Extensive impact of non-antibiotic drugs on human gut bacteria A screen of more than 1,000 drugs shows that about a quarter of the non-antibiotic drugs inhibit the growth of at least one commensal bacterial strain in vitro. Lisa MaierMihaela PruteanuAthanasios Typas Article19 Mar 2018 Nature
Gut bacterial phospholipase Ds support disease-associated metabolism by generating choline Phospholipase Ds (PLDs) transform phosphatidylcholine to choline, which can then be converted to disease-associated trimethylamine. Here, PLDs are identified in gut bacteria that support growth of other bacteria and are potential therapeutic targets. Carina L. ChittimAna Martínez del CampoEmily P. Balskus Article19 Nov 2018 Nature Microbiology
Infant diet and maternal gestational weight gain predict early metabolic maturation of gut microbiomes Infant nutrition and maternal weight gain during pregnancy impact early-life acquisition and function of the gut microbiome . Aimee M. Baumann-DudenhoefferAlaric W. D’SouzaGautam Dantas Letter29 Oct 2018 Nature Medicine
The fecal metabolome as a functional readout of the gut microbiome Comprehensive fecal metabolic profiling in 786 individuals from TwinsUK provides insights into the influence of host genetics and gut microbial composition on metabolites that may mediate microbiome-associated phenotypes. Jonas ZiererMatthew A. JacksonCristina Menni Letter28 May 2018 Nature Genetics
Best practices for analysing microbiomes Complex microbial communities shape the dynamics of various environments. In this Review, Knight and colleagues discuss the best practices for performing a microbiome study, including experimental design, choice of molecular analysis technology, methods for data analysis and the integration of multiple omics data sets. Rob KnightAlison VrbanacPieter C. Dorrestein Review Article23 May 2018 Nature Reviews Microbiology
Yakult’s research activities: The inheritance and practice of Shirota-ism We contribute to the health and happiness of people around the world through our pursuit of excellence in life sciences and our research and experience in microorganisms. Osamu Chonan Advertisement Feature25 Jan 2019
Temporal development of the gut microbiome in early childhood from the TEDDY study Metagenomic sequencing analysis of stool samples from 903 children as part of the TEDDY study shows that breastfeeding was the most important factor associated with microbiome structure, and the cessation of breast milk resulted in faster maturation of the gut microbiome. Christopher J. StewartNadim J. AjamiJoseph F. Petrosino LetterOpen Access24 Oct 2018 Nature
The human gut microbiome in early-onset type 1 diabetes from the TEDDY study An analysis of more than 10,000 metagenomes from the TEDDY study provides a detailed functional profile of the gut microbiome in relation to islet autoimmunity, and supports the protective effects of short-chain fatty acids in early-onset type 1 diabetes. Tommi VatanenEric A. FranzosaRamnik J. Xavier LetterOpen Access24 Oct 2018 Nature
Complex virome in feces from Amerindian children in isolated Amazonian villages The authors compare human fecal viromes from three isolated villages of the Amazon rain forest with those from city dwellers. They report that the diversity of human viruses is not reduced in isolated villages, suggesting frequent viral introductions or increased susceptibility to enteric infections. Juliana D. SiqueiraMaria Gloria Dominguez-BelloEric Delwart ArticleOpen Access15 Oct 2018 Nature Communications
Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential The effects of caesarean section delivery on mother-to-neonate transmission of microbiota are unclear. Here the authors show that caesarean section delivery can affect the transmission of specific microbial strains and the immunomodulatory potential of the microbiota. Linda WampachAnna Heintz-BuschartPaul Wilmes ArticleOpen Access30 Nov 2018 Nature Communications
Delayed gut microbiota development in high-risk for asthma infants is temporarily modifiable by Lactobacillus supplementation 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 DurackNikole E. KimesSusan V. Lynch ArticleOpen Access16 Feb 2018 Nature Communications
Gut microbiota associations with common diseases and prescription medications in a population-based cohort The human gut microbiome has been associated with many health factors, but variability between studies limits exploration of these effects. Here, Jackson et al. analyse gut microbiota associations for 38 common diseases and 51 medications within >2700 members of the TwinsUK cohort. Matthew A. JacksonSerena VerdiClaire J. Steves ArticleOpen Access9 Jul 2018 Nature Communications
Human genetic variation and the gut microbiome in disease Recent microbiome genome-wide association studies have identified numerous associations between human genetic variants and the gut microbiome. Here, the authors review how genetic variation in the host can alter the composition of the gut microbiome towards a disease state, with a focus on disorders of immunity and metabolism. Andrew Brantley HallAndrew C. TolonenRamnik J. Xavier Review Article21 Aug 2017 Nature Reviews Genetics
Precision identification of diverse bloodstream pathogens in the gut microbiome A new bioinformatic tool identifies a candidate source of bloodstream infection for better management and prevention of hospital-acquired infections. Fiona B. TamburiniTessa M. AndermannAmi S. Bhatt Letter15 Oct 2018 Nature Medicine
Pathogen elimination by probiotic Bacillus via signalling interference Lipopeptides secreted by Bacillus bacteria block quorum sensing by Staphylococcus aureus and thereby inhibit the growth of this opportunistic pathogen in the gut, suggesting why people in rural Thailand who are colonized by Bacillus are not also colonized by S. aureus. Pipat PiewngamYue ZhengMichael Otto Article10 Oct 2018 Nature
Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome Genome-wide and metagenome-wide association study of 92 cardiovascular-diseases-related proteins identifies genetic and microbial factors that explain 76.6% of inter-individual variation, highlighting the role of gut microbiome in cardiovascular disease. Daria V. ZhernakovaTrang H. LeBIOS consortium Article24 Sep 2018 Nature Genetics
You are what you eat: diet, health and the gut microbiota Current nutritional approaches to prevent and treat various diseases have limited effectiveness. Here, Zmora et al. review the major principles underlying effects of dietary constituents on the gut microbiota, resolving aspects of the diet–microbiota–host crosstalk, and present the promises and challenges of incorporating microbiome data into dietary planning. Niv ZmoraJotham SuezEran Elinav Review Article27 Sep 2018 Nature Reviews Gastroenterology & Hepatology
Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota Antimicrobial peptide resistance genes are found to be widespread in the gut microbiome but are exchanged at lower rates compared to antibiotic resistance genes, with functional compatibility between bacteria being important for gene exchange. Bálint KintsesOrsolya MéhiCsaba Pál Article17 Dec 2018 Nature Microbiology
Gut pathobionts underlie intestinal barrier dysfunction and liver T helper 17 cell immune response in primary sclerosing cholangitis Klebsiella pneumoniae from the gut microbiota of patients with primary sclerosing cholangitis (PSC) can damage the intestinal epithelial barrier, resulting in bacterial translocation and T helper 17 cell responses in the liver, indicating a role in PSC pathogenesis. Nobuhiro NakamotoNobuo SasakiTakanori Kanai Article14 Jan 2019 Nature Microbiology
Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life Integration of longitudinal gut metagenomic datasets from children in Finland, Estonia and Russian Karelia reveals high strain-level diversity, which consequently impacts the functional capabilities of the early life microbiome. Tommi VatanenDamian R. PlichtaRamnik J. Xavier Article17 Dec 2018 Nature Microbiology
Environment dominates over host genetics in shaping human gut microbiota Statistical analyses of a metagenomics-sequenced human cohort identify a relatively minor role for genetics in determining microbiome composition and show that several human phenotypes are as strongly associated with the gut microbiome as with host genetics. Daphna RothschildOmer WeissbrodEran Segal Article28 Feb 2018 Nature
Depicting the composition of gut microbiota in a population with varied ethnic origins but shared geography Stool microbiota composition correlates with the ethnic backgrounds of people living in the same city, suggesting that geographical location and ethnicity have distinct effects on microbiota. Mélanie DeschasauxKristien E. BouterMax Nieuwdorp Letter27 Aug 2018 Nature Medicine
Regional variation limits applications of healthy gut microbiome reference ranges and disease models The definition of a 'healthy' microbiome is impacted by geographic regional variations. Yan HeWei WuHong-Wei Zhou Letter27 Aug 2018 Nature Medicine
Recovery of gut microbiota of healthy adults following antibiotic exposure Here the authors show that the human gut microbiome can recover after a clinically relevant, broad-spectrum antibiotic treatment and characterization of the resistome indicates that antibiotic resistance genes can impact the recovery process. Albert PallejaKristian H. MikkelsenOluf Pedersen Article22 Oct 2018 Nature Microbiology
An exclusive metabolic niche enables strain engraftment in the gut microbiota Finely tuned control of strain engraftment and abundance in the mouse gut microbiota was achieved using the marine polysaccharide porphyran, which could exclusively be used by an introduced subset of wild-type or genetically modified Bacteroides strains. Elizabeth Stanley ShepherdWilliam C. DeLoacheJustin L. Sonnenburg Letter9 May 2018 Nature
Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies Here the authors have characterized the growth of 96 human gut bacteria on a range of defined media, providing valuable insights into their metabolic capabilities and unique media for future studies. Melanie TramontanoSergej AndrejevKiran Raosaheb Patil Article19 Mar 2018 Nature Microbiology
Interactions between Roseburia intestinalis and diet modulate atherogenesis in a murine model Roseburia intestinalis is a butyrate-producing member of the gut microbiome that can use dietary plant polysaccharides to alter host metabolism, transcription and epigenetics, and lower inflammation and endotoxaemia, resulting in reduced atherosclerosis. Kazuyuki KasaharaKimberly A. KrautkramerFederico E. Rey Article5 Nov 2018 Nature Microbiology
Fecal microbiota transplantation for refractory immune checkpoint inhibitor-associated colitis Preliminary evidence from two cases suggests that fecal microbiota transplantation may provide a viable treatment option for a severe adverse effect of immune checkpoint blockade therapy in patients with cancer. Yinghong WangDiana H. WiesnoskiRobert R. Jenq Brief Communication12 Nov 2018 Nature Medicine
Precision editing of the gut microbiota ameliorates colitis Tungstate inhibits molybdenum-cofactor-dependent microbial respiratory pathways and shows potential as a selective treatment for microbial imbalances that occur during inflammation of the gastrointestinal tract. Wenhan ZhuMaria G. WinterSebastian E. Winter Letter3 Jan 2018 Nature
Murine colitis reveals a disease-associated bacteriophage community Quantitative metagenomics reveals an altered bacteriophage community in a mouse model of colitis, which overlaps with that observed in humans with inflammatory bowel disease (IBD), providing a tool for interrogating phage dynamics in IBD. Breck A. DuerkopManuel KleinerLora V. Hooper Article23 Jul 2018 Nature Microbiology
The gut–liver axis and the intersection with the microbiome Attention has turned to the gut microbiota in liver disease, including alcoholic and nonalcoholic fatty liver disease and hepatocellular carcinoma. This Review describes gut–liver communications, including evidence from animal and human studies, compares conditions within the liver disease spectrum and highlights key points for designing microbiome-based studies for liver disease research. Anupriya TripathiJustine DebeliusRob Knight Review Article10 May 2018 Nature Reviews Gastroenterology & Hepatology
Richness and ecosystem development across faecal snapshots of the gut microbiota Faecal microbiota richness is considered a hallmark of gut health and stability. However, in healthy hosts, richness would primarily reflect the stage of ecosystem development through the gut, rather than community resilience. This Comment discusses the need to rethink microbiome biomarkers in the context of gut ecology. Gwen FalonySara Vieira-SilvaJeroen Raes Comment24 Apr 2018 Nature Microbiology
Culturing the human microbiota and culturomics Culturomics was developed to culture and identify unknown bacteria that inhabit the human gut. In this Review, Raoult and colleagues discuss the development of culturomics and how it has extended our understanding of bacterial diversity, and highlight the potential implications for human health. Jean-Christophe LagierGrégory DubourgDidier Raoult Review Article24 Jun 2018 Nature Reviews Microbiology
A great-ape view of the gut microbiome Comparing the microbiomes of great apes enables an evolutionary perspective on microbial communities. This approach is revealing not only new insights about humans and what differentiates us from our closest relatives but also the factors that influence microbiome composition and the ways in which microbiomes diverge. Alex H. NishidaHoward Ochman Review Article8 Jan 2019 Nature Reviews Genetics