Microbiome articles within Nature Communications

Featured

• Article
  20 September 2023 | Open Access

  A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil

  Rewetting of seasonally dry soils induces dramatic shifts in viral biomass and diversity. Combining stable isotope probing, metagenomics, and viromics Nicolas et al. provide evidence that viral lysis contributes to microbial turnover and the associated CO₂ efflux.

  • Alexa M. Nicolas
  • , Ella T. Sieradzki
  •  & Steven J. Blazewicz

• Article
  18 September 2023 | Open Access

  Ecophysiology and interactions of a taurine-respiring bacterium in the mouse gut

  Authors utilise a multi-omics approach for the ecophysiological characterization of a taurine-respiring mouse gut bacterium.

  • Huimin Ye
  • , Sabrina Borusak
  •  & Alexander Loy

• Article
  16 September 2023 | Open Access

  Bridging of host-microbiota tryptophan partitioning by the serotonin pathway in fungal pneumonia

  Serotonin regulates mood as well as intestinal homeostasis, but its role in lung immune homeostasis is less clear. Here, Renga et al. show that serotonin regulates immune and microbial metabolic functions in respiratory pneumonia, beyond its mood regulatory function, by modulating tryptophan metabolism in the cystic fibrosis lung.

  • Giorgia Renga
  • , Fiorella D’Onofrio
  •  & Luigina Romani

• Article
  14 September 2023 | Open Access

  Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes

  Here, the authors present a novel approach for inferring in vivo growth phases of human gut bacteria from metagenomic time series data. These inferences can be used to better-constrain community scale metabolic modeling in the gut.

  • Joe J. Lim
  • , Christian Diener
  •  & Sean M. Gibbons

• Article
  01 September 2023 | Open Access

  The interplay between dietary fatty acids and gut microbiota influences host metabolism and hepatic steatosis

  Here, Schoeler et al. investigate how interaction between dietary lipids and the gut microbiota affect hepatic steatosis and host metabolism, showing that dietary lipids impact the gut microbiota composition independent on fiber intake in humans and mice.

  • Marc Schoeler
  • , Sandrine Ellero-Simatos
  •  & Robert Caesar

• Article
  29 August 2023 | Open Access

  Delayed gut microbiota maturation in the first year of life is a hallmark of pediatric allergic disease

  Here, using participants in the CHILD birth cohort, the authors reveal that impaired 1-year microbiota maturation may be universal to 5-year pediatric allergies, mediated by functional and metabolic imbalances of compromised mucous integrity, elevated oxidative activity, decreased fermentation, and elevated trace amines.

  • Courtney Hoskinson
  • , Darlene L. Y. Dai
  •  & Stuart E. Turvey

• Article
  24 August 2023 | Open Access

  Fiber supplementation protects from antibiotic-induced gut microbiome dysbiosis by modulating gut redox potential

  Here, the authors show that fiber supplementation protects from antibiotic-induced gut microbiome damage by reducing the abundance of aerobic bacteria as well as metabolic pathways associated with oxidative metabolism.

  • Swathi Penumutchu
  • , Benjamin J. Korry
  •  & Peter Belenky

• Article
  22 August 2023 | Open Access

  Antibiotics promote intestinal growth of carbapenem-resistant Enterobacteriaceae by enriching nutrients and depleting microbial metabolites

  Broad-spectrum antibiotics can kill harmless bacteria in our intestine, thus facilitating invasion by antibiotic-resistant bacteria such as carbapenem-resistant Enterobacteriaceae (CRE). Here, Yip et al. show that killing gut bacteria with antibiotics leads to enrichment of nutrients and depletion of inhibitory microbial metabolites, which overall potentiates CRE growth.

  • Alexander Y. G. Yip
  • , Olivia G. King
  •  & Julie A. K. McDonald

• Article
  14 August 2023 | Open Access

  Systematic review of cnidarian microbiomes reveals insights into the structure, specificity, and fidelity of marine associations

  This study unified cnidarian microbiome data from 186 studies (~ 6.5 billion sequence reads), providing novel insights into cnidarian microbial communities and highlighting key bacteria across sub-phylum, geography, depth and microhabitat. Understanding factors governing microbiome health will support ongoing and future coral preservation efforts.

  • M. McCauley
  • , T. L. Goulet
  •  & S. Loesgen

• Article
  12 August 2023 | Open Access

  Characterization of the pig lower respiratory tract antibiotic resistome

  Antibiotic resistance is a risk for human and pig health. Here, the authors profile the antibiotic resistome of the pig lower respiratory tract and evaluate potential mobile genetic elements mediating antibiotic resistance gene transfer.

  • Yunyan Zhou
  • , Jingquan Li
  •  & Lusheng Huang

• Article
  08 August 2023 | Open Access

  Nutritional and host environments determine community ecology and keystone species in a synthetic gut bacterial community

  Here, characterizing a synthetic gut bacterial community, the authors reveal a context dependency of keystone functions and bacterial interaction networks, challenging the concept of universal keystone species in the gastrointestinal ecosystem.

  • Anna S. Weiss
  • , Lisa S. Niedermeier
  •  & Bärbel Stecher

• Article
  26 July 2023 | Open Access

  Tapping the rhizosphere metabolites for the prebiotic control of soil-borne bacterial wilt disease

  Prebiotics can be used to encourage beneficial organisms. Here, the authors select rhizosphere metabolites that can be used as prebiotics to reduce the effect of the plant pathogen Ralstonia.

  • Tao Wen
  • , Penghao Xie
  •  & Jun Yuan

• Article
  18 July 2023 | Open Access

  Characterization of crAss-like phage isolates highlights Crassvirales genetic heterogeneity and worldwide distribution

  Here, the authors report the isolation and genetic characterization of 25 unique crAss-like phages (termed “crAssBcn”) infecting Bacteroides intestinalis, and show that CrAssBcn phages are commonly found in fecal samples from people around the globe, indicating their wide distribution.

  • María Dolores Ramos-Barbero
  • , Clara Gómez-Gómez
  •  & Maite Muniesa

• Article
  14 July 2023 | Open Access

  Genetic strategies for sex-biased persistence of gut microbes across human life

  Here, via analyses of shotgun metagenomic sequencing data of more than 12,000 fecal microbiomes from healthy individuals, the authors reveal the presence of microbiome genetic traits involved in host mucin metabolism, supporting colonization and persistence of specific bacterial strains preferentially in the intestinal environment of women compared to men.

  • Chiara Tarracchini
  • , Giulia Alessandri
  •  & Marco Ventura

• Article
  12 July 2023 | Open Access

  Abrupt perturbation and delayed recovery of the vaginal ecosystem following childbirth

  Childbirth prompts a vaginal inflammatory response and loss of Lactobacillus dominance. This disturbance, the authors show, reverberates deep into the first postpartum year, with evidence of recovery in only 49% of women by year’s end.

  • Elizabeth K. Costello
  • , Daniel B. DiGiulio
  •  & David A. Relman

• Article
  06 July 2023 | Open Access

  TET2 and TET3 loss disrupts small intestine differentiation and homeostasis

  DNA demethylation is known to be critical for the development and function of many tissues. Here the authors show that it is also required for intestinal lineage differentiation, and that mice lacking DNA demethylases have altered microbiomes and a predisposition to inflammation.

  • Ihab Ansari
  • , Llorenç Solé-Boldo
  •  & Yehudit Bergman

• Article
  20 June 2023 | Open Access

  Gut microbiota Turicibacter strains differentially modify bile acids and host lipids

  Mechanisms by which the gut microbiota affects its host are a main research focus. Here, Lynch et al. characterize bile acid modifications performed by a prevalent bacterial taxon from the gut, the genus Turicibacter, and found they broadly altered host lipids, connecting Turicibacter functions and host physiology.

  • Jonathan B. Lynch
  • , Erika L. Gonzalez
  •  & Elaine Y. Hsiao

• Article
  20 June 2023 | Open Access

  Global branches and local states of the human gut microbiome define associations with environmental and intrinsic factors

  Here, applying an ecological framework to cross-sectional and longitudinal data, the authors identify major branches of the human gut microbiome across the lifespan that connect local ecological states, allowing to better capture associations with health, diet, and lifestyle.

  • Julien Tap
  • , Franck Lejzerowicz
  •  & Muriel Derrien

• Article
  17 June 2023 | Open Access

  A data-driven approach for predicting the impact of drugs on the human microbiome

  Drugs can impact the gut microbiome. Here, Algavi and Borenstein developed a machine-learning framework that successfully predicts the impact of thousands of drugs on hundreds of gut microbes, explaining drug-induced dysbiosis and side effects.

  • Yadid M. Algavi
  •  & Elhanan Borenstein

• Article
  14 June 2023 | Open Access

  Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization

  The organization of gut microbes in lumen and mucosa and the microbial genes regulating this organization remain poorly understood. Here, using in vitro cultures incorporating a complex gut microbial community in mucin-hydrogel carriers, the authors show greater richness and strain-specific spatial organization, enabling discovery of associated genes.

  • Xiaofan Jin
  • , Feiqiao B. Yu
  •  & Katherine S. Pollard

• Article
  13 June 2023 | Open Access

  Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems

  Microbes in ancient groundwaters can be very diverse and productive. Some microbes seem to produce oxygen in the dark, which others use to consume the greenhouse gas methane. Their metabolisms are relevant for groundwater health and global change.

  • S. Emil Ruff
  • , Pauline Humez
  •  & Marc Strous

• Article
  10 June 2023 | Open Access

  Revealing proteome-level functional redundancy in the human gut microbiome using ultra-deep metaproteomics

  Here, Li et al. show that functional redundancy, which has not previously been quantified at the proteome level, can arise when different microbes play similar roles in the gut microbiome, revealing that proteomes are nested among gut microbes, favoring high functional redundancy.

  • Leyuan Li
  • , Tong Wang
  •  & Daniel Figeys

• Article
  07 June 2023 | Open Access

  A probiotic bi-functional peptidoglycan hydrolase sheds NOD2 ligands to regulate gut homeostasis in female mice

  Lactobacillus-based probiotics have been reported to be beneficial for colitis through incompletely understood mechanisms. Here the authors identify an uncharacterized secreted enzyme named LPH from multiple probiotic Lactobacillus strains, which protects female mice from chemically induced colitis and colorectal cancer via NOD2 signalling.

  • Jie Gao
  • , Lei Wang
  •  & Xiaolong He

• Article
  01 June 2023 | Open Access

  Diversity of the Pacific Ocean coral reef microbiome

  Using data from the Tara Pacific expedition, this study reports the biogeography and the diversity of microbiomes collected from corals, fish and plankton in 99 reefs across the Pacific Ocean. The large richness of Pacific Ocean reef microorganisms, when extrapolated to all fish and corals of the Pacific, represents the current estimated total prokaryotic diversity for the entire Earth.

  • Pierre E. Galand
  • , Hans-Joachim Ruscheweyh
  •  & Serge Planes

• Article
  31 May 2023 | Open Access

  Host-diet-gut microbiome interactions influence human energy balance: a randomized clinical trial

  The gut microbiome is causally linked to body weight in preclinical models. Here, in a controlled feeding study, the authors show that greater delivery of gut-microbiome fermentable dietary substrates to the colon leads to a net negative energy balance that is accompanied by robust microbial and host responses.

  • Karen D. Corbin
  • , Elvis A. Carnero
  •  & Steven R. Smith

• Article
  25 May 2023 | Open Access

  Detailed mapping of Bifidobacterium strain transmission from mother to infant via a dual culture-based and metagenomic approach

  Here, the authors combine isolation and sequencing of bacteria from both mothers and infants and to show that several microbial strains are commonly transferred, including from the genus Bifidobacterium, with factors that influencing transfer including delivery mode and exposure to antibiotics in labour.

  • Conor Feehily
  • , Ian J. O’Neill
  •  & Paul D. Cotter

• Article
  17 May 2023 | Open Access

  Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater

  Sapoval et al. introduce QuaID, a bioinformatics tool for SARS-CoV-2 variant detection based on quasi-unique mutations. QuaID leverages all mutations, including insertions and deletions, and provides precise detection of variants early in their spread.

  • Nicolae Sapoval
  • , Yunxi Liu
  •  & Todd J. Treangen

• Article
  26 April 2023 | Open Access

  Modulation of antibiotic effects on microbial communities by resource competition

  Antibiotics impact the gut microbiota in complex ways. Here, employing ecological models of resource competition, Newton et al. elucidate species coexistence patterns under resource competition and species-specific death rates, providing a model to predict microbiota dynamics under deleterious perturbations.

  • Daniel P. Newton
  • , Po-Yi Ho
  •  & Kerwyn Casey Huang

• Article
  13 April 2023 | Open Access

  Previously uncharacterized rectangular bacterial structures in the dolphin mouth

  Dudek et al. describe rectangular bacterial structures in the mouths of dolphins. Using various genomic and microscopy techniques, they show that the structures consist of bacterial cells that appear to divide along the longitudinal axis and display other unusual features.

  • Natasha K. Dudek
  • , Jesus G. Galaz-Montoya
  •  & David A. Relman

• Article
  11 April 2023 | Open Access

  Anaerobic thiosulfate oxidation by the Roseobacter group is prevalent in marine biofilms

  Thiosulfate oxidation by microbes has a major impact on global sulfur cycling. Here, Ding et al. provide evidence that bacteria of the Roseobacter group are major thiosulfate-oxidizers in marine biofilms, where anaerobic thiosulfate metabolism is preferred.

  • Wei Ding
  • , Shougang Wang
  •  & Weipeng Zhang

• Article
  01 April 2023 | Open Access

  Sialidases and fucosidases of Akkermansia muciniphila are crucial for growth on mucin and nutrient sharing with mucus-associated gut bacteria

  This study offers molecular insight into the sialidase and fucosidase decapping apparatus that initiates growth on mucin and promotes nutrient sharing by the dedicated mucolytic symbiont Akkermansia muciniphila with the mucus-associated microbiota.

  • Bashar Shuoker
  • , Michael J. Pichler
  •  & Maher Abou Hachem

• Article
  01 April 2023 | Open Access

  Parabacteroides distasonis ameliorates hepatic fibrosis potentially via modulating intestinal bile acid metabolism and hepatocyte pyroptosis in male mice

  Parabacteroides distasonis (P. distasonis), part of the gut microbiome, was reported to play a role in diabetes, colorectal cancer and inflammatory bowel disease. Here the authors report that P. distasonis ameliorates liver fibrosis in studies with male mice, potentially via altered bile acid metabolism and hepatocyte pyroptosis.

  • Qi Zhao
  • , Man-Yun Dai
  •  & Fei Li

• Article
  24 March 2023 | Open Access

  The core metabolome and root exudation dynamics of three phylogenetically distinct plant species

  Root exudates display a diurnal signature, change with growth environment, and can be divided into a core metabolome common to multiple plant species, and specialized exudates produced by distinct species.

  • Sarah McLaughlin
  • , Kateryna Zhalnina
  •  & Joelle Sasse

• Article
  11 March 2023 | Open Access

  Clinical NEC prevention practices drive different microbiome profiles and functional responses in the preterm intestine

  Here, the authors comparatively analyze the impact of three successful clinical preventive interventions against NEC in preterm, VLBW infants and demonstrate a major impact of especially probiotic-based strategies on the development and maturation of the gut microbiome.

  • Charlotte J. Neumann
  • , Alexander Mahnert
  •  & Christine Moissl-Eichinger

• Article
  09 March 2023 | Open Access

  Gut microbiota alters host bile acid metabolism to contribute to intrahepatic cholestasis of pregnancy

  Intrahepatic cholestasis of pregnancy (ICP) is a liver disease that sometimes develops during pregnancy and is characterized by increased serum bile acid levels. Here the authors report that the gut microbiome species B. fragilis is enriched in patients with ICP and promotes ICP development in mice via inhibition of signalling though the bile acid receptor FXR.

  • Bo Tang
  • , Li Tang
  •  & Shiming Yang

• Article
  23 February 2023 | Open Access

  Seasonal activities of the phyllosphere microbiome of perennial crops

  Understanding the interactions between plants and microorganisms can inform microbiome management to enhance crop productivity and resilience to stress. Here, Howe et al. use metagenomics and metatranscriptomics to study changes in the leaf microbiome of perennial crops over two growing seasons.

  • Adina Howe
  • , Nejc Stopnisek
  •  & Ashley Shade

• Article
  18 February 2023 | Open Access

  An open label, non-randomized study assessing a prebiotic fiber intervention in a small cohort of Parkinson’s disease participants

  This study found that a prebiotic intervention was well-tolerated and safe, beneficially changed the microbiome, decreased inflammation and a marker of neurodegeneration, with possible clinical effects in Parkinson’s disease (PD) patients. This study offers the rationale for further investigations using prebiotic fibers in PD.

  • Deborah A. Hall
  • , Robin M. Voigt
  •  & Ali Keshavarzian

• Article
  14 February 2023 | Open Access

  The gut microbiome and early-life growth in a population with high prevalence of stunting

  Here, using metagenomics, the authors show that the gut microbiome of rural Zimbabwean infants undergoes programmed maturation that is unresponsive to sanitation and nutrition interventions but is strongly associated with maternal HIV infection and can moderately predict linear growth.

  • Ruairi C. Robertson
  • , Thaddeus J. Edens
  •  & Amee R. Manges

• Article
  14 February 2023 | Open Access

  Impact of diet and host genetics on the murine intestinal mycobiome

  In this study, 591 mice from an advanced-intercross mouse line were used to provide evidence that fungi are regulated by host genetics, while uncovering a regulatory role of diet on the composition of fungi in the murine gut.

  • Yask Gupta
  • , Anna Lara Ernst
  •  & Tanya Sezin

• Article
  06 February 2023 | Open Access

  Microbiota-derived acetate enhances host antiviral response via NLRP3

  The NLRP3 inflammasome plays a pivotal role in clearing viral respiratory infection, but the molecular mechanism is not fully known. Here authors show that acetate, produced by gut bacteria, may enhance NLRP3-mediated type I interferon production following influenza infection in mice.

  • Junling Niu
  • , Mengmeng Cui
  •  & Guangxun Meng

• Article
  30 January 2023 | Open Access

  Microbially produced vitamin B12 contributes to the lipid-lowering effect of silymarin

  Silymarin has been used for improving hepatic damage and lipid disorders, but its action mechanism remains to be clarified. Here, the authors reveal a mechanism of action underpinning the lipid-lowering effect of silymarin via the gut microbiota and its vitamin B12 producing capabilities.

  • Wen-Long Sun
  • , Sha Hua
  •  & Hong-Fang Ji

• Article
  30 January 2023 | Open Access

  Copper intrauterine device increases vaginal concentrations of inflammatory anaerobes and depletes lactobacilli compared to hormonal options in a randomized trial

  Here, in a randomized trial, the authors comparatively evaluate the effect of a copper intrauterine device versus other contraceptive options on the vaginal environment after one and six consecutive months of use, finding to exert changes on the vaginal microbiota that may potentially lead to detrimental sex and reproductive health.

  • Bryan P. Brown
  • , Colin Feng
  •  & Heather B. Jaspan

• Article
  13 January 2023 | Open Access

  Gut microbiome dysbiosis drives metabolic dysfunction in Familial dysautonomia

  Familial dysautonomia is a rare genetic disease caused in part by neurodegeneration. Here, the authors show that the gut-metabolism axis is altered in both patients and transgenic mice and that disease pathology is ameliorated by controlling microbiome divergence.

  • Alexandra M. Cheney
  • , Stephanann M. Costello
  •  & Seth T. Walk

• Article
  05 January 2023 | Open Access

  Gut colonisation with multidrug-resistant Klebsiella pneumoniae worsens Pseudomonas aeruginosa lung infection

  Gut microbiome dysbiosis has been shown to alter the immune response to lung infection. Authors utilise a murine model to investigate if gut colonisation with carbapenemase-producing Enterobacterales altered the outcomes of Pseudomonas aeruginosa lung infection.

  • Rémi Le Guern
  • , Teddy Grandjean
  •  & Rodrigue Dessein

• Article
  22 December 2022 | Open Access

  Cross-kingdom synthetic microbiota supports tomato suppression of Fusarium wilt disease

  Rhizosphere microbiota can influence plant pathogen interactions. Here the authors use field- and lab-based approaches to show that rhizosphere bacteria and fungi of healthy tomatoes can enhance tomato resistance against Fusarium wilt disease and formulate synthetic microbial communities that could help to control soil-borne disease.

  • Xin Zhou
  • , Jinting Wang
  •  & Lei Cai

• Article
  20 December 2022 | Open Access

  Chronic exposure to synthetic food colorant Allura Red AC promotes susceptibility to experimental colitis via intestinal serotonin in mice

  Allura Red AC is a dye used in food products. Here the authors report that chronic, long-term exposure to Allura Red AC increases susceptibility to experimental colitis in mice dependent on the serotonin biosynthetic enzyme TPH1, while intermittent exposure more typical for the human setting did not increase susceptibility to experimental colitis.

  • Yun Han Kwon
  • , Suhrid Banskota
  •  & Waliul I. Khan

• Article
  06 December 2022 | Open Access

  The gut microbiota and depressive symptoms across ethnic groups

  Here, by studying a multi-ethnic cross-sectional urban cohort (N = 3211, 6 ethnic groups), the authors show that depressive symptom levels are related to the gut microbiota taxonomic characteristics but that these are largely invariant across ethnic groups.

  • Jos A. Bosch
  • , Max Nieuwdorp
  •  & Anja Lok

• Article
  06 December 2022 | Open Access

  Gut microbiome-wide association study of depressive symptoms

  Here, the authors analyze the relation of fecal microbiota diversity and composition with depressive symptoms in 1,054 participants from the Rotterdam Study cohort and in 1,539 subjects of the Amsterdam HELIUS cohort, finding associations with bacteria known to be involved in the synthesis of key neurotransmitters for depression.

  • Djawad Radjabzadeh
  • , Jos A. Bosch
  •  & Najaf Amin

• Article
  05 December 2022 | Open Access

  Impact of international travel and diarrhea on gut microbiome and resistome dynamics

  Here, the authors characterize the microbiome and resistome in a longitudinal cohort of 159 international students visiting the Andean city of Cusco, Peru. They find that international travel associates with spread of antimicrobial resistance, and that travelers’ diarrhea increases a persons’ risk for acquiring antimicrobial-resistant pathogens, while a diverse, “healthy” microbiome can be protective against diarrhea.

  • Manish Boolchandani
  • , Kevin S. Blake
  •  & Gautam Dantas

• Article
  01 December 2022 | Open Access

  Strong pathogen competition in neonatal gut colonisation

  Opportunistic bacterial pathogen species frequently colonise the human gut as a normal part of the ecosystem but strain-level colonisation and competition dynamics in healthy hosts is yet to be established. Authors seek to understand the relationship between colonisation potential and ecological factors modulating pathogen prevalence in disease in a longitudinal cohort.

  • Tommi Mäklin
  • , Harry A. Thorpe
  •  & Jukka Corander