Microbial communities articles within Nature Communications

Featured

  • Article
    | Open Access

    The role of ecosystem structure in microbial activity related to greenhouse gas production is poorly understood. Here, Taş and colleagues show that microbial communities and ecosystem function vary across fine-scale topography in a polygonal tundra.

    • Neslihan Taş
    • , Emmanuel Prestat
    •  & Janet K. Jansson

  • Article
    | Open Access

    Gut microbial dysbiosis in infancy is associated with childhood atopy and the development of asthma. Here, the authors show that gut microbiota perturbation is evident in the very earliest stages of postnatal life, continues throughout infancy, and can be partially rescued by Lactobacillus supplementation in high-risk for asthma infants.

    • Juliana Durack
    • , Nikole E. Kimes
    •  & Susan V. Lynch

  • Article
    | Open Access

    Oral microbial communities are excellent sites for examining the mechanisms of structural variation in the microbiota. Here, the authors use spatial and ecological analysis to examine over 9000 dental and mucosal microbiota samples. They find that saliva plays a key role in structuring bacterial communities in the mouth.

    • Diana M. Proctor
    • , Julia A. Fukuyama
    •  & David A. Relman

  • Article
    | Open Access

    Colonization of commensal bacteria is thought to impact immune development, especially in the earliest years of life. Here, the authors show, by analyzing the development of the gut microbiome of 690 children, that microbial composition at the age of 1 year is associated with asthma diagnosed in the first 5 years of life.

    • Jakob Stokholm
    • , Martin J. Blaser
    •  & Hans Bisgaard

  • Article
    | Open Access

    Metagenomic sequencing provides a window into microbial community structure and metabolic potential. Here, Swenson et al. integrate metabolomics and shotgun sequencing to functionally link microbial community structure with environmental chemistry in biological soil crust (biocrust).

    • Tami L. Swenson
    • , Ulas Karaoz
    •  & Trent R. Northen

  • Article
    | Open Access

    Microbiota is often a complex mixture of multiple coexisting species and strains with high level of phenotypic and genomic variability. Here, Albanese and Donati develop StrainEst for estimating the number and identity of coexisting strains and their relative abundances in mixed metagenomic samples.

    • Davide Albanese
    •  & Claudio Donati

  • Article
    | Open Access

    Understanding ecological interactions in microbial communities is limited by lack of informative longitudinal abundance data necessary for reliable inference. Here, Xiao et al. develop a method to infer the interactions between microbes based on their abundances in steady-state samples.

    • Yandong Xiao
    • , Marco Tulio Angulo
    •  & Yang-Yu Liu

  • Article
    | Open Access

    Reported associations between the human microbiome and disease are often inconsistent. Here, Duvallet et al. perform a meta-analysis of 28 gut microbiome studies spanning ten diseases, and find associations that are likely not disease-specific but potentially part of a shared response to disease.

    • Claire Duvallet
    • , Sean M. Gibbons
    •  & Eric J. Alm

  • Article
    | Open Access

    It is thought that the hospital environment may contribute to infant microbiome development. Here, Brooks et al. present a genome-resolved metagenomic study of microbial genotypes from the infant gut and from neonatal intensive care unit rooms, showing that some strains are found in both infants and rooms.

    • Brandon Brooks
    • , Matthew R. Olm
    •  & Jillian F. Banfield

  • Article
    | Open Access

    There is a need for improved in vitro models of host-microbe interactions in the lung. Here, Barkal et al. present a microscale organotypic model of the human bronchiole for studying pulmonary infection, including volatile compound communication between microbial populations and host cells.

    • Layla J. Barkal
    • , Clare L. Procknow
    •  & David J. Beebe

  • Article
    | Open Access

    It is unclear whether the transfer of plasmids carrying antibiotic resistance genes can explain their persistence when antibiotics are not present. Here, Lopatkin et al. show that conjugal plasmids, even when costly, are indeed transferred at sufficiently high rates to be maintained in the absence of antibiotics.

    • Allison J. Lopatkin
    • , Hannah R. Meredith
    •  & Lingchong You

  • Article
    | Open Access

    Variations in the gut microbiota may affect the host’s performance in changing environments. Here, Macke et al. show, in the freshwater crustacean Daphnia magna, that host genotype and external microbial inoculum interact to shape the gut microbiota, which in turns mediates tolerance to toxic cyanobacteria.

    • Emilie Macke
    • , Martijn Callens
    •  & Ellen Decaestecker

  • Article
    | Open Access

    Convenient methods for assessing microbial community structure in terms of biomass are lacking. Here, the authors present a metaproteomics-based approach for assessing microbial community structure using protein abundance as a measure for biomass contributions of individual populations.

    • Manuel Kleiner
    • , Erin Thorson
    •  & Marc Strous

  • Article
    | Open Access

    Little is known about Marinimicrobia, a group of bacteria that are prevalent in the oceans. Here, the authors study global populations of Marinimicrobia using single-cell genomics, metagenomics and metatranscriptomics, showing potential co-metabolic interactions and participation in the sulfur and nitrogen cycles.

    • Alyse K. Hawley
    • , Masaru K. Nobu
    •  & Steven J. Hallam

  • Article
    | Open Access

    The microbiota promotes resistance to respiratory infection through unclear mechanisms. Here, the authors identify members of the gut and upper airway microbiota that protect against respiratory infection by Streptococcus pneumoniae and Klebsiella pneumoniae by activating GM-CSF signaling.

    • Rebecca L. Brown
    • , Richard P. Sequeira
    •  & Thomas B. Clarke

  • Article
    | Open Access

    Microbes live in communities and exchange metabolites, but the resulting dynamics are poorly understood. Here, the authors study the interplay between metabolite production strategies and population dynamics, and find that complex and unexpected dynamics emerge even in simple microbial economies.

    • Yoav Kallus
    • , John H. Miller
    •  & Eric Libby

  • Article
    | Open Access

    Peptide CSP regulates natural competence in pneumococci and has been proposed as a quorum-sensing signal or a probe for sensing environmental cues. Here, the authors show that CSP levels can indeed act as an indicator of cell density and also incorporate information on environmental factors or cell history.

    • Stefany Moreno-Gámez
    • , Robin A. Sorg
    •  & Jan-Willem Veening

  • Article
    | Open Access

    The gut microbiota may play a role in cardiovascular diseases. Here, the authors perform a metagenome-wide association study on stools from individuals with atherosclerotic cardiovascular disease and healthy controls, identifying microbial strains and functions associated with the disease.

    • Zhuye Jie
    • , Huihua Xia
    •  & Karsten Kristiansen

  • Article
    | Open Access

    Certain neuropeptides, in addition to their neuromodulatory functions, display antibacterial activities of unclear significance. Here, the authors show that a secreted neuropeptide modulates the distribution of bacterial communities on the body surface during development of the model organism Hydra.

    • René Augustin
    • , Katja Schröder
    •  & Thomas C. G. Bosch

  • Article
    | Open Access

    High or multiple doses of macrolide antibiotics, when given early in life, can perturb the metabolic and immunological development of lab mice. Here, Ruiz et al. show that even a single macrolide course, given early in life, leads to long-lasting changes in the gut microbiota and immune system of mice.

    • Victoria E. Ruiz
    • , Thomas Battaglia
    •  & Martin J. Blaser

  • Article
    | Open Access

    Environmental factors often outweigh host heritable factors in structuring host-associated microbiomes. Here, Bowen et al. show that host lineage is crucial for determination of rhizosphere bacterial communities in Phragmites australis, a globally distributed invasive plant.

    • Jennifer L. Bowen
    • , Patrick J. Kearns
    •  & Laura A. Meyerson

  • Article
    | Open Access

    Some bacteria can feed on live fungi through unclear mechanisms. Here, the authors show that a T3SS-secreted protein, which is homologous to phage tail proteins, allows a Burkholderia gladioli strain to kill and feed on various fungal species.

    • Durga Madhab Swain
    • , Sunil Kumar Yadav
    •  & Gopaljee Jha

  • Article
    | Open Access

    Bacteria can exchange nutrients and macromolecules through tubular membranous structures called nanotubes. Here, the authors show that Bacillus subtilis can kill and prey on Bacillus megaterium by delivering a toxin and extracting nutrients in a nanotube-dependent manner.

    • Ofer Stempler
    • , Amit K. Baidya
    •  & Sigal Ben-Yehuda

  • Article
    | Open Access

    Cooperative behaviour among individuals provides a collective benefit, but is considered costly. Using Pseudomonas aeruginosa as a model system, the authors show that secretion of the siderophore pyoverdine only incurs a fitness cost and favours cheating when its building blocks carbon or nitrogen are growth-limiting.

    • D. Joseph Sexton
    •  & Martin Schuster

  • Article
    | Open Access

    Planktonic bacteria are untethered to surfaces or to each other, and thus are expected to move independently when at low cell densities. Here Sretenovic et al. show, using optical tweezers, that bacteria in dilute suspensions are mechanically coupled and show long-range correlated motion.

    • Simon Sretenovic
    • , Biljana Stojković
    •  & David Stopar

  • Article
    | Open Access

    Early-life microbiota alterations can affect infection susceptibility later in life, in animal models. Here, Knutie et al. show that manipulating the microbiota of tadpoles leads to increased susceptibility to parasitic infection in adult frogs, in the absence of substantial changes in the adults’ microbiota.

    • Sarah A. Knutie
    • , Christina L. Wilkinson
    •  & Jason R. Rohr

  • Article
    | Open Access

    Viruses play an important role in microbial communities but, due to limitations of available techniques, our understanding of viral diversity is limited. Here, the authors use SVGs and identify highly abundant viruses in marine communities that have been previously overlooked.

    • Francisco Martinez-Hernandez
    • , Oscar Fornas
    •  & Manuel Martinez-Garcia

  • Article
    | Open Access

    The metabolic interactions between gut microbes and host cells play roles in human health. Here, Sunget al. present a literature-curated metabolic network of the human gut microbiota and three human cell types, together with a mathematical approach to identify distinct microbial and metabolic features in gut microbiomes.

    • Jaeyun Sung
    • , Seunghyeon Kim
    •  & Pan-Jun Kim

  • Article
    | Open Access

    Crystalline uraninite is believed to be the dominant form in uranium deposits. Here, the authors find that non-crystalline U(IV) generated through biologically mediated U(VI) reduction is the predominant U(IV)species in ore deposits, implying that biogenic processes are more important than previously thought.

    • Amrita Bhattacharyya
    • , Kate M. Campbell
    •  & Thomas Borch

  • Article
    | Open Access

    There is concern about potential long-term effects of antibiotics on children’s health. Here Leclercqet al. show, in mice, that low doses of penicillin during late pregnancy and early life induce lasting effects on the offspring, including alterations in gut microbiota, brain cytokine levels and behaviour.

    • Sophie Leclercq
    • , Firoz M. Mian
    •  & John Bienenstock

  • Article
    | Open Access

    Both host diet and phylogeny have been argued to shape mammalian microbiome communities. Here, the authors show that diet predicts the presence of ancient bacterial lineages in the microbiome, but that co-speciation between more recent bacterial lineages and their hosts may drive associations between microbiome composition and phylogeny.

    • Mathieu Groussin
    • , Florent Mazel
    •  & Eric J. Alm

  • Article
    | Open Access

    Currently available metagenomic data analysis relies on reference genomes. Here, the authors describe a newde novometagenomic assembly method, metaSort, that constructs bacterial genomes from metagenomic samples to reduce microbial community complexity while increasing genome recovery and assembly.

    • Peifeng Ji
    • , Yanming Zhang
    •  & Fangqing Zhao

  • Article
    | Open Access

    Host-associated microbial communities can shift in structure or function when hosts change locations. Bletzet al. reciprocally transfer salamander larvae between pond and stream habitats to show that gut microbiomes shift in function, but not necessarily taxonomic identities, when hosts encounter a new environment.

    • Molly C. Bletz
    • , Daniel J. Goedbloed
    •  & Sebastian Steinfartz

  • Article
    | Open Access

    Crohn’s disease is associated with altered intestinal microbiota. Here, the authors show that the microbe Atopobium parvulumis associated with Crohn’s disease patients, triggers colitis in a mouse model, and that scavenging microbe-induced hydrogen sulfide improved symptoms in mice.

    • Walid Mottawea
    • , Cheng-Kang Chiang
    •  & Alain Stintzi

Browse broader subjects

Browse narrower subjects

Browse Microbial communities across other nature.com journals