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Huang J, Lin Y, Ding X, Lin S, Li X, Yan W, Chen M. Alteration of the gut microbiome in patients with heart failure: A systematic review and meta-analysis. Microb Pathog 2024; 192:106647. [PMID: 38788811 DOI: 10.1016/j.micpath.2024.106647] [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: 12/18/2023] [Revised: 04/02/2024] [Accepted: 04/13/2024] [Indexed: 05/26/2024]
Abstract
Recent research has revealed that alterations of the gut microbiome (GM) play a comprehensive role in the pathophysiology of HF. However, findings in this field remain controversial. In this study, we focus on differences in GM diversity and abundance between HF patients and non-HF people, based on previous 16 S ribosomal RNA (16rRNA) gene sequencing. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we conducted a comprehensive search of PubMed, Web of Science, Embase, Cochrane Library, and Ovid databases using the keyword "Heart failure" and "Gastrointestinal Microbiome". A significant decrease in alpha diversity was observed in the HF patients (Chao1, I2 = 87.5 %, p < 0.001; Shannon index, I2 = 62.8 %, p = 0.021). At the phylum level, the HF group exhibited higher abundances of Proteobacteria (I2 = 92.0 %, p = 0.004) and Actinobacteria (I2 = 82.5 %, p = 0.010), while Bacteroidetes (I2 = 45.1 %, p = 0.017) and F/B ratio (I2 = 0.0 %, p<0.001) were lower. The Firmicutes showed a decreasing trend but did not reach statistical significance (I2 = 82.3 %, p = 0.127). At the genus level, the relative abundances of Streptococcus, Bacteroides, Alistipes, Bifidobacterium, Escherichia-Shigella, Enterococcus and Klebsiella were increased in the HF group, whereas Ruminococcus, Faecalibacterium, Dorea and Megamona exhibited decreased relative abundances. Dialister, Blautia and Prevotella showed decreasing trends but without statistical significance. This observational meta-analysis suggests that GM changes are associated with HF, manifesting as alterations in GM abundance, disruptions in the production of short-chain fatty acids (SCFAs) bacteria, and an increase in trimethylamine N-oxide (TMAO) producing bacteria.
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Affiliation(s)
- Jiayi Huang
- Department of Cardiology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, China
| | - Yongping Lin
- Department of Cardiology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, China
| | - Xiangwei Ding
- Department of Cardiology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, China
| | - Song Lin
- Department of Cardiology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, China
| | - Xin Li
- Department of Cardiology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, China
| | - Wei Yan
- Department of Cardiology, Nanjing Pukou People's Hospital, Nanjing, 211800, China
| | - Minglong Chen
- Department of Cardiology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, China; Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China.
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Ji J, Gu Z, Li N, Dong X, Wang X, Yao Q, Zhang Z, Zhang L, Cao L. Gut microbiota alterations in postmenopausal women with osteoporosis and osteopenia from Shanghai, China. PeerJ 2024; 12:e17416. [PMID: 38832037 PMCID: PMC11146318 DOI: 10.7717/peerj.17416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/28/2024] [Indexed: 06/05/2024] Open
Abstract
Background The importance of the gut microbiota in maintaining bone homeostasis has been increasingly emphasized by recent research. This study aimed to identify whether and how the gut microbiome of postmenopausal women with osteoporosis and osteopenia may differ from that of healthy individuals. Methods Fecal samples were collected from 27 individuals with osteoporosis (OP), 44 individuals with osteopenia (ON), and 23 normal controls (NC). The composition of the gut microbial community was analyzed by 16S rRNA gene sequencing. Results No significant difference was found in the microbial composition between the three groups according to alpha and beta diversity. At the phylum level, Proteobacteria and Fusobacteriota were significantly higher and Synergistota was significantly lower in the ON group than in the NC group. At the genus level, Roseburia, Clostridia_UCG.014, Agathobacter, Dialister and Lactobacillus differed between the OP and NC groups as well as between the ON and NC groups (p < 0.05). Linear discriminant effect size (LEfSe) analysis results showed that one phylum community and eighteen genus communities were enriched in the NC, ON and OP groups, respectively. Spearman correlation analysis showed that the abundance of the Dialister genus was positively correlated with BMD and T score at the lumbar spine (p < 0.05). Functional predictions revealed that pathways relevant to amino acid biosynthesis, vitamin biosynthesis, and nucleotide metabolism were enriched in the NC group. On the other hand, pathways relevant to metabolites degradation and carbohydrate metabolism were mainly enriched in the ON and OP groups respectively. Conclusions Our findings provide new epidemiologic evidence regarding the relationship between the gut microbiota and postmenopausal bone loss, laying a foundation for further exploration of therapeutic targets for the prevention and treatment of postmenopausal osteoporosis (PMO).
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Affiliation(s)
- Jiaqing Ji
- Department of Orthopedics, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhengrong Gu
- Department of Orthopedics, Luodian Hospital, Baoshan District, Shanghai, China
| | - Na Li
- School of Medicine, Shanghai University, Shanghai, China
| | - Xin Dong
- School of Medicine, Shanghai University, Shanghai, China
| | - Xiong Wang
- Department of Orthopedics, Luodian Hospital, Baoshan District, Shanghai, China
| | - Qiang Yao
- Department of Orthopedics, Luodian Hospital, Baoshan District, Shanghai, China
| | - Zhongxiao Zhang
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Zhang
- Department of Orthopedics, Luodian Hospital, Baoshan District, Shanghai, China
| | - Liehu Cao
- Department of Orthopedics, Luodian Hospital, Baoshan District, Shanghai, China
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Kuster R, Staton M. Readsynth: short-read simulation for consideration of composition-biases in reduced metagenome sequencing approaches. BMC Bioinformatics 2024; 25:191. [PMID: 38750423 PMCID: PMC11095026 DOI: 10.1186/s12859-024-05809-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 05/10/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND The application of reduced metagenomic sequencing approaches holds promise as a middle ground between targeted amplicon sequencing and whole metagenome sequencing approaches but has not been widely adopted as a technique. A major barrier to adoption is the lack of read simulation software built to handle characteristic features of these novel approaches. Reduced metagenomic sequencing (RMS) produces unique patterns of fragmentation per genome that are sensitive to restriction enzyme choice, and the non-uniform size selection of these fragments may introduce novel challenges to taxonomic assignment as well as relative abundance estimates. RESULTS Through the development and application of simulation software, readsynth, we compare simulated metagenomic sequencing libraries with existing RMS data to assess the influence of multiple library preparation and sequencing steps on downstream analytical results. Based on read depth per position, readsynth achieved 0.79 Pearson's correlation and 0.94 Spearman's correlation to these benchmarks. Application of a novel estimation approach, fixed length taxonomic ratios, improved quantification accuracy of simulated human gut microbial communities when compared to estimates of mean or median coverage. CONCLUSIONS We investigate the possible strengths and weaknesses of applying the RMS technique to profiling microbial communities via simulations with readsynth. The choice of restriction enzymes and size selection steps in library prep are non-trivial decisions that bias downstream profiling and quantification. The simulations investigated in this study illustrate the possible limits of preparing metagenomic libraries with a reduced representation sequencing approach, but also allow for the development of strategies for producing and handling the sequence data produced by this promising application.
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Affiliation(s)
- Ryan Kuster
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA.
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
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Liao F, Xia Y, Gu W, Fu X, Yuan B. Comparative analysis of shotgun metagenomics and 16S rDNA sequencing of gut microbiota in migratory seagulls. PeerJ 2023; 11:e16394. [PMID: 37941936 PMCID: PMC10629391 DOI: 10.7717/peerj.16394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 10/11/2023] [Indexed: 11/10/2023] Open
Abstract
Background Shotgun metagenomic and 16S rDNA sequencing are commonly used methods to identify the taxonomic composition of microbial communities. Previously, we analysed the gut microbiota and intestinal pathogenic bacteria configuration of migratory seagulls by using 16S rDNA sequencing and culture methods. Methods To continue in-depth research on the gut microbiome and reveal the applicability of the two methods, we compared the metagenome and 16S rDNA amplicon results to further demonstrate the features of this animal. Results The number of bacterial species detected by metagenomics gradually increased from the phylum to species level, consistent with 16S rDNA sequencing. Several taxa were commonly shared by both sequencing methods. However, Escherichia, Shigella, Erwinia, Klebsiella, Salmonella, Escherichia albertii, Shigella sonnei, Salmonella enterica, and Shigella flexneri were unique taxa for the metagenome compared with Escherichia-Shigella, Hafnia-Obesumbacterium, Catellicoccus marimammalium, Lactococcus garvieae, and Streptococcus gallolyticus for 16S rDNA sequencing. The largest differences in relative abundance between the two methods were identified at the species level, which identified many pathogenic bacteria to humans using metagenomic sequencing. Pearson correlation analysis indicated that the correlation coefficient for the two methods gradually decreased with the refinement of the taxonomic levels. The high consistency of the correlation coefficient was identified at the genus level for the beta diversity of the two methods. Conclusions In general, relatively consistent patterns and reliability could be identified by both sequencing methods, but the results varied following the refinement of taxonomic levels. Metagenomic sequencing was more suitable for the discovery and detection of pathogenic bacteria of gut microbiota in seagulls. Although there were large differences in the numbers and abundance of bacterial species of the two methods in terms of taxonomic levels, the patterns and reliability results of the samples were consistent.
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Affiliation(s)
- Feng Liao
- Department of Respiratory Medicine, The First People’s Hospital of Yunnan Province, Kunming, Yunnan, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yilan Xia
- Department of Infectious Diseases and Hepatology, The First People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Wenpeng Gu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, Yunnan, China
| | - Xiaoqing Fu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, Yunnan, China
| | - Bing Yuan
- Department of Respiratory Medicine, The First People’s Hospital of Yunnan Province, Kunming, Yunnan, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
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Leo S, Cetiner OF, Pittet LF, Messina NL, Jakob W, Falquet L, Curtis N, Zimmermann P. Metagenomics analysis of the neonatal intestinal resistome. Front Pediatr 2023; 11:1169651. [PMID: 37397142 PMCID: PMC10313230 DOI: 10.3389/fped.2023.1169651] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 04/25/2023] [Indexed: 07/04/2023] Open
Abstract
Introduction The intestinal microbiome forms a major reservoir for antibiotic resistance genes (ARGs). Little is known about the neonatal intestinal resistome. Objective The objective of this study was to investigate the intestinal resistome and factors that influence the abundance of ARGs in a large cohort of neonates. Methods Shotgun metagenomics was used to analyse the resistome in stool samples collected at 1 week of age from 390 healthy, term-born neonates who did not receive antibiotics. Results Overall, 913 ARGs belonging to 27 classes were identified. The most abundant ARGs were those conferring resistance to tetracyclines, quaternary ammonium compounds, and macrolide-lincosamide-streptogramin-B. Phylogenetic composition was strongly associated with the resistome composition. Other factors that were associated with the abundance of ARGs were delivery mode, gestational age, birth weight, feeding method, and antibiotics in the last trimester of pregnancy. Sex, ethnicity, probiotic use during pregnancy, and intrapartum antibiotics had little effect on the abundance of ARGs. Conclusion Even in the absence of direct antibiotic exposure, the neonatal intestine harbours a high abundance and a variety of ARGs.
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Affiliation(s)
- Stefano Leo
- Department for Community Health, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Department of Paediatrics, Fribourg Hospital, Fribourg, Switzerland
| | - Omer F. Cetiner
- Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Laure F. Pittet
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
- Infectious Diseases Research Group, Murdoch Children’s Research Institute, Parkville, VIC, Australia
- Pediatric Infectious Diseases Unit, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Nicole L. Messina
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
- Infectious Diseases Research Group, Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | - William Jakob
- Microbiology Laboratory, Fribourg Hospital, Fribourg, Switzerland
| | - Laurent Falquet
- Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Nigel Curtis
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
- Infectious Diseases Research Group, Murdoch Children’s Research Institute, Parkville, VIC, Australia
- Infectious Diseases Unit, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
| | - Petra Zimmermann
- Department for Community Health, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Department of Paediatrics, Fribourg Hospital, Fribourg, Switzerland
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
- Infectious Diseases Research Group, Murdoch Children’s Research Institute, Parkville, VIC, Australia
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Huang R, Liu P, Bai Y, Huang J, Pan R, Li H, Su Y, Zhou Q, Ma R, Zong S, Zeng G. Changes in the gut microbiota of osteoporosis patients based on 16S rRNA gene sequencing: a systematic review and meta-analysis. J Zhejiang Univ Sci B 2022; 23:1002-1013. [PMID: 36518053 PMCID: PMC9758719 DOI: 10.1631/jzus.b2200344] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/11/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND: Osteoporosis (OP) has become a major public health issue, threatening the bone health of middle-aged and elderly people from all around the world. Changes in the gut microbiota (GM) are correlated with the maintenance of bone mass and bone quality. However, research results in this field remain highly controversial, and no systematic review or meta-analysis of the relationship between GM and OP has been conducted. This paper addresses this shortcoming, focusing on the difference in the GM abundance between OP patients and healthy controls based on previous 16S ribosomal RNA (rRNA) gene sequencing results, in order to provide new clinical reference information for future customized prevention and treatment options of OP. METHODS: According to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA), we comprehensively searched the databases of PubMed, Web of Science, Embase, Cochrane Library, and China National Knowledge Infrastructure (CNKI). In addition, we applied the R programming language version 4.0.3 and Stata 15.1 software for data analysis. We also implemented the Newcastle-Ottawa Scale (NOS), funnel plot analysis, sensitivity analysis, Egger's test, and Begg's test to assess the risk of bias. RESULTS: This research ultimately considered 12 studies, which included the fecal GM data of 2033 people (604 with OP and 1429 healthy controls). In the included research papers, it was observed that the relative abundance of Lactobacillus and Ruminococcus increased in the OP group, while the relative abundance for Bacteroides of Bacteroidetes increased (except for Ireland). Meanwhile, Firmicutes, Blautia, Alistipes, Megamonas, and Anaerostipes showed reduced relative abundance in Chinese studies. In the linear discriminant analysis Effect Size (LEfSe) analysis, certain bacteria showed statistically significant results consistently across different studies. CONCLUSIONS: This observational meta-analysis revealed that changes in the GM were correlated with OP, and variations in some advantageous GM might involve regional differences.
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Affiliation(s)
- Rui Huang
- College of Public Hygiene of Guangxi Medical University, Nanning 530021, China
| | - Pan Liu
- Department of Spine Osteopathic, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
- Department of Orthopaedics, the Third Affiliated Hospital of Xinxiang Medical University, Xinxiang 453000, China
| | - Yiguang Bai
- Department of Spine Osteopathic, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
- Department of Orthopaedics, Nanchong Central Hospital, the Second Clinical Institute of North Sichuan Medical College, Nanchong 637000, China
| | - Jieqiong Huang
- College of Public Hygiene of Guangxi Medical University, Nanning 530021, China
| | - Rui Pan
- College of Public Hygiene of Guangxi Medical University, Nanning 530021, China
| | - Huihua Li
- College of Public Hygiene of Guangxi Medical University, Nanning 530021, China
| | - Yeping Su
- College of Public Hygiene of Guangxi Medical University, Nanning 530021, China
| | - Quan Zhou
- Department of Wound Repair, the First People's Hospital of Nanning, Nanning 530022, China
| | - Ruixin Ma
- Department of Spine Osteopathic, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Shaohui Zong
- Department of Spine Osteopathic, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China.
| | - Gaofeng Zeng
- College of Public Hygiene of Guangxi Medical University, Nanning 530021, China. ,
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Leo S, Curtis N, Zimmermann P. The neonatal intestinal resistome and factors that influence it - a systematic review. Clin Microbiol Infect 2022; 28:1539-1546. [PMID: 35868586 DOI: 10.1016/j.cmi.2022.07.014] [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: 05/17/2022] [Revised: 06/21/2022] [Accepted: 07/14/2022] [Indexed: 11/03/2022]
Abstract
BACKGROUND The intestinal microbiome provides a reservoir for antibiotic resistance genes (ARGs). The neonatal microbiome is more susceptible to disturbance from external factors than the established microbiome. OBJECTIVES In this review, we systematically summarise studies which investigated the intestinal resistome in neonates. DATA SOURCES MEDLINE and Embase databases were searched. STUDY ELIGIBILITY CRITERIA We included original studies which investigated ARGs in stool or rectal swabs in neonates using molecular diagnostics. METHODS OF DATA SYNTHESIS Two authors independently extracted data. Data was summarised in tables. RESULTS Our search identified 2,701 studies, of which 23 (22 cohorts) were included. The studies show that the neonatal intestine harbours a high abundance and variety of ARGs, even in the absence of direct antibiotic exposure. The most-commonly found ARGs confer resistance to aminoglycosides, beta-lactams, macrolides, tetracyclines or multi-drug resistance. There is evidence that ARGs can be transferred from mothers to neonates. Interestingly, however, compared to mothers, neonates are reported to have a higher abundance of ARGs. One likely reason for this is the bacterial phylogenetic composition with a high abundance of Gammaproteobacteria in neonatal stool. Factors that have been associated with a higher abundance of ARGs are intrapartum and neonatal antibiotic use. Breastfeeding and neonatal probiotic use have been associated with a lower abundance of ARGs. Antibiotics during pregnancy, delivery mode or sex are reported to have little effect. However, this might be because studies were underpowered and because it is difficult to account for effect modifiers. DISCUSSION The neonatal intestine seems to have a lower colonisation resistance, which could make it easier for antibiotic-resistant populations to establish themselves. Future studies will help in the development of evidence-based interventions to modulate the abundance of ARGs in neonates, for example, by the use of pre- and probiotics and bacteriophages.
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Affiliation(s)
- Stefano Leo
- Department for Community Health, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; Department of Paediatrics, Fribourg Hospital, Fribourg, Switzerland
| | - Nigel Curtis
- Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, Australia; Department of Paediatrics, The University of Melbourne, Parkville, Australia; Infectious Diseases Unit, The Royal Children's Hospital Melbourne, Parkville, Australia
| | - Petra Zimmermann
- Department for Community Health, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; Department of Paediatrics, Fribourg Hospital, Fribourg, Switzerland; Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, Australia.
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Peterson D, Bonham KS, Rowland S, Pattanayak CW, Klepac-Ceraj V. Comparative Analysis of 16S rRNA Gene and Metagenome Sequencing in Pediatric Gut Microbiomes. Front Microbiol 2021; 12:670336. [PMID: 34335499 PMCID: PMC8320171 DOI: 10.3389/fmicb.2021.670336] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 05/28/2021] [Indexed: 01/04/2023] Open
Abstract
The colonization of the human gut microbiome begins at birth, and over time, these microbial communities become increasingly complex. Most of what we currently know about the human microbiome, especially in early stages of development, was described using culture-independent sequencing methods that allow us to identify the taxonomic composition of microbial communities using genomic techniques, such as amplicon or shotgun metagenomic sequencing. Each method has distinct tradeoffs, but there has not been a direct comparison of the utility of these methods in stool samples from very young children, which have different features than those of adults. We compared the effects of profiling the human infant gut microbiome with 16S rRNA amplicon vs. shotgun metagenomic sequencing techniques in 338 fecal samples; younger than 15, 15-30, and older than 30 months of age. We demonstrate that observed changes in alpha-diversity and beta-diversity with age occur to similar extents using both profiling methods. We also show that 16S rRNA profiling identified a larger number of genera and we find several genera that are missed or underrepresented by each profiling method. We present the link between alpha diversity and shotgun metagenomic sequencing depth for children of different ages. These findings provide a guide for selecting an appropriate method and sequencing depth for the three studied age groups.
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Affiliation(s)
- Danielle Peterson
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Kevin S Bonham
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Sophie Rowland
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Cassandra W Pattanayak
- Department of Mathematics, Quantitative Reasoning Program, and the Quantitative Analysis Institute at Wellesley College, Wellesley, MA, United States
| | | | - Vanja Klepac-Ceraj
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
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Wei M, Li C, Dai Y, Zhou H, Cui Y, Zeng Y, Huang Q, Wang Q. High-Throughput Absolute Quantification Sequencing Revealed Osteoporosis-Related Gut Microbiota Alterations in Han Chinese Elderly. Front Cell Infect Microbiol 2021; 11:630372. [PMID: 33996619 PMCID: PMC8120270 DOI: 10.3389/fcimb.2021.630372] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 04/19/2021] [Indexed: 12/06/2022] Open
Abstract
Objective Accumulative evidence suggests that gut microbiota play an important role in bone remodeling and hence bone health maintenance. This study aimed to explore the association of gut microbiota with the risk of osteoporosis and to identify potential disease-related taxa, which may be promising targets in osteoporosis prevention and treatment in the future. Methods Absolute quantification 16S ribosomal RNA gene sequencing was used to detect absolute and relative abundances of gut microbiota in 44 patients with osteoporosis and 64 controls. In combination with one of our previous studies, a total of 175 samples were involved in the relative abundance analysis. Results Compared with the controls, the patients with osteoporosis had higher absolute and relative abundances of Bacteroidetes phylum, and Bacteroides and Eisenbergiella genera. The absolute abundances of Clostridium_XlVa, Coprococcus, Lactobacillus, and Eggerthella genera increased, and that of the Veillonella genus decreased in the osteoporosis group. As for relative abundance, that of the Parabacteroides and Flavonifractor genera increased, whereas that of the Raoultella genus decreased in the osteoporosis group. Controlling for potential confounders, the associations of Clostridium_XlVa, Coprococcus, and Veillonella genera with the risk of osteoporosis did not maintain significance. Ridge regression analysis suggested that Bacteroides is associated with reduced bone mineral density (BMD) and T-score at lumbar spines, and Anaerovorax is associated with increased BMD at the femoral neck. Functional predictions revealed that 10 Kyoto Encyclopedia of Genes and Genomes pathways were enriched in the osteoporosis group. Conclusions Gut microbiota compositions may contribute to the risk of osteoporosis. Several specific taxa and functional pathways are identified to associate with reduced bone density, thus providing epidemiologic evidence for the potential role of aberrant gut microbiota in osteoporosis pathogenesis.
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Affiliation(s)
- Muhong Wei
- MOE Key Lab of Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Can Li
- MOE Key Lab of Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Dai
- Department of Nuclear Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Haolong Zhou
- MOE Key Lab of Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuan Cui
- MOE Key Lab of Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yun Zeng
- Department of Medical Record Statistics, Wuhan NO.1 Hospital, Wuhan, China
| | - Qin Huang
- Department of Rehabilitation Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qi Wang
- MOE Key Lab of Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Snipen L, Angell IL, Rognes T, Rudi K. Reduced metagenome sequencing for strain-resolution taxonomic profiles. MICROBIOME 2021; 9:79. [PMID: 33781324 PMCID: PMC8008692 DOI: 10.1186/s40168-021-01019-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 02/02/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Studies of shifts in microbial community composition has many applications. For studies at species or subspecies levels, the 16S amplicon sequencing lacks resolution and is often replaced by full shotgun sequencing. Due to higher costs, this restricts the number of samples sequenced. As an alternative to a full shotgun sequencing we have investigated the use of Reduced Metagenome Sequencing (RMS) to estimate the composition of a microbial community. This involves the use of double-digested restriction-associated DNA sequencing, which means only a smaller fraction of the genomes are sequenced. The read sets obtained by this approach have properties different from both amplicon and shotgun data, and analysis pipelines for both can either not be used at all or not explore the full potential of RMS data. RESULTS We suggest a procedure for analyzing such data, based on fragment clustering and the use of a constrained ordinary least square de-convolution for estimating the relative abundance of all community members. Mock community datasets show the potential to clearly separate strains even when the 16S is 100% identical, and genome-wide differences is < 0.02, indicating RMS has a very high resolution. From a simulation study, we compare RMS to shotgun sequencing and show that we get improved abundance estimates when the community has many very closely related genomes. From a real dataset of infant guts, we show that RMS is capable of detecting a strain diversity gradient for Escherichia coli across time. CONCLUSION We find that RMS is a good alternative to either metabarcoding or shotgun sequencing when it comes to resolving microbial communities at the strain level. Like shotgun metagenomics, it requires a good database of reference genomes and is well suited for studies of the human gut or other communities where many reference genomes exist. A data analysis pipeline is offered, as an R package at https://github.com/larssnip/microRMS . Video abstract.
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Affiliation(s)
- Lars Snipen
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway
| | - Inga-Leena Angell
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway
| | - Torbjørn Rognes
- Department of Informatics, University of Oslo, P.O. Box 1080, Blindern, NO-0316 Oslo, Norway
| | - Knut Rudi
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway
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11
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Zhang M, Cui Z, Liu F, Chen N. Definition of a High-Resolution Molecular Marker for Tracking the Genetic Diversity of the Harmful Algal Species Eucampia zodiacus Through Comparative Analysis of Mitochondrial Genomes. Front Microbiol 2021; 12:631144. [PMID: 33841358 PMCID: PMC8024477 DOI: 10.3389/fmicb.2021.631144] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/23/2021] [Indexed: 11/13/2022] Open
Abstract
The cosmopolitan phytoplankton species Eucampia zodiacus is a common harmful algal bloom (HAB) species that have been found to cause HABs in essentially all coastal regions except the Polar regions. However, molecular information for this HAB species is limited with only a few molecular markers. In this project, we constructed the mitochondrial genome (mtDNA) of E. zodiacus, which was also the first mtDNA constructed for any species in the order Hemiaulales that includes 145 reported species (including two additional HAB species Cerataulina bicornis and Cerataulina pelagica). Comparative analysis of eight E. zodiacus strains revealed that they could not be distinguished using common molecular markers, suggesting that common molecular markers do not have adequate resolution for distinguishing E. zodiacus strains. However, these E. zodiacus strains could be distinguished using whole mtDNAs, suggesting the presence of different genotypes due to evolutionary divergence. Through comparative analysis of the mtDNAs of multiple E. zodiacus strains, we identified a new molecular marker ezmt1 that could adequately distinguish different E. zodiacus strains isolated in various coastal regions in China. This molecular marker ezmt1, which was ∼400 bp in size, could be applied to identify causative genotypes during E. zodiacus HABs through tracking the dynamic changes of genetic diversity of E. zodiacus in HABs.
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Affiliation(s)
- Mengjia Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Oceanology, University of Chinese Academy of Sciences, Beijing, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Zongmei Cui
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Oceanology, University of Chinese Academy of Sciences, Beijing, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Feng Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
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12
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Li Z, Shen J, Xu Y, Zhu W. Metagenomic analysis reveals significant differences in microbiome and metabolic profiles in the rumen of sheep fed low N diet with increased urea supplementation. FEMS Microbiol Ecol 2021; 96:5861934. [PMID: 32578861 DOI: 10.1093/femsec/fiaa117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 06/23/2020] [Indexed: 11/13/2022] Open
Abstract
Urea is a cost-effective replacement for feed proteins in ruminant diets. However, its metabolism by the rumen microbiome is not fully understood. Here, rumen contents were collected from 18 male sheep fed one of the following three treatments: a low N basal diet with no urea (UC, 0 g/kg dry matter (DM)), low urea (LU, 10 g/kg DM) and high urea (HU, 30 g/kg DM). Principal coordinate analysis showed that the microbial composition and functional profiles of the LU treatment significantly differed from the UC and HU treatments. The genera Prevotella, Succinivibrio, Succinatimonas and Megasphaera were higher in the LU rumen, while the genera Clostridium, Ruminococcus and Butyrivibrio were enriched in the UC and HU rumen. The aspartate-glutamate and arginine-proline metabolic pathways and valine, leucine and isoleucine biosynthesis were higher in the LU rumen. The cysteine and methionine metabolism, lysine degradation and fructose and pentose phosphate metabolism pathways were higher in the UC and HU rumen. The protozoa population in the HU treatment was higher than in the UC and LU treatments. These findings suggest that the rumen microbiome of sheep fed low N diet with different urea supplementation are significantly different.
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Affiliation(s)
- Zhipeng Li
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, China.,Department of Special Animal Nutrition and Feed Science, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, Jilin Province, China
| | - Junshi Shen
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, China.,National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, China
| | - Yixuan Xu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, China.,National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, China
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13
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Nilsen M, Lokmic A, Angell IL, Lødrup Carlsen KC, Carlsen KH, Haugen G, Hedlin G, Jonassen CM, Marsland BJ, Nordlund B, Rehbinder EM, Saunders CM, Skjerven HO, Snipen L, Staff AC, Söderhäll C, Vettukattil R, Rudi K. Fecal Microbiota Nutrient Utilization Potential Suggests Mucins as Drivers for Initial Gut Colonization of Mother-Child-Shared Bacteria. Appl Environ Microbiol 2021; 87:e02201-20. [PMID: 33452029 PMCID: PMC8105027 DOI: 10.1128/aem.02201-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/04/2021] [Indexed: 01/04/2023] Open
Abstract
The nutritional drivers for mother-child sharing of bacteria and the corresponding longitudinal trajectory of the infant gut microbiota development are not yet completely settled. We therefore aimed to characterize the mother-child sharing and the inferred nutritional utilization potential for the gut microbiota from a large unselected cohort. We analyzed in depth gut microbiota in 100 mother-child pairs enrolled antenatally from the general population-based Preventing Atopic Dermatitis and Allergies in Children (PreventADALL) cohort. Fecal samples collected at gestational week 18 for mothers and at birth (meconium), 3, 6, and 12 months for infants were analyzed by reduced metagenome sequencing to determine metagenome size and taxonomic composition. The nutrient utilization potential was determined based on the Virtual Metabolic Human (VMH, www.vmh.life) database. The estimated median metagenome size was ∼150 million base pairs (bp) for mothers and ∼20 million bp at birth for the children. Longitudinal analyses revealed mother-child sharing (P < 0.05, chi-square test) from birth up to 6 months for 3 prevalent Bacteroides species (prevalence, >25% for all age groups). In a multivariate analysis of variance (ANOVA), the mother-child-shared Bacteroides were associated with vaginal delivery (1.7% explained variance, P = 0.0001). Both vaginal delivery and mother-child sharing were associated with host-derived mucins as nutrient sources. The age-related increase in metagenome size corresponded to an increased diversity in nutrient utilization, with dietary polysaccharides as the main age-related factor. Our results support host-derived mucins as potential selection means for mother-child sharing of initial colonizers, while the age-related increase in diversity was associated with dietary polysaccharides.IMPORTANCE The initial bacterial colonization of human infants is crucial for lifelong health. Understanding the factors driving this colonization will therefore be of great importance. Here, we used a novel high-taxonomic-resolution approach to deduce the nutrient utilization potential of the infant gut microbiota in a large longitudinal mother-child cohort. We found mucins as potential selection means for the initial colonization of mother-child-shared bacteria, while the transition to a more adult-like microbiota was associated with dietary polysaccharide utilization potential. This knowledge will be important for a future understanding of the importance of diet in shaping the gut microbiota composition and development during infancy.
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Affiliation(s)
- Morten Nilsen
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Asima Lokmic
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Inga Leena Angell
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Karin C Lødrup Carlsen
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- University of Oslo, Faculty of Medicine, Institute of Clinical Medicine, Oslo, Norway
| | - Kai-Håkon Carlsen
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- University of Oslo, Faculty of Medicine, Institute of Clinical Medicine, Oslo, Norway
| | - Guttorm Haugen
- University of Oslo, Faculty of Medicine, Institute of Clinical Medicine, Oslo, Norway
- Division of Obstetrics and Gynaecology, Oslo University Hospital, Oslo, Norway
| | - Gunilla Hedlin
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Christine Monceyron Jonassen
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Genetic Unit, Centre for Laboratory Medicine, Østfold Hospital Trust, Kalnes, Norway
| | - Benjamin J Marsland
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Björn Nordlund
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Eva Maria Rehbinder
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- University of Oslo, Faculty of Medicine, Institute of Clinical Medicine, Oslo, Norway
- Division of Obstetrics and Gynaecology, Oslo University Hospital, Oslo, Norway
| | - Carina Madelen Saunders
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- University of Oslo, Faculty of Medicine, Institute of Clinical Medicine, Oslo, Norway
| | - Håvard O Skjerven
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- University of Oslo, Faculty of Medicine, Institute of Clinical Medicine, Oslo, Norway
| | - Lars Snipen
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Anne Cathrine Staff
- University of Oslo, Faculty of Medicine, Institute of Clinical Medicine, Oslo, Norway
- Division of Obstetrics and Gynaecology, Oslo University Hospital, Oslo, Norway
| | - Cilla Söderhäll
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Riyas Vettukattil
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- University of Oslo, Faculty of Medicine, Institute of Clinical Medicine, Oslo, Norway
| | - Knut Rudi
- Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, Ås, Norway
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14
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Mueller NT, Differding MK, Østbye T, Hoyo C, Benjamin-Neelon SE. Association of birth mode of delivery with infant faecal microbiota, potential pathobionts, and short chain fatty acids: a longitudinal study over the first year of life. BJOG 2021; 128:1293-1303. [PMID: 33338292 DOI: 10.1111/1471-0528.16633] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Caesarean section (CS) interrupts mother-to-newborn microbial transfer at birth. Beyond the neonatal period, the impact of CS on offspring gut microbiota and their short-chain fatty acids (SCFAs) remains unclear. Here, we examine birth delivery mode (CS versus vaginal delivery) with the infant gut microbiota and faecal SCFAs measured 3 and 12 months after birth. DESIGN Longitudinal study. SETTING North Carolina. POPULATION In 2013-15, we enrolled pregnant women and followed up their offspring for 12 months. We asked a subset of participants, enrolled over a 3-month period, to provide faecal samples at the 3- and 12-month follow-up visits. METHODS AND MAIN OUTCOMES We sequenced the 16S rRNA V4 region with Illumina MiSeq and quantified SCFA concentrations using gas chromatography. We examined delivery mode with differential abundance of microbiota amplicon sequence variants (ASVs) using beta-binomial regression and faecal SCFAs using linear regression. We adjusted models for confounders. RESULTS Of the 70 infants in our sample, 25 (36%) were delivered by CS. Compared with vaginal delivery, CS was associated with differential abundance of 14 infant bacterial ASVs at 3 months and 13 ASVs at 12 months (all FDR P < 0.05). Of note, CS infants had a higher abundance of the potential pathobionts Clostridium neonatale (P = 0.04) and Clostridium perfringens (P = 0.04) and a lower abundance of potentially beneficial Bifidobacterium and Bacteroides spp. (both P < 0.05) at 3 months. Other ASVs were differentially abundant at 12 months. Infants delivered by CS also had higher faecal butyrate concentration at 3 months (P < 0.005) but not at 12 months. CONCLUSIONS Caesarean section was associated with increased butyrate excretion, decreased Bifidobacterium and Bacteroides spp., and more colonisation of the infant gut by pathobionts at 3 months of age. CS was also associated with altered gut microbiota composition, but not faecal SCFAs, at 12 months. TWEETABLE ABSTRACT Caesarean section delivery was associated with increased butyrate excretion, decreased Bifidobacterium, and increased colonisation of the infant gut by pathobionts at 3 months of age.
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Affiliation(s)
- N T Mueller
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.,Welch Center for Prevention, Epidemiology and Clinical Research, Johns Hopkins University, Baltimore, MD, USA
| | - M K Differding
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - T Østbye
- Department of Family Medicine and Community Health, Duke University, Durham, NC, USA
| | - C Hoyo
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - S E Benjamin-Neelon
- Department of Health, Behavior and Society, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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15
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Hupfauf S, Etemadi M, Fernández-Delgado Juárez M, Gómez-Brandón M, Insam H, Podmirseg SM. CoMA - an intuitive and user-friendly pipeline for amplicon-sequencing data analysis. PLoS One 2020; 15:e0243241. [PMID: 33264369 PMCID: PMC7710066 DOI: 10.1371/journal.pone.0243241] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 11/17/2020] [Indexed: 12/23/2022] Open
Abstract
In recent years, there has been a veritable boost in next-generation sequencing (NGS) of gene amplicons in biological and medical studies. Huge amounts of data are produced and need to be analyzed adequately. Various online and offline analysis tools are available; however, most of them require extensive expertise in computer science or bioinformatics, and often a Linux-based operating system. Here, we introduce "CoMA-Comparative Microbiome Analysis" as a free and intuitive analysis pipeline for amplicon-sequencing data, compatible with any common operating system. Moreover, the tool offers various useful services including data pre-processing, quality checking, clustering to operational taxonomic units (OTUs), taxonomic assignment, data post-processing, data visualization, and statistical appraisal. The workflow results in highly esthetic and publication-ready graphics, as well as output files in standardized formats (e.g. tab-delimited OTU-table, BIOM, NEWICK tree) that can be used for more sophisticated analyses. The CoMA output was validated by a benchmark test, using three mock communities with different sample characteristics (primer set, amplicon length, diversity). The performance was compared with that of Mothur, QIIME and QIIME2-DADA2, popular packages for NGS data analysis. Furthermore, the functionality of CoMA is demonstrated on a practical example, investigating microbial communities from three different soils (grassland, forest, swamp). All tools performed well in the benchmark test and were able to reveal the majority of all genera in the mock communities. Also for the soil samples, the results of CoMA were congruent to those of the other pipelines, in particular when looking at the key microbial players.
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Affiliation(s)
- Sebastian Hupfauf
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Mohammad Etemadi
- Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz, Iran
| | | | - María Gómez-Brandón
- Department of Ecology and Animal Biology, GEA Group, University of Vigo, Vigo, Spain
| | - Heribert Insam
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
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16
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Angell IL, Rudi K. A game theory model for gut bacterial nutrient utilization strategies during human infancy. Proc Biol Sci 2020; 287:20200824. [PMID: 32673553 PMCID: PMC7423673 DOI: 10.1098/rspb.2020.0824] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022] Open
Abstract
Despite the fact that infant gut colonization patterns have been extensively studied, we have limited knowledge about the underlying ecological processes. This particularly relates to the ecological choice of nutrient utilization strategies. The aim of the current study was therefore to compare empirically determined nutrient utilization strategies with that expected from a combinatorial game theory model. Observational analyses for 100 mother-child pairs suggested mother-child transmission of specialists with the potential to use few nutrients. Generalists, on the other hand, with the potential to use many nutrients, peaked at three months of age for the children. The level of generalists was gradually replaced with specialists up to 12 months of age. Game theory simulation revealed a competitive advantage of generalists in an expanding population, while more specialized bacteria were favoured with the maturation of the population. This suggests that the observed increase in generalists in the three-month-old children could be due to an immature, expanding gut microbiota population while the increase of specialists at 12 months could be due to population maturation. The simulated and empirical data also correspond with respect to an increased α diversity and a decreased β diversity with the number of simulations and age, respectively. Taken together, game theory simulation of nutrient utilization strategies can therefore provide novel insight into the maturation of the human gut microbiota during infancy.
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Affiliation(s)
| | - Knut Rudi
- Faculty of Chemistry, Biotechnology and Food Science (KBM), Norwegian University of Life Sciences, Ås, Norway
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17
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Hess MK, Rowe SJ, Van Stijn TC, Henry HM, Hickey SM, Brauning R, McCulloch AF, Hess AS, Kirk MR, Kumar S, Pinares-Patiño C, Kittelmann S, Wood GR, Janssen PH, McEwan JC. A restriction enzyme reduced representation sequencing approach for low-cost, high-throughput metagenome profiling. PLoS One 2020; 15:e0219882. [PMID: 32243481 PMCID: PMC7122713 DOI: 10.1371/journal.pone.0219882] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 03/04/2020] [Indexed: 01/26/2023] Open
Abstract
Microbial community profiles have been associated with a variety of traits, including methane emissions in livestock. These profiles can be difficult and expensive to obtain for thousands of samples (e.g. for accurate association of microbial profiles with traits), therefore the objective of this work was to develop a low-cost, high-throughput approach to capture the diversity of the rumen microbiome. Restriction enzyme reduced representation sequencing (RE-RRS) using ApeKI or PstI, and two bioinformatic pipelines (reference-based and reference-free) were compared to bacterial 16S rRNA gene sequencing using repeated samples collected two weeks apart from 118 sheep that were phenotypically extreme (60 high and 58 low) for methane emitted per kg dry matter intake (n = 236). DNA was extracted from freeze-dried rumen samples using a phenol chloroform and bead-beating protocol prior to RE-RRS. The resulting sequences were used to investigate the repeatability of the rumen microbial community profiles, the effect of laboratory and analytical method, and the relationship with methane production. The results suggested that the best method was PstI RE-RRS analyzed with the reference-free approach, which accounted for 53.3±5.9% of reads, and had repeatabilities of 0.49±0.07 and 0.50±0.07 for the first two principal components (PC1 and PC2), phenotypic correlations with methane yield of 0.43±0.06 and 0.46±0.06 for PC1 and PC2, and explained 41±8% of the variation in methane yield. These results were significantly better than for bacterial 16S rRNA gene sequencing of the same samples (p<0.05) except for the correlation between PC2 and methane yield. A Sensitivity study suggested approximately 2000 samples could be sequenced in a single lane on an Illumina HiSeq 2500, meaning the current work using 118 samples/lane and future proposed 384 samples/lane are well within that threshold. With minor adaptations, our approach could be used to obtain microbial profiles from other metagenomic samples.
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Affiliation(s)
- Melanie K. Hess
- AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Suzanne J. Rowe
- AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand
| | | | - Hannah M. Henry
- AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Sharon M. Hickey
- AgResearch Limited, Ruakura Agricultural Centre, Hamilton, New Zealand
| | - Rudiger Brauning
- AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Alan F. McCulloch
- AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Andrew S. Hess
- AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Michelle R. Kirk
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Sandeep Kumar
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | | | - Sandra Kittelmann
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Graham R. Wood
- AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Peter H. Janssen
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - John C. McEwan
- AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand
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18
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Ramesh N, Archana L, Madurantakam Royam M, Manohar P, Eniyan K. Effect of various bacteriological media on the plaque morphology of Staphylococcus and Vibrio phages. Access Microbiol 2019; 1:e000036. [PMID: 32974524 PMCID: PMC7470289 DOI: 10.1099/acmi.0.000036] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/05/2019] [Indexed: 12/04/2022] Open
Abstract
The influence of media composition on the life cycle of bacteriophages to exhibit diverse plaque morphology on various bacteriological media was investigated by a double agar overlay method. Both Staphylococcus aureus phage and Vibrio parahaemolyticus phage showed altered plaque morphology from small to large and from clear to turbid, in different culture media used for the double agar overlay method.
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Affiliation(s)
- Nachimuthu Ramesh
- Antibiotic Resistance and Phage Therapy Laboratory, School of Bio Science and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
- *Correspondence: Nachimuthu Ramesh,
| | - Loganathan Archana
- Antibiotic Resistance and Phage Therapy Laboratory, School of Bio Science and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Madhav Madurantakam Royam
- Antibiotic Resistance and Phage Therapy Laboratory, School of Bio Science and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Prasanth Manohar
- Antibiotic Resistance and Phage Therapy Laboratory, School of Bio Science and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Kandasamy Eniyan
- Antibiotic Resistance and Phage Therapy Laboratory, School of Bio Science and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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19
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She Y, Cai H, Liu G. Effects of antibiotic on microflora in ileum and cecum for broilers by 16S rRNA sequence analysis. Anim Sci J 2018; 89:1680-1691. [PMID: 30362241 DOI: 10.1111/asj.13113] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/11/2018] [Accepted: 09/06/2018] [Indexed: 12/17/2022]
Abstract
An experiment was conducted to analyze and compare the microbial composition, abundance, dynamic distribution, and functions without and with antibiotic fed to broilers. A 16S rRNA-sequencing approach was used to evaluate the bacterial composition of the gut of male broilers under different groups. A total of 240 1-day old AA male broilers were randomly assigned to two groups, with 120 broilers per group. The treatment group was administered an antibiotic with their feed, while the control group was not administered antibiotic (control group). A total of 10 replicates were assessed per treatment. The control group was fed a basal diet containing corn, soybean meal, and cottonseed meal and met the nutritional requirement. The antibiotic group was fed 100 mg/kg aureomycin (based on the basal diet). The trial lasted 42 days. Operational taxonomic unit partition and classification, alpha diversity, taxonomic composition, beta diversity, and microflora comparative analyses along with key species screening were performed for all of the treatment groups. Our data indicate that aureomycin treatment in broilers is directly correlated with variations of the gut content of specific bacterial taxa, and herein provide insights into the impact of antibiotic on microbial communities in cecum and ileum of broiler chickens.
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Affiliation(s)
- Yue She
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huiyi Cai
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guohua Liu
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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Low Maternal Microbiota Sharing across Gut, Breast Milk and Vagina, as Revealed by 16S rRNA Gene and Reduced Metagenomic Sequencing. Genes (Basel) 2018; 9:genes9050231. [PMID: 29724017 PMCID: PMC5977171 DOI: 10.3390/genes9050231] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 04/27/2018] [Accepted: 04/30/2018] [Indexed: 12/27/2022] Open
Abstract
The maternal microbiota plays an important role in infant gut colonization. In this work we have investigated which bacterial species are shared across the breast milk, vaginal and stool microbiotas of 109 women shortly before and after giving birth using 16S rRNA gene sequencing and a novel reduced metagenomic sequencing (RMS) approach in a subgroup of 16 women. All the species predicted by the 16S rRNA gene sequencing were also detected by RMS analysis and there was good correspondence between their relative abundances estimated by both approaches. Both approaches also demonstrate a low level of maternal microbiota sharing across the population and RMS analysis identified only two species common to most women and in all sample types (Bifidobacterium longum and Enterococcus faecalis). Breast milk was the only sample type that had significantly higher intra- than inter- individual similarity towards both vaginal and stool samples. We also searched our RMS dataset against an in silico generated reference database derived from bacterial isolates in the Human Microbiome Project. The use of this reference-based search enabled further separation of Bifidobacterium longum into Bifidobacterium longum ssp. longum and Bifidobacterium longum ssp. infantis. We also detected the Lactobacillus rhamnosus GG strain, which was used as a probiotic supplement by some women, demonstrating the potential of RMS approach for deeper taxonomic delineation and estimation.
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