accepted: 06/01/2022] [Indexed: 11/10/2022] Open
Abstract
Background The transition period is a challenging period for high-producing dairy cattle. Cows in early lactation are considered as a group at risk of subacute ruminal acidosis (SARA). Variability in SARA susceptibility in early lactation is hypothesized to be reflected in fecal characteristics such as fecal pH, dry matter content, volatile and odd- and branched-chain fatty acids (VFA and OBCFA, respectively), as well as fecal microbiota. This was investigated with 38 periparturient dairy cows, which were classified into four groups differing in median and mean time of reticular pH below 6 as well as area under the curve of pH below 6. Furthermore, we investigated whether fecal differences were already obvious during a period prior to the SARA risk (prepartum). Results Variation in reticular pH during a 3-week postpartum period was not associated with differences in fecal pH and VFA concentration. In the postpartum period, the copy number of fecal bacteria and methanogens of unsusceptible (UN) cows was higher than moderately susceptible (MS) or susceptible (SU) cows, while the genera Ruminococcus and Prevotellacea_UCG-001 were proportionally less abundant in UN compared with SU cows. Nevertheless, only a minor reduction was observed in iso-BCFA proportions in fecal fatty acids of SU cows, particularly iso-C15:0 and iso-C16:0, compared with UN cows. Consistent with the bacterial changes postpartum, the lower abundance of Ruminococcus was already observed in the prepartum fecal bacterial communities of UN cows, whereas Lachnospiraceae_UCG-001 was increased. Nevertheless, no differences were observed in the prepartum fecal VFA or OBCFA profiles among the groups. Prepartum fecal bacterial communities of cows were clustered into two distinct clusters with 70% of the SU cows belonging to cluster 1, in which they represented 60% of the animals. Conclusions Inter-animal variation in postpartum SARA susceptibility was reflected in post- and prepartum fecal bacterial communities. Differences in prepartum fecal bacterial communities could alert for susceptibility to develop SARA postpartum. Our results generated knowledge on the association between fecal bacteria and SARA development which could be further explored in a prevention strategy. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s40104-022-00738-8.
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Affiliation(s)
- Hong Yang
- Laboratory for Animal Nutrition and Animal Product Quality, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Campus Coupure, building F, 1st floor, Coupure Links 653, 9000, Ghent, Belgium
| | - Stijn Heirbaut
- Laboratory for Animal Nutrition and Animal Product Quality, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Campus Coupure, building F, 1st floor, Coupure Links 653, 9000, Ghent, Belgium
| | - Xiaoping Jing
- Laboratory for Animal Nutrition and Animal Product Quality, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Campus Coupure, building F, 1st floor, Coupure Links 653, 9000, Ghent, Belgium.,State Key Laboratory of Grassland and Agro-Ecosystems, International Centre for Tibetan Plateau Ecosystem Management, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Nympha De Neve
- Laboratory for Animal Nutrition and Animal Product Quality, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Campus Coupure, building F, 1st floor, Coupure Links 653, 9000, Ghent, Belgium
| | - Leen Vandaele
- Animal Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Scheldeweg 68, 9090, Melle, Belgium
| | - Jeyamalar Jeyanathan
- Laboratory for Animal Nutrition and Animal Product Quality, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Campus Coupure, building F, 1st floor, Coupure Links 653, 9000, Ghent, Belgium
| | - Veerle Fievez
- Laboratory for Animal Nutrition and Animal Product Quality, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Campus Coupure, building F, 1st floor, Coupure Links 653, 9000, Ghent, Belgium.
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237
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Radojević D, Bekić M, Gruden-Movsesijan A, Ilić N, Dinić M, Bisenić A, Golić N, Vučević D, Đokić J, Tomić S. Myeloid-derived suppressor cells prevent disruption of the gut barrier, preserve microbiota composition, and potentiate immunoregulatory pathways in a rat model of experimental autoimmune encephalomyelitis. Gut Microbes 2022; 14:2127455. [PMID: 36184742 PMCID: PMC9543149 DOI: 10.1080/19490976.2022.2127455] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Over-activated myeloid cells and disturbance in gut microbiota composition are critical factors contributing to the pathogenesis of Multiple Sclerosis (MS). Myeloid-derived suppressor cells (MDSCs) emerged as promising regulators of chronic inflammatory diseases, including autoimmune diseases. However, it remained unclear whether MDSCs display any therapeutic potential in MS, and how this therapy modulates gut microbiota composition. Here, we assessed the potential of in vitro generated bone marrow-derived MDSCs to ameliorate experimental autoimmune encephalomyelitis (EAE) in Dark Agouti rats and investigated how their application associates with the changes in gut microbiota composition. MDSCs differentiated with prostaglandin (PG)E2 (MDSC-PGE2) and control MDSCs (differentiated without PGE2) displayed strong immunosuppressive properties in vitro, but only MDSC-PGE2 significantly ameliorated EAE symptoms. This effect correlated with a reduced infiltration of Th17 and IFN-γ-producing NK cells, and an increased proportion of regulatory T cells in the CNS and spleen. Importantly, both MDSCs and MDSC-PGE2 prevented EAE-induced reduction of gut microbiota diversity, but only MDSC-PGE2 prevented the extensive alterations in gut microbiota composition following their early migration into Payer's patches and mesenteric lymph nodes. This phenomenon was related to the significant enrichment of gut microbial taxa with potential immunoregulatory properties, as well as higher levels of butyrate, propionate, and putrescine in feces. This study provides new insights into the host-microbiota interactions in EAE, suggesting that activated MDSCs could be potentially used as an efficient therapy for acute phases of MS. Considering a significant association between the efficacy of MDSC-PGE2 and gut microbiota composition, our findings also provide a rationale for further exploring the specific microbial metabolites in MS therapy.
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Affiliation(s)
- Dušan Radojević
- Group for Probiotics and Microbiota-Host Interaction, Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Marina Bekić
- Department for Immunology and Immunoparasitology, Institute for the Application of Nuclear Energy, University of Belgrade, Belgrade, Serbia
| | - Alisa Gruden-Movsesijan
- Department for Immunology and Immunoparasitology, Institute for the Application of Nuclear Energy, University of Belgrade, Belgrade, Serbia
| | - Nataša Ilić
- Department for Immunology and Immunoparasitology, Institute for the Application of Nuclear Energy, University of Belgrade, Belgrade, Serbia
| | - Miroslav Dinić
- Group for Probiotics and Microbiota-Host Interaction, Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Aleksandar Bisenić
- Group for Probiotics and Microbiota-Host Interaction, Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Nataša Golić
- Group for Probiotics and Microbiota-Host Interaction, Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Dragana Vučević
- Medical Faculty of the Military Medical Academy, University of Defense in Belgrade, Belgrade, Serbia
| | - Jelena Đokić
- Group for Probiotics and Microbiota-Host Interaction, Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia,CONTACT Jelena Đokić Group for Probiotics and Microbiota-Host Interaction, Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, 111042 Belgrade, Vojvode Stepe 444a, Belgrade, Serbia
| | - Sergej Tomić
- Department for Immunology and Immunoparasitology, Institute for the Application of Nuclear Energy, University of Belgrade, Belgrade, Serbia,Sergej Tomić Institute for the Application of Nuclear Energy, 11080 Belgrade, Banatska 31b, Belgrade, Serbia
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238
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Valdes J, Gagné-Sansfaçon J, Reyes V, Armas A, Marrero G, Moyo-Muamba M, Ramanathan S, Perreault N, Ilangumaran S, Rivard N, Fortier LC, Menendez A. Defects in the expression of colonic host defense factors associate with barrier dysfunction induced by a high-fat/high-cholesterol diet. Anat Rec (Hoboken) 2022; 306:1165-1183. [PMID: 36196983 DOI: 10.1002/ar.25083] [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: 04/07/2022] [Revised: 08/25/2022] [Accepted: 09/11/2022] [Indexed: 11/07/2022]
Abstract
The effect of Western diets in the gastrointestinal system is largely mediated by their ability to promote alterations in the immunity and physiology of the intestinal epithelium, and to affect the composition of the commensal microbiota. To investigate the response of the colonic epithelium to high-fat/high-cholesterol diets (HFHCDs), we evaluated the synthesis of host defense factors involved in the maintenance of the colonic homeostasis. C57BL/6 mice were fed an HFHCD for 3 weeks and their colons were evaluated for histopathology, gene expression, and microbiota composition. In addition, intestinal permeability and susceptibility to Citrobacter rodentium were also studied. HFHCD caused colonic hyperplasia, loss of goblet cells, thinning of the mucus layer, moderate changes in the composition of the intestinal microbiota, and an increase in intestinal permeability. Gene expression analyses revealed significant drops in the transcript levels of Muc1, Muc2, Agr2, Atoh1, Spdef, Ang4, Camp, Tff3, Dmbt1, Fcgbp, Saa3, and Retnlb. The goblet cell granules of HFHCD-fed mice were devoid of Relmβ and Tff3, indicating defective production of those two factors critical for intestinal epithelial defense and homeostasis. In correspondence with these defects, colonic bacteria were in close contact with, and invading the epithelium. Fecal shedding of C. rodentium showed an increased bacterial burden in HFHCD-fed animals accompanied by increased epithelial damage. Collectively, our results show that HFHCD perturbs the synthesis of colonic host defense factors, which associate with alterations in the commensal microbiota, the integrity of the intestinal barrier, and the host's susceptibility to enteric infections.
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Affiliation(s)
- Jennifer Valdes
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Jessica Gagné-Sansfaçon
- Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Vilcy Reyes
- Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Anny Armas
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Gisela Marrero
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Mitterrand Moyo-Muamba
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Sheela Ramanathan
- Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Nathalie Perreault
- Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Subburaj Ilangumaran
- Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Nathalie Rivard
- Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Louis-Charles Fortier
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Alfredo Menendez
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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239
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Testerman T, Beka L, Reichley SR, King S, Welch TJ, Wiens GD, Graf J. A large-scale, multi-year microbial community survey of a freshwater trout aquaculture facility. FEMS Microbiol Ecol 2022; 98:6680245. [PMID: 36047934 DOI: 10.1093/femsec/fiac101] [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: 05/10/2022] [Revised: 07/15/2022] [Accepted: 08/30/2022] [Indexed: 12/14/2022] Open
Abstract
Aquaculture is an important tool for solving the growing worldwide food demand, but infectious diseases of farmed animals represent a serious roadblock to continued industry growth. Therefore, it is essential to understand the microbial communities that reside within the built environments of aquaculture facilities to identify reservoirs of bacterial pathogens and potential correlations between commensal species and specific disease agents. Here, we present the results from 3 years of sampling a commercial rainbow trout aquaculture facility. We observed that the microbial communities residing on the abiotic surfaces within the hatchery were distinct from those residing on the surfaces at the facility's water source as well as the production raceways, despite similar communities in the water column at each location. Also, a subset of the water community seeds the biofilm communities. Lastly, we detected a common fish pathogen, Flavobacterium columnare, within the hatchery, including at the source water inlet. Importantly, the relative abundance of this pathogen was correlated with clinical disease. Our results characterized the microbial communities in an aquaculture facility, established that the hatchery environment contains a unique community composition and demonstrated that a specific fish pathogen resides within abiotic surface biofilms and is seeded from the natural water source.
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Affiliation(s)
- Todd Testerman
- University of Connecticut, Department of Molecular and Cell Biology, Storrs, CT, 06269, USA
| | - Lidia Beka
- University of Connecticut, Department of Molecular and Cell Biology, Storrs, CT, 06269, USA
| | | | - Stacy King
- Riverence Provisions LLC, Buhl, ID 83316, USA
| | - Timothy J Welch
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service/U.S. Department of Agriculture, Kearneysville, WV, 25430, USA
| | - Gregory D Wiens
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service/U.S. Department of Agriculture, Kearneysville, WV, 25430, USA
| | - Joerg Graf
- University of Connecticut, Department of Molecular and Cell Biology, Storrs, CT, 06269, USA
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240
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Cárdenas A, Raina JB, Pogoreutz C, Rädecker N, Bougoure J, Guagliardo P, Pernice M, Voolstra CR. Greater functional diversity and redundancy of coral endolithic microbiomes align with lower coral bleaching susceptibility. THE ISME JOURNAL 2022; 16:2406-2420. [PMID: 35840731 PMCID: PMC9478130 DOI: 10.1038/s41396-022-01283-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/14/2022] [Accepted: 06/28/2022] [Indexed: 04/14/2023]
Abstract
The skeleton of reef-building coral harbors diverse microbial communities that could compensate for metabolic deficiencies caused by the loss of algal endosymbionts, i.e., coral bleaching. However, it is unknown to what extent endolith taxonomic diversity and functional potential might contribute to thermal resilience. Here we exposed Goniastrea edwardsi and Porites lutea, two common reef-building corals from the central Red Sea to a 17-day long heat stress. Using hyperspectral imaging, marker gene/metagenomic sequencing, and NanoSIMS, we characterized their endolithic microbiomes together with 15N and 13C assimilation of two skeletal compartments: the endolithic band directly below the coral tissue and the deep skeleton. The bleaching-resistant G. edwardsi was associated with endolithic microbiomes of greater functional diversity and redundancy that exhibited lower N and C assimilation than endoliths in the bleaching-sensitive P. lutea. We propose that the lower endolithic primary productivity in G. edwardsi can be attributed to the dominance of chemolithotrophs. Lower primary production within the skeleton may prevent unbalanced nutrient fluxes to coral tissues under heat stress, thereby preserving nutrient-limiting conditions characteristic of a stable coral-algal symbiosis. Our findings link coral endolithic microbiome structure and function to bleaching susceptibility, providing new avenues for understanding and eventually mitigating reef loss.
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Affiliation(s)
- Anny Cárdenas
- Department of Biology, University of Konstanz, Konstanz, 78457, Germany.
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
| | - Claudia Pogoreutz
- Department of Biology, University of Konstanz, Konstanz, 78457, Germany
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland
| | - Nils Rädecker
- Department of Biology, University of Konstanz, Konstanz, 78457, Germany
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland
| | - Jeremy Bougoure
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, WA, 6009, Australia
| | - Paul Guagliardo
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, WA, 6009, Australia
| | - Mathieu Pernice
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Christian R Voolstra
- Department of Biology, University of Konstanz, Konstanz, 78457, Germany.
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.
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241
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Jackson AC, Jorna J, Chaston JM, Adams BJ. Glacial Legacies: Microbial Communities of Antarctic Refugia. BIOLOGY 2022; 11:biology11101440. [PMID: 36290344 PMCID: PMC9598129 DOI: 10.3390/biology11101440] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/26/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022]
Abstract
In the cold deserts of the McMurdo Dry Valleys (MDV) the suitability of soil for microbial life is determined by both contemporary processes and legacy effects. Climatic changes and accompanying glacial activity have caused local extinctions and lasting geochemical changes to parts of these soil ecosystems over several million years, while areas of refugia may have escaped these disturbances and existed under relatively stable conditions. This study describes the impact of historical glacial and lacustrine disturbance events on microbial communities across the MDV to investigate how this divergent disturbance history influenced the structuring of microbial communities across this otherwise very stable ecosystem. Soil bacterial communities from 17 sites representing either putative refugia or sites disturbed during the Last Glacial Maximum (LGM) (22-17 kya) were characterized using 16 S metabarcoding. Regardless of geographic distance, several putative refugia sites at elevations above 600 m displayed highly similar microbial communities. At a regional scale, community composition was found to be influenced by elevation and geographic proximity more so than soil geochemical properties. These results suggest that despite the extreme conditions, diverse microbial communities exist in these putative refugia that have presumably remained undisturbed at least through the LGM. We suggest that similarities in microbial communities can be interpreted as evidence for historical climate legacies on an ecosystem-wide scale.
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Affiliation(s)
- Abigail C. Jackson
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
- Correspondence: (A.C.J.); (J.J.)
| | - Jesse Jorna
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
- Correspondence: (A.C.J.); (J.J.)
| | - John M. Chaston
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA
| | - Byron J. Adams
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
- Monte L. Bean Museum, Brigham Young University, Provo, UT 84602, USA
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242
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Fuerniss LK, Kreikemeier KK, Reed LD, Cravey MD, Johnson BJ. Cecal microbiota of feedlot cattle fed a four-species Bacillus supplement. J Anim Sci 2022; 100:skac258. [PMID: 35953238 PMCID: PMC9576023 DOI: 10.1093/jas/skac258] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/09/2022] [Indexed: 11/14/2022] Open
Abstract
As commercial fed cattle consume large amounts of concentrate feedstuffs, hindgut health can be challenged. The objective of this study was to evaluate the effects of a commercially available Bacillus feed additive on cattle health outcomes and cecal microbiota of fed cattle at the time of harvest. Commercial cattle from a single feedlot were identified for characterization of cecal microbial communities using 16S ribosomal ribonucleic acid gene sequencing. All cattle were fed a common corn-based finishing diet. Control cattle (CON) were administered no treatment while treated cattle (TRT) were supplemented daily with 0.050 g of MicroSaf 4C 40 (2 billion colony forming units of Bacillus spp.; Phileo by Lesaffre, Milwaukee, WI). Immediately after harvest and evisceration, the cecal contents of cattle were sampled. After DNA extraction, amplification, and sequencing, reads from CON samples (N = 12) and TRT samples (N = 12) were assigned taxonomy using the SILVA 138 database. Total morbidity, first treatment of atypical interstitial pneumonia, and early shipments for harvest were decreased among TRT cattle compared to CON cattle (P ≤ 0.021). On average, cecal microbiota from TRT cattle had greater alpha diversity than microbiota from CON cattle as measured by Shannon diversity, Pielou's evenness, and feature richness (P < 0.010). Additionally, TRT microbial communities were different (P = 0.001) and less variable (P < 0.001) than CON microbial communities when evaluated by unweighted UniFrac distances. By relative abundance across all samples, the most prevalent phyla were Firmicutes (55.40%, SD = 15.97) and Bacteroidetes (28.17%, SD = 17.74) followed by Proteobacteria (6.75%, SD = 10.98), Spirochaetes (4.54%, SD = 4.85), and Euryarchaeota (1.77%, SD = 3.00). Spirochaetes relative abundance in TRT communities was greater than that in CON communities and was differentially abundant between treatments by ANCOM testing (W = 11); Monoglobaceae was the only family-level taxon identified as differentially abundant (W = 59; greater mean relative abundance in TRT group by 2.12 percentage points). Half (N = 6) of the CON samples clustered away from all other samples based on principal coordinates and represented cecal dysbiosis among CON cattle. The results of this study indicated that administering a four-species blend of Bacillus positively supported the cecal microbial communities of finishing cattle. Further research is needed to explore potential mechanisms of action of Bacillus DFM products in feedlot cattle.
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Affiliation(s)
- Luke K Fuerniss
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | | | - Lynn D Reed
- Phileo by Lesaffre, Milwaukee, WI 52404, USA
| | | | - Bradley J Johnson
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, TX 79409, USA
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243
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Hernandez AR, Watson C, Federico QP, Fletcher R, Brotgandel A, Buford TW, Carter CS, Burke SN. Twelve Months of Time-Restricted Feeding Improves Cognition and Alters Microbiome Composition Independent of Macronutrient Composition. Nutrients 2022; 14:3977. [PMID: 36235630 PMCID: PMC9572159 DOI: 10.3390/nu14193977] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/12/2022] [Accepted: 09/22/2022] [Indexed: 02/01/2023] Open
Abstract
Declining health, gut dysbiosis, and cognitive impairments are hallmarks of advanced age. While caloric restriction is known to robustly extend the healthspan and alter gut microbiome composition, it is difficult maintain. Time-restricted feeding or changes in dietary macronutrient composition could be feasible alternatives for enhancing late life cognitive and physical health that are easier to comply with for extended periods of time. To investigate this possibility, 8-month-old rats were placed on time-restricted feeding with a ketogenic or micronutrient- and calorically matched control diet for 13 months. A third group of rats was permitted to eat standard chow ad libitum during this time. At 22 months, all rats were tested on a biconditional association task and fecal samples were collected for microbiome composition analysis. Regardless of dietary composition, time-restricted-fed rats had better cognitive performance than ad libitum-fed rats. This observation could not be accounted for by differences in motivation, procedural or sensorimotor impairments. Additionally, there were significant differences in gut microbiome diversity and composition between all diet conditions. Allobaculum abundance was associated with cognitive task performance, indicating a link between gut health and cognitive outcomes in aged subjects. Overall, time restricted feeding had the largest influence on cognitive performance in aged rats.
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Affiliation(s)
- Abbi R. Hernandez
- Department of Medicine, Division of Gerontology, Geriatrics, and Palliative Care, University of Alabama at Birmingham, Birmingham, AL 35205, USA
| | - Cory Watson
- Department of Neuroscience and McKnight, Brain Institute College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Quinten P. Federico
- Department of Neuroscience and McKnight, Brain Institute College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Rachel Fletcher
- Department of Neuroscience and McKnight, Brain Institute College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Armen Brotgandel
- Department of Neuroscience and McKnight, Brain Institute College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Thomas W. Buford
- Department of Medicine, Division of Gerontology, Geriatrics, and Palliative Care, University of Alabama at Birmingham, Birmingham, AL 35205, USA
- Birmingham/Atlanta Geriatric Research, Education, and Clinical Center, Birmingham VA Medical Center, Birmingham, AL 35205, USA
| | - Christy S. Carter
- Department of Medicine, Division of Gerontology, Geriatrics, and Palliative Care, University of Alabama at Birmingham, Birmingham, AL 35205, USA
| | - Sara N. Burke
- Department of Neuroscience and McKnight, Brain Institute College of Medicine, University of Florida, Gainesville, FL 32610, USA
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244
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Two modes of evolution shape bacterial strain diversity in the mammalian gut for thousands of generations. Nat Commun 2022; 13:5604. [PMID: 36153389 PMCID: PMC9509342 DOI: 10.1038/s41467-022-33412-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
How and at what pace bacteria evolve when colonizing healthy hosts remains unclear. Here, by monitoring evolution for more than six thousand generations in the mouse gut, we show that the successful colonization of an invader Escherichia coli depends on the diversity of the existing microbiota and the presence of a closely related strain. Following colonization, two modes of evolution were observed: one in which diversifying selection leads to long-term coexistence of ecotypes and a second in which directional selection propels selective sweeps. These modes can be quantitatively distinguished by the statistics of mutation trajectories. In our experiments, diversifying selection was marked by the emergence of metabolic mutations, and directional selection by acquisition of prophages, which bring their own benefits and costs. In both modes, we observed parallel evolution, with mutation accumulation rates comparable to those typically observed in vitro on similar time scales. Our results show how rapid ecotype formation and phage domestication can be in the mammalian gut. Here, the authors show that a colonizing bacterial strain evolves in the gut by either generating ecotypes or continuously fixing beneficial mutations. They associate the first mode to metabolic mutations and the second to domestication of bacteriophages that are incorporated into the bacterial genome.
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Liu Y, Zeng Y, Liu Y, Wang X, Chen Y, Lepp D, Tsao R, Sadakiyo T, Zhang H, Mine Y. Regulatory Effect of Isomaltodextrin on a High-Fat Diet Mouse Model with LPS-Induced Low-Grade Chronic Inflammation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:11258-11273. [PMID: 36041062 DOI: 10.1021/acs.jafc.2c03391] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This study aimed to identify the effects of isomaltodextrin (IMD) on sustaining the gut integrity and microbiota composition in a high-fat diet (HFD) with a lipopolysaccharide (LPS)-induced low-grade inflammation mouse model. The homeostasis of the immune response is important to reduce the risk of developing metabolic syndromes. The results of this study showed that pre-treatment of IMD at 5% (w/v) suppressed the concentration of endotoxin and pro-inflammatory mediators TNF-α, MCP-1, and IL-6 while increasing the adiponectin level in the plasma. Subsequently, IMD supplementation maintained the structural integrity and intestinal permeability by upregulating the tight junction protein expressions, leading to reducing D-mannitol concentration in the blood. In addition, dysbiosis was observed in mice induced by HFD plus LPS, suggesting that unhealthy dietary factors elicit metabolic endotoxemia and associated dysbiosis to impair the barrier function. However, IMD supplementation was shown to restore the microbial diversity, promote the growth of Bacteroides-Prevotella, and upregulate the related d-glucarate and d-galactarate degradation pathways, together demonstrating the benefits of IMD as a prebiotic able to promote energy homeostasis. Our results also showed that the blood lipid profile and glucose level in the low-grade inflammation mouse model were modulated by IMD. Moreover, IMD supplementation effectively prevented the metabolic disorder and modulated immune responses in inflamed white adipose tissues by inhibiting the macrophage infiltration and restoring the adiponectin, PPAR-γ, and IRS-1 expression. These findings provide strong evidence for IMD to be a potential prebiotic that acts to sustain a healthy gut microbiota composition and barrier function. By protecting against an unhealthy diet-impaired metabolic balance and maintaining immune homeostasis, IMD may affect the development of metabolic disorders.
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Affiliation(s)
- Yijun Liu
- Department of Food Nutrition and Safety, College of Pharmacy, Jiangxi University of Traditional Chinese Medicine, Nanchang 330004, China
| | - Yuhan Zeng
- Department of Food Science, University of Guelph, Guelph Ontario N1G2W1, Canada
| | - Yixin Liu
- Department of Food Nutrition and Safety, College of Pharmacy, Jiangxi University of Traditional Chinese Medicine, Nanchang 330004, China
| | - Xiaoya Wang
- Department of Food Nutrition and Safety, College of Pharmacy, Jiangxi University of Traditional Chinese Medicine, Nanchang 330004, China
| | - Yuhuan Chen
- Department of Food Nutrition and Safety, College of Pharmacy, Jiangxi University of Traditional Chinese Medicine, Nanchang 330004, China
| | - Dion Lepp
- Guelph Food Research and Development Centre, Agriculture and Agri-Food Canada, 93 Stone Road West, Guelph Ontario N1G 5C9, Canada
| | - Rong Tsao
- Guelph Food Research and Development Centre, Agriculture and Agri-Food Canada, 93 Stone Road West, Guelph Ontario N1G 5C9, Canada
| | - Tsuyoshi Sadakiyo
- Food System Solutions Division, Hayashibara CO., LTD., 525-3 Kuwano, Naka-ku, Okayama 702-8002, Japan
| | - Hua Zhang
- Department of Food Nutrition and Safety, College of Pharmacy, Jiangxi University of Traditional Chinese Medicine, Nanchang 330004, China
| | - Yoshinori Mine
- Department of Food Science, University of Guelph, Guelph Ontario N1G2W1, Canada
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Wang H, Dong P, Liu X, Zhang Z, Li H, Li Y, Zhang J, Dai L, Wang S. Active Peptide AR-9 From Eupolyphaga sinensis Reduces Blood Lipid and Hepatic Lipid Accumulation by Restoring Gut Flora and Its Metabolites in a High Fat Diet–Induced Hyperlipidemia Rat. Front Pharmacol 2022; 13:918505. [PMID: 36176455 PMCID: PMC9514323 DOI: 10.3389/fphar.2022.918505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/04/2022] [Indexed: 11/13/2022] Open
Abstract
The dysbiosis of gut flora and its metabolites plays important roles in the progression of hyperlipidemia (HL), and some bioactive peptides are available for HL treatment. In this study, we aimed to isolate an active peptide (AR-9) from active peptides of E. sinensis (APE) and determine whether AR-9 could improve many symptoms of a HL rat induced by a high-fat diet (HFD) by modulating gut flora and its metabolites. Above all, AR-9 was derived from APE using ion-exchange chromatography, and its structure was deconstructed by Fourier transform infrared spectrometer (FT-IR), circular dichroism (CD) spectroscopy, and UHPLC-Q-Exactive-Orbitrap MS. Then, an HFD-induced HL model in SD rats was established and used to clarify the regulatory effects of AR-9 (dose of 3 mg/kg) on HL. Normal diet–fed rats were taken as the control. The plasma samples and liver were harvested for biochemical and histopathological examinations. 16S rRNA gene sequencing and untargeted metabolomics were sequenced to assess changes in gut flora and its metabolites from rat fecal samples. Finally, Spearman’s correlation analysis was used to assess the relationship between lipid-related factors, gut flora, and its metabolites so as to evaluate the mechanism of AR-9 against HL. The results of the separation experiments showed that the amino acid sequence of AR-9 was AVFPSIVGR, which was a fragment of the actin protein from Blattaria insects. Moreover, HFD rats developed exaltation of index factors, liver lipid accumulation, and simple fibrosis for 8 weeks, and the profiles of gut flora and its metabolites were significantly altered. After treatment, AR-9 decreased the levels of lipid factors in plasma and the extent of liver damage. 16S rRNA gene sequencing results indicated that AR-9 significantly increased the relative abundance of beneficial bacteria Bacteroidetes and reduced the relative abundance of the obesity-associated bacteria Firmicutes. Furthermore, AR-9 changed gut microbiota composition and increased the relative abundance of beneficial bacteria: Lactobacillus, Clostridium, Dehalobacterium, and Candidatus arthromitus. Fecal metabolomics showed that the pathway regulated by AR-9 was “arginine biosynthesis”, in which the contents were citrulline and ornithine. Spearman’s correlation analysis revealed that two metabolites (ornithine and citrulline) showed significantly negative correlations with obesity-related parameters and positive correlations with the gut genera (Clostridium) enriched by AR-9. Overall, our results suggested interactions between gut microbial shifts and fecal amino acid/lipid metabolism and revealed the mechanisms underlying the anti-HL effect of AR-9. The abovementioned results not only reveal the initial anti-HL mechanism of AR-9 but also provide a theoretical basis for the continued development of AR-9.
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Affiliation(s)
- Hong Wang
- School of Pharmacy, Binzhou Medical University, Yantai, China
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Pingping Dong
- School of Pharmacy, Binzhou Medical University, Yantai, China
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
- State Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Avenida Wai Long, Macao SAR, China
| | - Xin Liu
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Zhen Zhang
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Huajian Li
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yanan Li
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jiayu Zhang
- School of Pharmacy, Binzhou Medical University, Yantai, China
- *Correspondence: Jiayu Zhang, ; Long Dai, ; Shaoping Wang,
| | - Long Dai
- School of Pharmacy, Binzhou Medical University, Yantai, China
- *Correspondence: Jiayu Zhang, ; Long Dai, ; Shaoping Wang,
| | - Shaoping Wang
- School of Pharmacy, Binzhou Medical University, Yantai, China
- *Correspondence: Jiayu Zhang, ; Long Dai, ; Shaoping Wang,
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Longitudinal Changes in Campylobacter and the Litter Microbiome throughout the Broiler Production Cycle. Appl Environ Microbiol 2022; 88:e0066722. [PMID: 35943254 PMCID: PMC9469715 DOI: 10.1128/aem.00667-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Broiler chickens are an important source of Campylobacter to humans and become colonized on the farm, but the role of the litter in the ecology of Campylobacter is still not clear. The aim of this study was to examine the relationship between Campylobacter and the changes in the litter microbiome throughout the broiler production cycle. Twenty-six commercial broiler flocks representing two production types (small and big broilers) were followed from 1 to 2 weeks after placement to the end of the production cycle. Composite litter samples from the broiler chicken house were collected weekly. Litter DNA was extracted and used for Campylobacter jejuni and Campylobacter coli qPCR as well as for 16S rRNA gene V4 region sequencing. Campylobacter jejuni concentration in litter significantly differed by production type and flock age. Campylobacter jejuni concentration in litter from big broilers was 2.4 log10 units higher, on average, than that of small broilers at 3 weeks of age. Sixteen amplicon sequence variants (ASVs) differentially abundant over time were detected in both production types. A negative correlation of Campylobacter with Bogoriella and Pseudogracilibacillus was observed in the litter microbiome network at 6 weeks of flock age. Dynamic Bayesian networks provided evidence of negative associations between Campylobacter and two bacterial genera, Ornithinibacillus and Oceanobacillus, at 2 and 4 weeks of flock age, respectively. In conclusion, dynamic associations between Campylobacter and the litter microbiome were observed during grow-out, suggesting a potential role of the litter microbiome in the ecology of Campylobacter colonization and persistence on farm. IMPORTANCE This study interrogated the longitudinal association between Campylobacter and broiler litter microbiome in commercial broiler flocks. The results of this investigation highlighted differences in Campylobacter dynamics in the litter throughout the broiler production cycle and between small and big broilers. Besides documenting the changing nature of the microbial networks in broiler litter during grow-out, we detected bacterial genera (Oceanobacillus and Ornithinibacillus) negatively associated with Campylobacter abundance and concentration in litter via the Bayesian network framework. These bacteria should be investigated as possible antagonists to Campylobacter colonization of the broiler environment.
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Prat M, Guenezan J, Drugeon B, Burucoa C, Mimoz O, Pichon M. Impact of Skin Disinfection on Cutaneous Microbiota, before and after Peripheral Venous Catheter Insertion. Antibiotics (Basel) 2022; 11:antibiotics11091209. [PMID: 36139988 PMCID: PMC9495181 DOI: 10.3390/antibiotics11091209] [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: 07/20/2022] [Revised: 08/25/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
Introduction. Patients with invasive medical devices are at high risk for infection. Skin colonization is the initial stage of these infections, leading to the recommendation of practices requiring disinfection using antiseptics. Microbial communities playing a major role in skin health could be impacted by antiseptic procedures. Aim. To characterize and compare the bacterial communities of skin samples from patients before an antisepsis procedure, and after removal of the medical device itself, according to the nature of the antiseptic molecule (povidone iodine or chlorhexidine). Methods. The study focused on alterations in bacterial communities depending on the nature of the antiseptic procedure and type of intravascular device. After amplification of 16S rDNA, libraries (n = 498 samples) were sequenced using MiSeq platform. Results. Using an in-house pipeline (QIIME2 modules), while no alteration in skin microbiota diversity was associated with antiseptic procedure or PVC type, according to culture results (p < 0.05), alterations were at times associated with restricted diversity and higher dissimilarity (p < 0.05). Antiseptic procedures and PVC types were associated with the modification of specific bacterial representations with modulation of the Bacillota/Bacteroidota (Firmicutes/Bacteroidetes) ratio (modulation of C. acnes, Prevotella, Lagierella, and Actinomyces spp.) (p < 0.05). At baseline, the microbiota shows certain bacteria that are significantly associated with future PVC colonization and/or bacteremia (p < 0.05). All of these modulations were associated with altered expression of metabolic pathways (p < 0.05). Discussion. Finally, this work highlights the need to optimize the management of patients requiring intravascular devices, possibly by modulating the skin microbiota.
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Affiliation(s)
- Manon Prat
- CHU Poitiers, Bacteriology Laboratory, Infectious Agents Department, 86021 Poitiers, France
- INSERM U1070, Pharmacology of Antimicrobial Agents and Antibiotic Resistance, University of Poitiers, 86073 Poitiers, France
| | - Jeremy Guenezan
- INSERM U1070, Pharmacology of Antimicrobial Agents and Antibiotic Resistance, University of Poitiers, 86073 Poitiers, France
- CHU Poitiers, Emergency Room Department, 86021 Poitiers, France
| | - Bertrand Drugeon
- INSERM U1070, Pharmacology of Antimicrobial Agents and Antibiotic Resistance, University of Poitiers, 86073 Poitiers, France
| | - Christophe Burucoa
- CHU Poitiers, Bacteriology Laboratory, Infectious Agents Department, 86021 Poitiers, France
- INSERM U1070, Pharmacology of Antimicrobial Agents and Antibiotic Resistance, University of Poitiers, 86073 Poitiers, France
| | - Olivier Mimoz
- INSERM U1070, Pharmacology of Antimicrobial Agents and Antibiotic Resistance, University of Poitiers, 86073 Poitiers, France
- CHU Poitiers, Emergency Room Department, 86021 Poitiers, France
| | - Maxime Pichon
- INSERM U1070, Pharmacology of Antimicrobial Agents and Antibiotic Resistance, University of Poitiers, 86073 Poitiers, France
- CHU Poitiers, Emergency Room Department, 86021 Poitiers, France
- Correspondence: ; Tel.: +33-(0)5-4944-4143
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Ke S, Weiss ST, Liu YY. Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes. Nat Commun 2022; 13:5235. [PMID: 36068270 PMCID: PMC9446638 DOI: 10.1038/s41467-022-32991-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/24/2022] [Indexed: 11/14/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), primarily a respiratory disease caused by infection with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is often accompanied by gastrointestinal symptoms. However, little is known about the relation between the human microbiome and COVID-19, largely due to the fact that most previous studies fail to provide high taxonomic resolution to identify microbes that likely interact with SARS-CoV-2 infection. Here we used whole-metagenome shotgun sequencing data together with assembly and binning strategies to reconstruct metagenome-assembled genomes (MAGs) from 514 COVID-19 related nasopharyngeal and fecal samples in six independent cohorts. We reconstructed a total of 11,584 medium-and high-quality microbial MAGs and obtained 5403 non-redundant MAGs (nrMAGs) with strain-level resolution. We found that there is a significant reduction of strain richness for many species in the gut microbiome of COVID-19 patients. The gut microbiome signatures can accurately distinguish COVID-19 cases from healthy controls and predict the progression of COVID-19. Moreover, we identified a set of nrMAGs with a putative causal role in the clinical manifestations of COVID-19 and revealed their functional pathways that potentially interact with SARS-CoV-2 infection. Finally, we demonstrated that the main findings of our study can be largely validated in three independent cohorts. The presented results highlight the importance of incorporating the human gut microbiome in our understanding of SARS-CoV-2 infection and disease progression.
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Affiliation(s)
- Shanlin Ke
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
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Sandeu MM, Maffo CGT, Dada N, Njiokou F, Hughes GL, Wondji CS. Seasonal variation of microbiota composition in Anopheles gambiae and Anopheles coluzzii in two different eco-geographical localities in Cameroon. MEDICAL AND VETERINARY ENTOMOLOGY 2022; 36:269-282. [PMID: 35579271 DOI: 10.1111/mve.12583] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 05/03/2022] [Indexed: 06/15/2023]
Abstract
Understanding the environmental factors affecting the microbiota in malaria vectors may help in the development of novel vector control interventions, similar to paratransgenesis. This study evaluated seasonal and geographical variations in the microbial community of the two major malaria vectors. Adult Anopheles mosquitoes were collected across two different eco-geographical settings in Cameroon, during the dry and wet seasons. DNA was extracted from the whole individual mosquitoes from each group and processed for microbial analysis using Illumina Miseq sequencing of the V3-V4 region of the 16S rRNA gene. Data analysis was performed using QIIME2 and R software programs. A total of 1985 mosquitoes were collected and among them, 120 were selected randomly corresponding to 30 mosquitoes per season and locality. Overall, 97 bacterial taxa were detected across all mosquito samples, with 86 of these shared between dry and wet seasons in both localities and species. There were significant differences in bacterial composition between both seasons, with a clear separation observed between the dry and wet seasons (PERMANOVA comparisons of beta diversity, Pseudo-F = 10.45; q-value = 0.01). This study highlights the influence of seasonal variation on microbial communities and this variation's impact on mosquito biology and vectorial capacity should be further investigated.
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Affiliation(s)
- Maurice Marcel Sandeu
- Department of Medical Entomology, Centre for Research in Infectious Diseases (CRID), LSTM Research Unit, Yaoundé, Cameroon
- Department of Microbiology and Infectious Diseases, School of Veterinary Medicine and Sciences, University of Ngaoundéré, Ngaoundéré, Cameroon
| | - Claudine Grâce Tatsinkou Maffo
- Department of Medical Entomology, Centre for Research in Infectious Diseases (CRID), LSTM Research Unit, Yaoundé, Cameroon
- Department of Animal Biology and Physiology, Faculty of Science, University of Yaoundé 1, Yaoundé, Cameroon
| | - Nsa Dada
- Faculty of Science and Technology, Norwegian University of Life Science, Aas, Norway
- Tropical Infectious Disease Research Center, University of Abomey-Calavi, Cotonou, Benin
| | - Flobert Njiokou
- Department of Medical Entomology, Centre for Research in Infectious Diseases (CRID), LSTM Research Unit, Yaoundé, Cameroon
- Department of Animal Biology and Physiology, Faculty of Science, University of Yaoundé 1, Yaoundé, Cameroon
| | - Grant L Hughes
- Departments of Vector Biology and Tropical Disease Biology, Centre for Neglected Tropical Diseases, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Charles S Wondji
- Department of Medical Entomology, Centre for Research in Infectious Diseases (CRID), LSTM Research Unit, Yaoundé, Cameroon
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
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