Primate microbiomes over time: Longitudinal answers to standing questions in microbiome research

Conservation biology needs a microbial renaissance: a call for the consideration of host-associated microbiota in wildlife management practices

(2019) Brian K. Trevelline et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Interbirth intervals in wild baboons: Environmental predictors and hormonal correlates

(2018) Laurence R. Gesquiere et al.   AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY

Season, age, and sex affect the fecal mycobiota of free-ranging Tibetan macaques (Macaca thibetana )

(2018) Binghua Sun et al.   AMERICAN JOURNAL OF PRIMATOLOGY

Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation

(2018) Christopher S. Smillie et al.   Cell Host & Microbe

Microbial communities as dynamical systems

(2018) Didier Gonze et al.   CURRENT OPINION IN MICROBIOLOGY

Selective maternal seeding and environment shape the human gut microbiome

(2018) Katri Korpela et al.   GENOME RESEARCH

The ecosystem services of animal microbiomes

(2018) E. A. McKenney et al.   MOLECULAR ECOLOGY

Uncovering the drivers of host-associated microbiota with joint species distribution modelling

(2018) Johannes R. Björk et al.   MOLECULAR ECOLOGY

Role of priority effects in the early-life assembly of the gut microbiota

(2018) Daniel Sprockett et al.   Nature Reviews Gastroenterology & Hepatology

Embracing Community Ecology in Plant Microbiome Research

(2018) Francisco Dini-Andreote et al.   TRENDS IN PLANT SCIENCE

Gut microbiomes of wild great apes fluctuate seasonally in response to diet

(2018) Allison L. Hicks et al.   Nature Communications

‘TIME’: A Web Application for Obtaining Insights into Microbial Ecology Using Longitudinal Microbiome Data

(2018) Krishanu D. Baksi et al.   Frontiers in Microbiology

Multilevel social structure and diet shape the gut microbiota of the gelada monkey, the only grazing primate

(2018) Pål Trosvik et al.   Microbiome

MetaLonDA: a flexible R package for identifying time intervals of differentially abundant features in metagenomic longitudinal studies

(2018) Ahmed A. Metwally et al.   Microbiome

Genetic Markers Are Associated with the Ruminal Microbiome and Metabolome in Grain and Sugar Challenged Dairy Heifers

(2018) Helen M. Golder et al.   Frontiers in Genetics

Early and Adult Social Environments Shape Sex-Specific Actuarial Senescence Patterns in a Cooperative Breeder

(2018) Vérane Berger et al.   AMERICAN NATURALIST

Environment dominates over host genetics in shaping human gut microbiota

(2018) Daphna Rothschild et al.   NATURE

Experimental evaluation of the importance of colonization history in early-life gut microbiota assembly

(2018) Inés Martínez et al.   eLife

Divergence of Fecal Microbiota and Their Associations With Host Phylogeny in Cervinae

(2018) Jiaying Li et al.   Frontiers in Microbiology

The microbiome in threatened species conservation

(2018) Annie G. West et al.   BIOLOGICAL CONSERVATION

Coordinated change at the colony level in fruit bat fur microbiomes through time

(2018) Oren Kolodny et al.   Nature Ecology & Evolution

Group Living and Male Dispersal Predict the Core Gut Microbiome in Wild Baboons

(2017) Laura E. Grieneisen et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Modeling time-series data from microbial communities

(2017) Benjamin J Ridenhour et al.   ISME Journal

Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey Species

(2017) Vanessa L. Hale et al.   MICROBIAL ECOLOGY

Patterns in Gut Microbiota Similarity Associated with Degree of Sociality among Sex Classes of a Neotropical Primate

(2017) Katherine R. Amato et al.   MICROBIAL ECOLOGY

Codiversification of gastrointestinal microbiota and phylogeny in passerines is not explained by ecological divergence

(2017) Lucie Kropáčková et al.   MOLECULAR ECOLOGY

Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery

(2017) Derrick M Chu et al.   NATURE MEDICINE

The resilience of the intestinal microbiota influences health and disease

(2017) Felix Sommer et al.   NATURE REVIEWS MICROBIOLOGY

Dispersal limitation promotes the diversification of the mammalian gut microbiota

(2017) Andrew H. Moeller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interhost dispersal alters microbiome assembly and can overwhelm host innate immunity in an experimental zebrafish model

(2017) Adam R. Burns et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hierarchical social networks shape gut microbial composition in wild Verreaux's sifaka

(2017) Amanda C. Perofsky et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Unraveling the processes shaping mammalian gut microbiomes over evolutionary time

(2017) Mathieu Groussin et al.   Nature Communications

Host Genotype and Gut Microbiome Modulate Insulin Secretion and Diet-Induced Metabolic Phenotypes

(2017) Julia H. Kreznar et al.   Cell Reports

Patterns of seasonality and group membership characterize the gut microbiota in a longitudinal study of wild Verreaux's sifakas (Propithecus verreauxi )

(2017) Andrea Springer et al.   Ecology and Evolution

Research priorities for harnessing plant microbiomes in sustainable agriculture

(2017) Posy E. Busby et al.   PLOS BIOLOGY

Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment

(2017) Julia Fukuyama et al.   PLoS Computational Biology

Phenome-wide heritability analysis of the UK Biobank

(2017) Tian Ge et al.   PLoS Genetics

Regulation of life span by the gut microbiota in the short-lived African turquoise killifish

(2017) Patrick Smith et al.   eLife

Evolutionary Biology Needs Wild Microbiomes

(2017) Sarah M. Hird   Frontiers in Microbiology

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

Patterns of Early-Life Gut Microbial Colonization during Human Immune Development: An Ecological Perspective

(2017) Isabelle Laforest-Lapointe et al.   Frontiers in Immunology

The Gut Microbiota of Healthy Aged Chinese Is Similar to That of the Healthy Young

(2017) Gaorui Bian et al.   mSphere

Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling

(2017) Francesco Asnicar et al.   mSystems

The microbiome beyond the horizon of ecological and evolutionary theory

(2017) Britt Koskella et al.   Nature Ecology & Evolution

The multilayer nature of ecological networks

(2017) Shai Pilosof et al.   Nature Ecology & Evolution

Fiber-utilizing capacity varies in Prevotella- versus Bacteroides-dominated gut microbiota

(2017) Tingting Chen et al.   Scientific Reports

Host age, social group, and habitat type influence the gut microbiota of wild ring-tailed lemurs (Lemur catta)

(2016) Genevieve Bennett et al.   AMERICAN JOURNAL OF PRIMATOLOGY

Maternal effects on offspring stress physiology in wild chimpanzees

(2016) Carson M. Murray et al.   AMERICAN JOURNAL OF PRIMATOLOGY

Compositional data analysis of the microbiome: fundamentals, tools, and challenges

(2016) Matthew C.B. Tsilimigras et al.   ANNALS OF EPIDEMIOLOGY

Population- and Individual-Level Dynamics of the Intestinal Microbiota of a Small Primate

(2016) Tuomas Aivelo et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study

(2016) Toshitaka Odamaki et al.   BMC MICROBIOLOGY

Genetic Determinants of the Gut Microbiome in UK Twins

(2016) Julia K. Goodrich et al.   Cell Host & Microbe

Gut microbiota signatures of longevity

(2016) Fanli Kong et al.   CURRENT BIOLOGY

Gut Microbiota and Extreme Longevity

(2016) Elena Biagi et al.   CURRENT BIOLOGY

Navigating the complexity of ecological stability

(2016) Ian Donohue et al.   ECOLOGY LETTERS

When can positive interactions cause alternative stable states in ecosystems?

(2016) Sonia Kéfi et al.   FUNCTIONAL ECOLOGY

Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples

(2016) N. Snyder-Mackler et al.   GENETICS

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

(2016) Stephen Nayfach et al.   GENOME RESEARCH

Fecal Bacterial Composition of Sichuan Snub-Nosed Monkeys (Rhinopithecus roxellana)

(2016) Chun Su et al.   INTERNATIONAL JOURNAL OF PRIMATOLOGY

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

(2016) Sophie Weiss et al.   ISME Journal

Reduced intestinal motility, mucosal barrier function, and inflammation in aged monkeys

(2016) E. L. Mitchell et al.   Journal of Nutrition Health & Aging

Transitioning From Descriptive to Mechanistic Understanding of the Microbiome: The Need for a Prospective Longitudinal Approach to Predicting Disease

(2016) Victoria J. Martin et al.   JOURNAL OF PEDIATRICS

Why are there lasting effects from exposure to stress during development? An analysis of current models of early stress

(2016) Lauren E. Chaby   PHYSIOLOGY & BEHAVIOR

Captivity humanizes the primate microbiome

(2016) Jonathan B. Clayton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prenatal stress effects in a wild, long-lived primate: predictive adaptive responses in an unpredictable environment

(2016) Andreas Berghänel et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Cospeciation of gut microbiota with hominids

(2016) A. H. Moeller et al.   SCIENCE

Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability

(2016) Moran Yassour et al.   Science Translational Medicine

Host genotype and age shape the leaf and root microbiomes of a wild perennial plant

(2016) Maggie R. Wagner et al.   Nature Communications

Signatures of early frailty in the gut microbiota

(2016) Matthew A. Jackson et al.   Genome Medicine

The Woodrat Gut Microbiota as an Experimental System for Understanding Microbial Metabolism of Dietary Toxins

(2016) Kevin D. Kohl et al.   Frontiers in Microbiology

Tracking Strains in the Microbiome: Insights from Metagenomics and Models

(2016) Ilana L. Brito et al.   Frontiers in Microbiology

Female and male life tables for seven wild primate species

(2016) Anne M. Bronikowski et al.   Scientific Data

Social behavior shapes the chimpanzee pan-microbiome

(2016) A. H. Moeller et al.   Science Advances

Early-Life Events, Including Mode of Delivery and Type of Feeding, Siblings and Gender, Shape the Developing Gut Microbiota

(2016) Rocio Martin et al.   PLoS One

Historical Contingency in Community Assembly: Integrating Niches, Species Pools, and Priority Effects

(2015) Tadashi Fukami   Annual Review of Ecology Evolution and Systematics

Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life

(2015) Fredrik Bäckhed et al.   Cell Host & Microbe

The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes

(2015) Aleksandar D. Kostic et al.   Cell Host & Microbe

Metagenomics meets time series analysis: unraveling microbial community dynamics

(2015) Karoline Faust et al.   CURRENT OPINION IN MICROBIOLOGY

Development, diet and dynamism: longitudinal and cross-sectional predictors of gut microbial communities in wild baboons

(2015) Tiantian Ren et al.   ENVIRONMENTAL MICROBIOLOGY

Asynchrony of senescence among phenotypic traits in a wild mammal population

(2015) Adam D. Hayward et al.   EXPERIMENTAL GERONTOLOGY

Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development

(2015) Adam R Burns et al.   ISME Journal

Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species

(2015) Katherine R. Amato et al.   OECOLOGIA

The ecology of the microbiome: Networks, competition, and stability

(2015) K. Z. Coyte et al.   SCIENCE

So Many Variables: Joint Modeling in Community Ecology

(2015) David I. Warton et al.   TRENDS IN ECOLOGY & EVOLUTION

Proportionality: A Valid Alternative to Correlation for Relative Data

(2015) David Lovell et al.   PLoS Computational Biology

Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by Entamoeba and Subsistence

(2015) Elise R. Morton et al.   PLoS Genetics

Social networks predict gut microbiome composition in wild baboons

(2015) Jenny Tung et al.   eLife

Variable responses of human and non-human primate gut microbiomes to a Western diet

(2015) Katherine R. Amato et al.   Microbiome

Ecology of bacteria in the human gastrointestinal tract—identification of keystone and foundation taxa

(2015) Pål Trosvik et al.   Microbiome

Patterns of Gut Bacterial Colonization in Three Primate Species

(2015) Erin A. McKenney et al.   PLoS One

The Evolution of Stomach Acidity and Its Relevance to the Human Microbiome

(2015) DeAnna E. Beasley et al.   PLoS One

Genome-Wide Association Studies of the Human Gut Microbiota

(2015) Emily R. Davenport et al.   PLoS One

Priming for health: gut microbiota acquired in early life regulates physiology, brain and behaviour

(2014) G Clarke et al.   ACTA PAEDIATRICA

The role of gut microbes in satisfying the nutritional demands of adult and juvenile wild, black howler monkeys (Alouatta pigra)

(2014) Katherine R. Amato et al.   AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY

You Are What You Host: Microbiome Modulation of the Aging Process

(2014) Caroline Heintz et al.   CELL

The dynamic microbiome

(2014) Georg K. Gerber   FEBS LETTERS

Compositional and Functional Features of the Gastrointestinal Microbiome and Their Effects on Human Health

(2014) Emily B. Hollister et al.   GASTROENTEROLOGY

Longitudinal study of murine microbiota activity and interactions with the host during acute inflammation and recovery

(2014) Clarissa Schwab et al.   ISME Journal

Biogeography and individuality shape function in the human skin metagenome

(2014) Julia Oh et al.   NATURE

Persistent gut microbiota immaturity in malnourished Bangladeshi children

(2014) Sathish Subramanian et al.   NATURE

Members of the human gut microbiota involved in recovery from Vibrio cholerae infection

(2014) Ansel Hsiao et al.   NATURE

Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression

(2014) Charles K. Fisher et al.   PLoS One

Rapid changes in the gut microbiome during human evolution

(2014) Andrew H. Moeller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Longitudinal analysis of microbial interaction between humans and the indoor environment

(2014) S. Lax et al.   SCIENCE

Diet and the development of the human intestinal microbiome

(2014) Noah Voreades et al.   Frontiers in Microbiology

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

(2014) David Berry et al.   Frontiers in Microbiology

Host lifestyle affects human microbiota on daily timescales

(2014) Lawrence A David et al.   GENOME BIOLOGY

Diversity and Composition of the Adult Fecal Microbiome Associated with History of Cesarean Birth or Appendectomy: Analysis of the American Gut Project

(2014) James J. Goedert et al.   EBioMedicine

Fecal microbiomes of non-human primates in Western Uganda reveal species-specific communities largely resistant to habitat perturbation

(2013) Aleia I. McCord et al.   AMERICAN JOURNAL OF PRIMATOLOGY

Rank effects on social stress in lactating chimpanzees

(2013) A. Catherine Markham et al.   ANIMAL BEHAVIOUR

The importance of species sorting differs between habitat generalists and specialists in bacterial communities

(2013) Anna J. Székely et al.   FEMS MICROBIOLOGY ECOLOGY

Sympatric chimpanzees and gorillas harbor convergent gut microbial communities

(2013) A. H. Moeller et al.   GENOME RESEARCH

Speedy speciation in a bacterial microcosm: new species can arise as frequently as adaptations within a species

(2013) Alexander F Koeppel et al.   ISME Journal

Need for Prospective Cohort Studies to Establish Human Gut Microbiome Contributions to Disease Risk

(2013) V. Mai et al.   JNCI-Journal of the National Cancer Institute

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor

(2013) M. I. Smith et al.   SCIENCE

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Quantitative Genetic Background of the Host Influences Gut Microbiomes in Chickens

(2013) Lele Zhao et al.   Scientific Reports

Cohabiting family members share microbiota with one another and with their dogs

(2013) Se Jin Song et al.   eLife

Senescence in natural populations of animals: Widespread evidence and its implications for bio-gerontology

(2012) Daniel H. Nussey et al.   AGEING RESEARCH REVIEWS

Maternal Effects and the Endocrine Regulation of Mandrill Growth

(2012) ROBIN M. BERNSTEIN et al.   AMERICAN JOURNAL OF PRIMATOLOGY

Effect of Mother's Dominance Rank on Offspring Temperament in Infant Rhesus Monkeys (Macaca mulatta)

(2012) BENJAMIN SUAREZ-JIMENEZ et al.   AMERICAN JOURNAL OF PRIMATOLOGY

Gut microbial colonisation in premature neonates predicts neonatal sepsis

(2012) Juliette C Madan et al.   Archives of Disease in Childhood-Fetal and Neonatal Edition

Gut microbiota composition correlates with diet and health in the elderly

(2012) Marcus J. Claesson et al.   NATURE

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

The keystone-pathogen hypothesis

(2012) George Hajishengallis et al.   NATURE REVIEWS MICROBIOLOGY

Ageing and gut microbes: Perspectives for health maintenance and longevity

(2012) Elena Biagi et al.   PHARMACOLOGICAL RESEARCH

Factors associated with the diversification of the gut microbial communities within chimpanzees from Gombe National Park

(2012) P. H. Degnan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Application of Ecological Theory Toward an Understanding of the Human Microbiome

(2012) E. K. Costello et al.   SCIENCE

Ageing of the human metaorganism: the microbial counterpart

(2011) Elena Biagi et al.   AGE

Generalized linear mixed models for phylogenetic analyses of community structure

(2011) Anthony R. Ives et al.   ECOLOGICAL MONOGRAPHS

Profound Alterations of Intestinal Microbiota following a Single Dose of Clindamycin Results in Sustained Susceptibility to Clostridium difficile-Induced Colitis

(2011) Charlie G. Buffie et al.   INFECTION AND IMMUNITY

Bayesian community-wide culture-independent microbial source tracking

(2011) Dan Knights et al.   NATURE METHODS

Unravelling the effects of the environment and host genotype on the gut microbiome

(2011) Aymé Spor et al.   NATURE REVIEWS MICROBIOLOGY

Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease

(2011) S. Greenblum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aging in the Natural World: Comparative Data Reveal Similar Mortality Patterns Across Primates

(2011) A. M. Bronikowski et al.   SCIENCE

Guidelines for estimating repeatability

(2011) Matthew E. Wolak et al.   Methods in Ecology and Evolution

Moving pictures of the human microbiome

(2011) J Gregory Caporaso et al.   GENOME BIOLOGY

Life history context of reproductive aging in a wild primate model

(2010) Jeanne Altmann et al.   Annals of the New York Academy of Sciences

The Human Gut Microbiome: Ecology and Recent Evolutionary Changes

(2010) Jens Walter et al.   Annual Review of Microbiology

Exposure to a social stressor alters the structure of the intestinal microbiota: Implications for stressor-induced immunomodulation

(2010) Michael T. Bailey et al.   BRAIN BEHAVIOR AND IMMUNITY

Through Ageing, and Beyond: Gut Microbiota and Inflammatory Status in Seniors and Centenarians

(2010) Elena Biagi et al.   PLoS One

Characterization of the Fecal Microbiome from Non-Human Wild Primates Reveals Species Specific Microbial Communities

(2010) Suleyman Yildirim et al.   PLoS One

Strain-resolved community genomic analysis of gut microbial colonization in a premature infant

(2010) M. J. Morowitz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Composition, variability, and temporal stability of the intestinal microbiota of the elderly

(2010) M. J. Claesson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

(2010) L. Dethlefsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns

(2010) M. G. Dominguez-Bello et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conceptual Synthesis in Community Ecology

(2010) Mark Vellend   QUARTERLY REVIEW OF BIOLOGY

The Seven Ages of Pan

(2010) T. Clutton-Brock et al.   SCIENCE

Individuals and populations: the role of long-term, individual-based studies of animals in ecology and evolutionary biology

(2010) Tim Clutton-Brock et al.   TRENDS IN ECOLOGY & EVOLUTION

The Primate Life History Database: a unique shared ecological data resource

(2010) Karen B. Strier et al.   Methods in Ecology and Evolution

Evolutionary Relationships of Wild Hominids Recapitulated by Gut Microbial Communities

(2010) Howard Ochman et al.   PLOS BIOLOGY

The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age

(2009) D Mariat et al.   BMC MICROBIOLOGY

The benefits of social capital: close social bonds among female baboons enhance offspring survival

(2009) J. B. Silk et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Persistence of maternal effects in baboons: Mother's dominance rank at son's conception predicts stress hormone levels in subadult males

(2008) Patrick Ogola Onyango et al.   HORMONES AND BEHAVIOR

Nutritional programming of disease: unravelling the mechanism

(2008) Simon C. Langley-Evans   JOURNAL OF ANATOMY

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE