Microbiota articles within Nature Communications

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  • Article
    | Open Access

    Gut bacteriome dysbiosis has been implicated in the pathogenesis of inflammatory bowel disease (IBD). Here, they authors characterize the small bowel (terminal ileum) virome and bacteriome of patients with Crohn´s Disease (CD), and show that ileal virions from CD patients causally exacerbate intestinal inflammation in IBD mouse models.

    • Zhirui Cao
    • , Dejun Fan
    •  & Tao Zuo

  • Article
    | Open Access

    Here, through parallel profiling of the mucosal transcriptome and microbiome of intestinal biopsies derived from patients with IBD and from non-IBD controls, the authors characterize interactions between gene expression and microbiota composition associated with traits of patients with inflammatory bowel diseases. Peer Review Information: Nature Communications thanks Robert Häsler, and the other, anonymous, reviewers for their contribution to the peer review of this work. A peer review file is available.

    • Shixian Hu
    • , Arno R. Bourgonje
    •  & Rinse K. Weersma

  • Article
    | Open Access

    IgA protects mucosal barriers by coating microorganisms, yet infection related complications are rare in human IgA deficiency. Authors here show that in humans lacking IgA, IgG assists IgM in coating of most bacterial families, thus contributing to gut mucosal defence.

    • Carsten Eriksen
    • , Janne Marie Moll
    •  & Susanne Brix

  • Comment
    | Open Access

    Resveratrol (REV) is a natural polyphenol with anti-obesity effects. However, the mechanisms remain unclear due to its low bioavailability and the lack of defined membrane-bound or nuclear receptors. Pang and colleagues reported that REV intervention (REV-I) alters gut microbiota and bile acid profile, leading to the inhibition of farnesoid X receptor (FXR) and attenuation of scavenger receptor class B type 1 (SR-B1)-mediated chylomicron secretion. This highlights a therapeutic potential of targeting gut microbiome and intestinal SR-B1 for obesity and diabetes treatment.

    • Eryun Zhang
    • , Alon Agua
    •  & Wendong Huang

  • Article
    | Open Access

    Commensal microbes contribute considerably to mammalian metabolism. Here the authors report the relative contributions of microbiome, age and sex to metabolism throughout the body and uncover age- and sex- specificity in how microbes affect metabolite levels in mice.

    • Kirsty Brown
    • , Carolyn A. Thomson
    •  & Kathy D. McCoy

  • Article
    | Open Access

    Dietary glycans are a major driver of the human gut microbiota composition. Here, the authors apply next-generation metabolic labeling coupled with fluorescence-activated cell sorting to identify and isolate gut bacteria consumers of dietary glycans in human stool samples, linking bacteria to the glycans they consume.

    • Lharbi Dridi
    • , Fernando Altamura
    •  & Bastien Castagner

  • Article
    | Open Access

    Gut microbiota composition is altered in patients with alcohol use disorder, and fecal microbiota transplant reduced alcohol craving in patients with alcohol use disorder and liver cirrhosis in a phase 1 clinical trial. Here the authors used stool samples collected in the trial to report that this phenotype is transmissible via microbial transfer to germ free mice, as assessed by reduced ethanol acceptance, intake and preference.

    • Jennifer T. Wolstenholme
    • , Justin M. Saunders
    •  & Jasmohan S. Bajaj

  • Article
    | Open Access

    In a large prospective cohort of liver transplantation (LT) recipients, the authors identify associations between colonization by multidrug-resistant bacteria (MDRB) and microbiome dysbiosis pre- and post-LT, suggesting colonizing MDRB as an important target for microbiome-informed therapeutic approaches post-LT.

    • Medini K. Annavajhala
    • , Angela Gomez-Simmonds
    •  & Anne-Catrin Uhlemann

  • Article
    | Open Access

    The roles played by thrombin in the human intestinal mucosa are unclear. Here, the authors show that the commensal microbiota modulates epithelial production of active thrombin, which controls biofilm growth and contributes to protection of the mucosa from bacterial invasion.

    • Jean-Paul Motta
    • , Alexandre Denadai-Souza
    •  & Nathalie Vergnolle

  • Article
    | Open Access

    The role of the gut microbiota in hepatic lipid metabolism is controversial and incompletely understood. Here the authors perform multi-omics analyses of altered lipid metabolic processes in germ-free and specific pathogen-free mice, revealing how the gut microbiota affects hepatic fatty acid desaturation and elongation.

    • Alida Kindt
    • , Gerhard Liebisch
    •  & Josef Ecker

  • Review Article
    | Open Access

    Gut microbial metabolites are known to impact many physiological processes of the host and play a critical role in immune-homeostasis. Here the authors review our current understanding and appreciation of the importance of microbially derived tryptophan catabolites during both health and disease.

    • Henrik M. Roager
    •  & Tine R. Licht

  • 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

    Short-chain fatty acids (SCFA) are a main class of metabolites derived from fermentation of dietary fibre in the intestine. Here, the authors show that dietary administration of SCFA is associated with inhibition of osteoclast differentiation, increased bone mass, and reduced pathological bone loss in mice.

    • Sébastien Lucas
    • , Yasunori Omata
    •  & Mario M. Zaiss

  • Article
    | Open Access

    Mice deficient in the pro-inflammatory cytokine IFNγ have improved glucose tolerance. Here, the authors show that this effect depends on the gut microbeAkkermansia muciniphila, whose abundance increases in the absence IFNγ, and which is known to have beneficial effects on host metabolism.

    • Renee L. Greer
    • , Xiaoxi Dong
    •  & Natalia Shulzhenko

  • Article
    | Open Access

    The interactions between gut bacteria and enteric pathogens are poorly understood. Here, Yoon et al. show that subinhibitory antibiotic treatment in a mouse model leads to overgrowth of an E. coli strain carrying a catalase-encoding gene that enhances infection with the human pathogen Vibrio cholerae.

    • Mi Young Yoon
    • , Kyung Bae Min
    •  & Sang Sun Yoon

  • Article
    | Open Access

    Commensal microbes are necessary for proper development of the immune system. Here Zanvit et al. show that neonatal antibiotics treatment causes long-term changes in the gut and skin microbiomes, and exacerbates immune-mediated skin pathology at adult age in mouse experimental models of psoriasis.

    • Peter Zanvit
    • , Joanne E. Konkel
    •  & WanJun Chen

  • Article
    | Open Access

    The potential recovery of the human gut microbiota after an antibiotic treatment, and its effects on our health, are poorly understood. Here, the authors use a mouse model mimicking paediatric antibiotic use to shed new light into these processes.

    • Yael R. Nobel
    • , Laura M. Cox
    •  & Martin J. Blaser

  • Article
    | Open Access

    Ganoderma lucidumis a medicinal mushroom used in Traditional Chinese Medicine with putative anti-diabetic properties. Here, the authors show that polysaccharides from a water extract of this mushroom exert beneficial metabolic effects by modulating the composition of the gut microbiota in mice.

    • Chih-Jung Chang
    • , Chuan-Sheng Lin
    •  & Hsin-Chih Lai

  • Article |

    Metabolites produced by the gut microbiota can potentially affect our physiology. Here, the authors present a metabolomics strategy that models microbiota metabolism as a reaction network and uses pathway analysis to facilitate identification and characterization of microbial metabolites.

    • Gautham V. Sridharan
    • , Kyungoh Choi
    •  & Arul Jayaraman

  • Article
    | Open Access

    Diet variations can alter gut microbial composition, but the potential influence of host genetic factors on these effects is unclear. Here, the authors show, in humans and in natural and laboratory fish populations, that such effects are dependent on the host’s sex, a genetically determined factor.

    • Daniel I. Bolnick
    • , Lisa K. Snowberg
    •  & Richard Svanbäck

  • Article
    | Open Access

    Intestinal microbes can have important effects on our health. Here, the authors analyse the gut microbiota composition in 1,000 western adults and find that certain bacteria are either abundant or nearly absent, and that these alternative states are associated with ageing and overweight.

    • Leo Lahti
    • , Jarkko Salojärvi
    •  & Willem M. de Vos

  • Article
    | Open Access

    Gut microbes influence our health and may contribute to human adaptation to different lifestyles. Here, the authors describe the gut microbiome of a community of hunter-gatherers and identify unique features that could be linked to a foraging lifestyle.

    • Stephanie L. Schnorr
    • , Marco Candela
    •  & Alyssa N. Crittenden

  • Article |

    Gut-associated Peyer’s patches are lymphoid tissues that generate IgA-secreting cells, however less is known about related caecal patches. Here, Masahata et al.show that caecal patches produce IgA-positive B cells that migrate to the intestines to maintain faecal microbiota homeostasis.

    • Kazunori Masahata
    • , Eiji Umemoto
    •  & Kiyoshi Takeda

  • Article |

    Antibiotics alter the intestinal microbiota and facilitate colonization of pathogens such as Clostridium difficile. Here, the authors show that antibiotic-induced shifts in the mouse gut microbiome are correlated with changes in levels of certain metabolites that C. difficilecan use for germination and growth.

    • Casey M. Theriot
    • , Mark J. Koenigsknecht
    •  & Vincent B. Young

  • Article
    | Open Access

    The structure of the human gut microbiota has been shown to vary between populations. Tyakht et al.analyse the gut microbiota assembly from Russian individuals living in urban and rural areas, and compare these with previously studied populations.

    • Alexander V. Tyakht
    • , Elena S. Kostryukova
    •  & Vadim M. Govorun

  • Article
    | Open Access

    Calorie restriction has been shown to extend lifespan in diverse model systems, however, the mechanisms underlying this effect remain unclear. Zhang et al.show that calorie restriction changes the structure of the gut microbiota in mice, enriching for phylotypes positively correlated with lifespan.

    • Chenhong Zhang
    • , Shoufeng Li
    •  & Liping Zhao

  • Article
    | Open Access

    The gut microbiota produces metabolites such as short-chain fatty acids (SCFAs), which can influence the development of obesity. Here Kimura et al.show that SCFAs act via the receptor GPR43, which acts as a sensor for excessive dietary energy and controls body energy utilization as well as metabolic homoeostasis.

    • Ikuo Kimura
    • , Kentaro Ozawa
    •  & Gozoh Tsujimoto

  • Article |

    Epithelial cells in the colon mainly use microbial fermentation products as energy sources. Here Okada et al. find that lactate produced by commensal Lactobacillus murinusregulates colonic epithelial cell proliferation and show that mice are more susceptible to carcinogens when refed after a period of starvation.

    • Toshihiko Okada
    • , Shinji Fukuda
    •  & Taeko Dohi

  • Article |

    Humans tend to adopt one of a limited number of different bacterial community structures in the gut, known as enterotypes. Moeller et al.now show that these microbial fingerprints are conserved in chimpanzees, and that individuals can switch between enterotypes over periods of several years.

    • Andrew H. Moeller
    • , Patrick H. Degnan
    •  & Howard Ochman

  • Article
    | Open Access

    The gut is populated by a myriad of microorganisms and how the immune system tolerates their presence is of great interest. Here, by studying colon morphology in multiple knockout mice, the authors demonstrate a potential role for prostaglandin E2 and SOCS1 in mediating immune tolerance.

    • Takatoshi Chinen
    • , Kyoko Komai
    •  & Akihiko Yoshimura

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