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Exploration of bacterial community classes in major human habitats

Published on Jan 1, 2014in Genome Biology 14.03
· DOI :10.1186/gb-2014-15-5-r66
Yanhua Zhou32
Estimated H-index: 32
(UW: University of Washington),
Kathie A. Mihindukulasuriya14
Estimated H-index: 14
(UW: University of Washington)
+ 8 AuthorsGeorge M. Weinstock98
Estimated H-index: 98
(University of Connecticut Health Center)
Cite
Abstract
Background Determining bacterial abundance variation is the first step in understanding bacterial similarity between individuals. Categorization of bacterial communities into groups or community classes is the subsequent step in describing microbial distribution based on abundance patterns. Here, we present an analysis of the groupings of bacterial communities in stool, nasal, skin, vaginal and oral habitats in a healthy cohort of 236 subjects from the Human Microbiome Project.
  • References (48)
  • Citations (38)
Cite
References48
Newest
Published on Sep 4, 2014
Martin Maechler1
Estimated H-index: 1
,
Peter J. Rousseeuw52
Estimated H-index: 52
+ 1 AuthorsMia Hubert4
Estimated H-index: 4
Published on Mar 1, 2013in The FASEB Journal 5.39
Kjersti Aagaard30
Estimated H-index: 30
(BCM: Baylor College of Medicine),
Joseph F. Petrosino47
Estimated H-index: 47
(BCM: Baylor College of Medicine)
+ 12 AuthorsHolli A. Hamilton3
Estimated H-index: 3
(NIH: National Institutes of Health)
The Human Microbiome Project used rigorous good clinical practice standards to complete comprehensive body site sampling in healthy 18- to 40-yr-old adults, creating an unparalleled reference set of microbiome specimens. To ensure that specimens represented minimally perturbed microbiomes, we first screened potential participants using exclusion criteria based on health history, including the presence of systemic diseases (e.g., hypertension, cancer, or immunodeficiency or autoimmune disorders),...
Published on Jan 10, 2013in PLOS Computational Biology
Omry Koren32
Estimated H-index: 32
(Cornell University),
Dan Knights41
Estimated H-index: 41
(CU: University of Colorado Boulder)
+ 5 AuthorsRuth E. Ley59
Estimated H-index: 59
(Cornell University)
Recent analyses of human-associated bacterial diversity have categorized individuals into ‘enterotypes’ or clusters based on the abundances of key bacterial genera in the gut microbiota. There is a lack of consensus, however, on the analytical basis for enterotypes and on the interpretation of these results. We tested how the following factors influenced the detection of enterotypes: clustering methodology, distance metrics, OTU-picking approaches, sequencing depth, data type (whole genome shotg...
Published on Jan 1, 2013in Genome Biology 14.03
Falk Hildebrand18
Estimated H-index: 18
(Vrije Universiteit Brussel),
Thi Loan Anh Nguyen2
Estimated H-index: 2
+ 5 AuthorsJeroen Raes64
Estimated H-index: 64
(Vrije Universiteit Brussel)
Background Murine models are a crucial component of gut microbiome research. Unfortunately, a multitude of genetic backgrounds and experimental setups, together with inter-individual variation, complicates cross-study comparisons and a global understanding of the mouse microbiota landscape. Here, we investigate the variability of the healthy mouse microbiota of five common lab mouse strains using 16S rDNA pyrosequencing.
Published on Jan 1, 2013in Genome Biology 14.03
Yanhua Zhou32
Estimated H-index: 32
(WashU: Washington University in St. Louis),
Hongyu Gao9
Estimated H-index: 9
(WashU: Washington University in St. Louis)
+ 13 AuthorsDavid E. Nelson43
Estimated H-index: 43
(IU: Indiana University Bloomington)
Background Characterizing the biogeography of the microbiome of healthy humans is essential for understanding microbial associated diseases. Previous studies mainly focused on a single body habitat from a limited set of subjects. Here, we analyzed one of the largest microbiome datasets to date and generated a biogeographical map that annotates the biodiversity, spatial relationships, and temporal stability of 22 habitats from 279 healthy humans.
Published on Sep 1, 2012in Nature Reviews Microbiology 34.65
Ian B. Jeffery21
Estimated H-index: 21
,
Marcus J. Claesson32
Estimated H-index: 32
+ 1 AuthorsFergus Shanahan100
Estimated H-index: 100
Grouping the microbiota of individual subjects into compositional categories, or enterotypes, based on the dominance of certain genera may have oversimplified a complex situation.
Published on Aug 15, 2012in PLOS ONE 2.78
Margaret L. Zupancic1
Estimated H-index: 1
(UMB: University of Maryland, Baltimore),
Brandi L. Cantarel26
Estimated H-index: 26
(UMB: University of Maryland, Baltimore)
+ 14 AuthorsDan Knights41
Estimated H-index: 41
(CU: University of Colorado Boulder)
Obesity has been linked to the human gut microbiota; however, the contribution of gut bacterial species to the obese phenotype remains controversial because of conflicting results from studies in different populations. To explore the possible dysbiosis of gut microbiota in obesity and its metabolic complications, we studied men and women over a range of body mass indices from the Old Order Amish sect, a culturally homogeneous Caucasian population of Central European ancestry. We characterized th...
Published on Jun 14, 2012in Nature 43.07
Barbara A. Methé5
Estimated H-index: 5
(JCVI: J. Craig Venter Institute),
Karen E. Nelson71
Estimated H-index: 71
(JCVI: J. Craig Venter Institute)
+ 245 AuthorsJonathan H. Badger32
Estimated H-index: 32
(JCVI: J. Craig Venter Institute)
The Human Microbiome Project Consortium has established a population-scale framework to study a variety of microbial communities that exist throughout the human body, enabling the generation of a range of quality-controlled data as well as community resources.
Published on Jun 14, 2012in Nature 43.07
Curtis Huttenhower68
Estimated H-index: 68
(Broad Institute),
Dirk Gevers66
Estimated H-index: 66
(Broad Institute)
+ 245 AuthorsRobert S. Fulton80
Estimated H-index: 80
(WashU: Washington University in St. Louis)
The Human Microbiome Project Consortium reports the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome.
Published on Jun 13, 2012in PLOS ONE 2.78
John Martin33
Estimated H-index: 33
(WashU: Washington University in St. Louis),
Sean Sykes22
Estimated H-index: 22
(Broad Institute)
+ 8 AuthorsGeorge M. Weinstock98
Estimated H-index: 98
(WashU: Washington University in St. Louis)
The Human Microbiome Project (HMP) aims to characterize the microbial communities of 18 body sites from healthy individuals. To accomplish this, the HMP generated two types of shotgun data: reference shotgun sequences isolated from different anatomical sites on the human body and shotgun metagenomic sequences from the microbial communities of each site. The alignment strategy for characterizing these metagenomic communities using available reference sequence is important to the success of HMP da...
Cited By38
Newest
Published in BMC Genomics 3.50
Ko Abe (Nagoya University), Masaaki Hirayama31
Estimated H-index: 31
(RMIT: RMIT University)
+ -3 AuthorsTeppei Shimamura21
Estimated H-index: 21
(Nagoya University)
Background One of the major challenges in microbial studies is detecting associations between microbial communities and a specific disease. A specialized feature of microbiome count data is that intestinal bacterial communities form clusters called as “enterotype”, which are characterized by differences in specific bacterial taxa, making it difficult to analyze these data under health and disease conditions. Traditional probabilistic modeling cannot distinguish between the bacterial differences ...
Published on Mar 26, 2019in PeerJ 2.35
Beatriz García-Jiménez2
Estimated H-index: 2
(UPM: Technical University of Madrid),
Mark D. Wilkinson34
Estimated H-index: 34
(UPM: Technical University of Madrid)
Published on Feb 1, 2019in Genomics, Proteomics & Bioinformatics
Mingyue Cheng (HUST: Huazhong University of Science and Technology), Kang Ning21
Estimated H-index: 21
(HUST: Huazhong University of Science and Technology)
Abstract In 2011, the term “ enterotype ” first appeared to the general public in Nature , which refers to stratification of human gut microbiota. However, with more studies on enterotypes conducted nowadays, doubts about the existence and robustness of enterotypes have also emerged. Here we reviewed current opinions about enterotypes from both conceptual and analytical points of view. We firstly illustrated the definition of the enterotype and various factors influencing enterotypes, such as di...
Published on Feb 1, 2019in Molecular Nutrition & Food Research 4.65
María Romo-Vaquero9
Estimated H-index: 9
(CSIC: Spanish National Research Council),
Adrián Cortés‐Martín2
Estimated H-index: 2
(CSIC: Spanish National Research Council)
+ 5 AuthorsMaría V. Selma32
Estimated H-index: 32
(CSIC: Spanish National Research Council)
Published on Jan 24, 2019in Nutrients 4.17
Nida Murtaza2
Estimated H-index: 2
(UQ: University of Queensland),
Louise M. Burke54
Estimated H-index: 54
(AIS: Australian Institute of Sport)
+ 6 AuthorsMark Morrison43
Estimated H-index: 43
(UQ: University of Queensland)
We investigated extreme changes in diet patterns on the gut microbiota of elite race walkers undertaking intensified training and its possible links with athlete performance. Numerous studies with sedentary subjects have shown that diet and/or exercise can exert strong selective pressures on the gut microbiota. Similar studies with elite athletes are relatively scant, despite the recognition that diet is an important contributor to sports performance. In this study, stool samples were collected ...
Published on Dec 1, 2018in Nature Communications 11.88
Allison L. Hicks7
Estimated H-index: 7
(Columbia University),
Kerry Jo Lee2
Estimated H-index: 2
(Columbia University)
+ 12 AuthorsAlain Ondzie5
Estimated H-index: 5
(WCS: Wildlife Conservation Society)
The microbiome is essential for extraction of energy and nutrition from plant-based diets and may have facilitated primate adaptation to new dietary niches in response to rapid environmental shifts. Here we use 16S rRNA sequencing to characterize the microbiota of wild western lowland gorillas and sympatric central chimpanzees and demonstrate compositional divergence between the microbiotas of gorillas, chimpanzees, Old World monkeys, and modern humans. We show that gorilla and chimpanzee microb...
Published on Aug 29, 2018in bioRxiv
Miguel Angel Galindo Martín13
Estimated H-index: 13
(UPM: Technical University of Madrid)
Abstract Background: Metagenomics has provided valuable insight into human gut microbiome composition together with its structure and function. Studies suggest that the adult gut microbial community possess a certain amount of stability and resilience. The architecture of host-microbial symbiotic states suggested by microbiome clustering findings and co-occurrence functional networks might be involved in these properties. Models for understanding the underlying structure (including enterotypes) ...
Published on May 1, 2018in British Journal of Dermatology 6.71
Ewan A. Langan13
Estimated H-index: 13
(University of Lübeck),
Griffiths Cem96
Estimated H-index: 96
(University of Manchester)
+ 3 AuthorsDiamant Thaçi35
Estimated H-index: 35
(University of Lübeck)
With several million microbes per cm2 of skin, the task of mapping the physiological cutaneous microbiome is enormous. Indeed, the reliance on bacterial culture to identify cutaneous bacterial communities has led to a systematic under-appreciation of cutaneous microbial diversity, potentially limiting our understanding of common inflammatory skin diseases including psoriasis. However, based heavily on developments in molecular biology and bioinformatics, including next generation sequencing, the...
Published on Jan 1, 2018
José E. Belizário14
Estimated H-index: 14
(USP: University of São Paulo),
Joel Faintuch28
Estimated H-index: 28
(USP: University of São Paulo)
The gastrointestinal (GI) tract is the residence of trillions of microorganisms that include bacteria, archaea, fungi and viruses. The collective genomes of whole microbial communities (microbiota) integrate the gut microbiome. Up to 100 genera and 1000 distinct bacterial species were identified in digestive tube niches. Gut microbiomes exert permanent pivotal functions by promoting food digestion, xenobiotic metabolism and regulation of innate and adaptive immunological processes. Proteins, pep...