Featured
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| Open AccessRemoval of false positives in metagenomics-based taxonomy profiling via targeting Type IIB restriction sites
Here, leveraging species-specific Type IIB restriction endonuclease digestion sites as reference instead of universal markers or whole microbial genomes, the authors introduce MAP2B, a metagenomic profiler, showing it can significantly remove false-positive identification and generate highly accurate taxonomic profiling results.
- Zheng Sun
- , Jiang Liu
- & Yang-Yu Liu
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Article
| Open AccessThe 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
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Article
| Open AccessDelayed 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
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Article
| Open AccessFiber 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
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Article
| Open AccessAntibiotics 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
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Article
| Open AccessMicrodiversity of the vaginal microbiome is associated with preterm birth
Here, Liao et al. analyze the vaginal microbiome during pregnancy, and find a unique population genetic structure associated with preterm birth, suggesting that evolutionary processes acting on vaginal bacteria may play a role in prematurity.
- Jingqiu Liao
- , Liat Shenhav
- & Tal Korem
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Perspective
| Open AccessExtreme environments offer an unprecedented opportunity to understand microbial eukaryotic ecology, evolution, and genome biology
The ecology and evolution of eukaryotic microbes in extreme environments are poorly understood. In this Perspective, Rappaport and Oliverio summarize data from over 80 studies of protists in extreme environments and identify lineages of particular interest as targets for future research.
- Hannah B. Rappaport
- & Angela M. Oliverio
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Article
| Open AccessSystematic 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
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Article
| Open AccessCharacterization 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
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Article
| Open AccessVitamin interdependencies predicted by metagenomics-informed network analyses and validated in microbial community microcosms
Metagenomic data and network analyses are often used to predict microbial interactions in complex communities, but these predictions are rarely explored experimentally. Here, Hessler et al. combine experiments with metagenome-informed, microbial consortia-based network analyses to identify interactions in microbial consortia grown under dozens of conditions.
- Tomas Hessler
- , Robert J. Huddy
- & Jillian F. Banfield
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Article
| Open AccessNutritional 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
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Article
| Open AccessTapping 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
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Article
| Open AccessCharacterization 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
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Article
| Open AccessGenetic 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
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Article
| Open AccessAbrupt 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
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Article
| Open AccessThree-dimensional images reveal the impact of the endosymbiont Midichloria mitochondrii on the host mitochondria
The mitochondrial symbiont, Candidatus Midichloria mitochondrii, exists in the hard tick Ixodus ricinus, the main vector for Lyme disease. Here, the authors use FIB-SEM to characterise mitochondrial morphology and bacterial interactions in the context of oocyte maturation and endosymbiosis.
- Zerrin Uzum
- , Dmitry Ershov
- & Fabrizia Stavru
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Article
| Open AccessTET2 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
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Article
| Open AccessTop-down identification of keystone taxa in the microbiome
Keystone taxa in ecological communities are native taxa that have an especially important role in the stability of their ecosystem. This study introduces a novel method for detecting keystones in microbial communities by comparing data with and without specific species.
- Guy Amit
- & Amir Bashan
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Article
| Open AccessCoexisting ecotypes in long-term evolution emerged from interacting trade-offs
Previous, a long-term evolution experiment in E.coli resulted in spontaneous emergence of ecotypes that coexisted for more than 14,000 generations. Here, the authors show that the emergence and persistence of this phenomenon results from two interacting trade-offs, rooted in biochemical constraints.
- Avik Mukherjee
- , Jade Ealy
- & Markus Basan
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Article
| Open AccessPatterns and determinants of the global herbivorous mycobiome
Anaerobic gut fungi are a functionally important component of mammalian herbivores’ microbiomes. Here, the authors surveys anaerobic gut fungi in 34 species of ruminants and hindgut fermenters, assessing their patterns and identifying 56 novel genera.
- Casey H. Meili
- , Adrienne L. Jones
- & Mostafa S. Elshahed
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Article
| Open AccessGlobal 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
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Article
| Open AccessGut 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
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Article
| Open AccessA 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
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Article
| Open AccessCulturing 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
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Article
| Open AccessHydrogen 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
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Article
| Open AccessRevealing 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
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Article
| Open AccessA 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
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Article
| Open AccessEcology of Endozoicomonadaceae in three coral genera across the Pacific Ocean
Bacterial symbionts of the Endozoicomonadaceae family are frequently found in marine animals but are poorly understood. Using data from the Tara Pacific expedition, this study of Endozoicomonadaceae ecology at an ocean basin-scale reveals that corals across the Pacific Ocean have different host-symbiont association strategies that are determined at the bacterial lineage level.
- Corentin Hochart
- , Lucas Paoli
- & Pierre E. Galand
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Article
| Open AccessDiversity 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
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Article
| Open AccessHost-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
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Article
| Open AccessStress-induced metabolic exchanges between complementary bacterial types underly a dynamic mechanism of inter-species stress resistance
Microbes can cooperate and share resources via metabolic cross-feeding. Here, the authors show that excretion of key metabolites following acid stress provides a collaborative, inter-species mechanism of stress resistance.
- Kapil Amarnath
- , Avaneesh V. Narla
- & Terence Hwa
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Article
| Open AccessDetailed 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
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Article
| Open AccessEngineered symbiotic bacteria interfering Nosema redox system inhibit microsporidia parasitism in honeybees
Microsporidia parasitism affect honeybees health and has been implicated in colony losses. Here, the authors show that members of the honeybee gut microbiota inhibit microsporidia proliferation, and engineer a gut symbiont that protects against Nosema ceranae infection via inhibiting its redox system.
- Haoyu Lang
- , Hao Wang
- & Hao Zheng
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Article
| Open AccessEnabling 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
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Article
| Open AccessCandida expansion in the gut of lung cancer patients associates with an ecological signature that supports growth under dysbiotic conditions
Here, Seelbinder et al. show high Candida levels in cancer patients’ stool to correlate with greater metabolically flexibility but less robust bacterial communities and, combined with machine learning models to predict Candida levels from bacterial data, suggest that lactate producing bacteria may fuel Candida overgrowth in the gut during dysbiosis.
- Bastian Seelbinder
- , Zoltan Lohinai
- & Gianni Panagiotou
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Article
| Open AccessModulation 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
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Article
| Open AccessTradeoff between lag time and growth rate drives the plasmid acquisition cost
Plasmid acquisition imposes a transient burden on bacterial hosts. Here, authors show this burden results in a tradeoff between growth and lag that dictates plasmid fate, favoring intermediate cost plasmids over both low and high cost counterparts.
- Mehrose Ahmad
- , Hannah Prensky
- & Allison J. Lopatkin
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Article
| Open AccessPreviously 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
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Article
| Open AccessAnaerobic 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
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Article
| Open AccessSialidases 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
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Article
| Open AccessParabacteroides 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
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Article
| Open AccessThe 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
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Article
| Open AccessCable bacteria with electric connection to oxygen attract flocks of diverse bacteria
Cable bacteria are centimeter-long filamentous microbes that conduct electrons via internal wires, thus coupling sulfide oxidation between sediment layers. Here, Bjerg et al. show that the anoxic part of oxygen-respiring cable bacteria attracts swarms of other bacteria, which appear to transfer electrons to cable bacteria via soluble metabolites.
- Jesper J. Bjerg
- , Jamie J. M. Lustermans
- & Andreas Schramm
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Article
| Open AccessA symbiotic physical niche in Drosophila melanogaster regulates stable association of a multi-species gut microbiota
Animal gut microbiomes are fairly stable over time despite large daily fluctuations in diet and introductions of environmental bacteria. Here the authors report that fruit flies maintain the stability of their microbiome in part through a physical niche in the esophagus.
- Ren Dodge
- , Eric W. Jones
- & William B. Ludington
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Article
| Open AccessAbiotic selection of microbial genome size in the global ocean
This study investigates the average genome size of planktonic prokaryotes across tropical and polar oceans and down to the hadal realm. Using hundreds of metagenomes of marine microorganisms, genome size was found to be highest in the perennially cold polar ocean, suggesting that environmental factors influence genome size selection and the ecological strategies of marine microbes.
- David K. Ngugi
- , Silvia G. Acinas
- & Carlos M. Duarte
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Article
| Open AccessClinical 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
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Article
| Open AccessGut 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
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Article
| Open AccessDevelopment of the oral resistome during the first decade of life
Here, the authors provide a longitudinal genetic surveillance of the antimicrobial resistance potential of the human oral microbiome in the first decade of life, revealing a dynamic environment altered by tooth decay with the increasing potential to mobilize genes as children grow.
- Smitha Sukumar
- , Fang Wang
- & Christina J. Adler
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Article
| Open AccessPopulation-level impacts of antibiotic usage on the human gut microbiome
Here, the authors study the population-level impact of antimicrobial resistance genes (ARGs). By analyzing 8972 metagenomes and 3,096 gut microbiomes from healthy individuals not taking antibiotics, they demonstrate significant correlations between both the total ARG abundance and diversity and per capita antibiotic usage rates across ten countries spanning three continents. Using a collection of 154,723 human-associated metagenome assembled genomes (MAGs) they link these ARGs to microbial taxa and horizontal gene transfer.
- Kihyun Lee
- , Sebastien Raguideau
- & Christopher Quince