Category Archives: Water microbiome

April 30, 2024

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Human microbiome

Safety and efficacy of faecal microbiota transplantation in patients with mild to moderate Parkinson’s disease (GUT-PARFECT): a double-blind, placebo-controlled, randomised, phase 2 trial – Anout Bruggeman – eClinicalMedicine

Implications of intestinal microecology and immune function alterations for immunotherapy outcomes in advanced unresectable lung adenocarcinoma – Shuang He – Clinical Respiratory Journal

Recipient microbiome-related features predicting metabolic improvement following fecal microbiota transplantation in adults with severe obesity and metabolic syndrome: a secondary analysis of a phase 2 clinical trial – Zhengxiao Zhang – Gut Microbes

Gut microbiome composition and metabolic activity in women with diverticulitis – Wenjie Ma – Nature Communications

Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development – Raúl Y. Tito – Nature Medicine

Prediction and causal inference of hyperuricemia using gut microbiota – Yuna Miyajima – Scientific Reports

Early-life gut microbiota associates with allergic rhinitis during 13-year follow-up in a Finnish probiotic intervention cohort – Sampo Kallio – Microbiology Spectrum

Food microbiome

The detailed analysis of the microbiome and resistome of artisanal blue-veined cheeses provides evidence on sources and patterns of succession linked with quality and safety traits – Elena A. Alexa – BMC Microbiome

Animal experiments

Sodium Propionate Oral Supplementation ameliorates Depressive-Like Behavior through Gut Microbiome and Histone 3 Epigenetic Regulation – Luiza Marques Prates Behrens – Journal of Nutritional Biochemistry

Colon impairments and inflammation driven by an altered gut microbiota leads to social behavior deficits rescued by hyaluronic acid and celecoxib – Oryan Agronyoni – BMC Medicine

Dissecting the respective roles of microbiota and host genetics in the susceptibility of Card9−/− mice to colitis – C. Danne – BMC Microbiome

Animal microbiome

Synergistic resistance of honeybee (Apis mellifera) and their gut microorganisms to fluvalinate stress – Jianhui Liu – Pesticide Biochemistry and Physiology

Determinants of microbiome composition: Insights from free-ranging hybrid zebras (Equus quagga × grevyi) – Joel O. Abraham – Molecular Ecology

Water & extremophile microbiomes

Phytoplankton-derived polysaccharides and microbial peptidoglycans are key nutrients for deep-sea microbes in the Mariana Trench – Yan-Ru Dang – BMC Microbiome

Rhizospheric bacteria from the Atacama Desert hyper-arid core: cultured community dynamics and plant growth promotion – Juan Castro-Severyn – Microbiology Spectrum

Tools & techniques

Variability and bias in microbiome metagenomic sequencing: an interlaboratory study comparing experimental protocols – Samuel P. Forry – Scientific Reports

Nanopore and Illumina sequencing reveal different viral populations from human gut samples – Ryan Cook – Microbial Genomics

April 12, 2024

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Today’s digest features human gut microbiome studies on dietary fiber and fasting glucose, ocean microbiome, pangenome approaches, and more.

See you at #MVIF!

Oral microbiome

Saliva sampling method influences oral microbiome composition and taxa distribution associated with oral diseases – Cristian Roca – PlosOne

Gut microbiome

Changes in the intestinal microbiota of individuals with non-alcoholic fatty liver disease based on sequencing: An updated systematic review and meta-analysis – Wenpin Cai – PlosOne

Gut microbiota differences in stunted and normal-lenght children aged 36–45 months in East Nusa Tenggara, Indonesia – Ingrid S. Surono – PlosOne

Integrating research on bacterial pathogens and commensals to fight infections—an ecological perspective – Lisa Maier – The Lancet Microbe

Recommendations for the Use of Dietary Fiber to Improve Blood Pressure Control – Hamdi A. Jama – Hypertension

Review: Prebiotic selection influencing inflammatory bowel disease treatment outcomes: a review of the preclinical and clinical evidence – Amin Ariaee – eGastroenterology

Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments – Torben Soelbeck Rasmussen – bioRxiv

Continuous glucose monitoring and intrapersonal variability in fasting glucose – Smadar Shilo – Nature Medicine

Animal microbiome

Intestinal microbiome profiles in broiler chickens raised without antibiotics exhibit altered microbiome dynamics relative to conventionally raised chickens – Seyed Hossien Kairmi – PlosOne

Microbial signatures and enterotype clusters in fattening pigs: implications for nitrogen utilization efficiency – Naomi Sarpong – Frontiers in Microbiology

A genome-centric view of the role of the Acropora kenti microbiome in coral health and resilience – Lauren F. Messer – Nature Communications

Varied microbial community assembly and specialization patterns driven by early life microbiome perturbation and modulation in young ruminants – Zhe Pan – ISME Communications

Ocean microbiome

Decoding populations in the ocean microbiome – Ramiro Logares – Microbiome

Bioinformatics

High-resolution Profiling of Bacterial and Fungal Communities using Pangenome-Informed Taxon-Specific Long-Read Amplicons – Luzia Stalder – bioRxiv

CELEBRIMBOR: Pangenomes from metagenomes – Joel Hellewell – bioRxiv

April 3, 2024

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Human Microbiome

Gut microbiome and metabolome profiling in Framingham heart study reveals cholesterol-metabolizing bacteria – Chenhao Li et al – Cell


Small Intestine Bacterial Overgrowth is associated with increased Campylobacter and epithelial injury in duodenal biopsies of Bangladeshi children – Shah Mohammad Fahim et al – PLOS Neglected Tropical Diseases


Placental TLR recognition of salivary and subgingival microbiota is associated with pregnancy complications – Kazune Pax et al – BMC Microbiome


Ecological patterns and processes of temporal turnover within lung infection microbiota – Helen Gavillet et al – BMC Microbiome


Integrative analysis with microbial modelling and machine learning uncovers potential alleviators for ulcerative colitis – Jinlin Zhu et al – Gut Microbes


A comparative study on dietary diversity and gut microbial diversity in children with autism spectrum disorder, attention-deficit hyperactivity disorder, their neurotypical siblings, and non-related neurotypical volunteers: a cross-sectional study – Shunya Kurokawa et al – Journal of Child Psychology & Psychiatry


Disrupted gut microecology after high-dose 131I therapy and radioprotective effects of arachidonic acid supplementation – Ganghua Lu et al – European Journal of Nuclear Medicine & Molecular Imaging


Pathogen-specific alterations in intestinal microbiota precede urinary tract infections in preterm infants: a longitudinal case-control study – Luyang Hong et al – Gut Microbes



Plant, soil, and root microbiome

Soil fungal communities varied across aspects of restored grassland in former mining areas of the Qinghai-Tibet Plateau – Xioqing Li et al – PLOS One


Integrated rice-yellow catfish farming resulting in variations in the agricultural environment, rice growth performance, and soil bacterial communities – Yiran Hou et al – Environmental Science & Pollution Research


Microbial terroir: associations between soil microbiomes and the flavor chemistry of mustard (Brassica juncea) – Corinne Walsh et al – New Phytologist


Animal experiments

The gut metabolite indole-3-propionic acid activates ERK1 to restore social function and hippocampal inhibitory synaptic transmission in a 16p11.2 microdeletion mouse model – Jian Jiang et al – BMC Microbiome


[PREPRINT] Supplier-origin gut microbiomes affect host body weight and select autism-related behaviors – Zachary L. McAdams et al – bioRxiv


Water & extremophile microbiome

Phenology and ecological role of aerobic anoxygenic phototrophs in freshwaters – Cristian Villena-Alemany et al – BMC Microbiome


The distinctive weathering crust habitat of a High Arctic glacier comprises discrete microbial micro-habitats – Sara M E Rassner et al – Environmental Microbiology


Animal Microbiome

Molecular-Weight-Dependent Degradation of Plastics: Deciphering Host-Microbiome Synergy Biodegradation of High-Purity Polypropylene Microplastics by Mealworms – Lei He et al – Environmental Science & Technology


Dispersion of antimicrobial resistant bacteria in pig farms and in the surrounding environment – Daniel Scicchitano et al – BMC Animal Microbiome


Tools & techniques

[PREPRINT] rRNA Operon Improves Species-Level Classification of Bacteria and Microbial Community Analysis Compared to 16S rRNA – Sohyoung Won et al – bioRxiv

March 20, 2024

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Human gut and general microbiome

Prevotella copri and microbiota members mediate the beneficial effects of a therapeutic food for malnutrition – Hao-Wei Chang et al – Nature Microbiology

Outcomes after Fecal Microbiota Transplantation in combination with Bezlotoxumab for Inflammatory Bowel Disease and Recurrent C. difficile Infection – Jessica R Allegretti – American Journal of Gastroenterology

Diosmin alleviates ulcerative colitis in mice by increasing Akkermansia muciniphila abundance, improving intestinal barrier function, and modulating the NF-κB and Nrf2 pathways – Maha Badr Salem et al – Cell Heliyon

Gut microbiota profiling in obese children from Southeastern China – Jingjing Wang et al – BMC Pediatrics

A flexible high-throughput cultivation protocol to assess the response of individuals’ gut microbiota to diet-, drug-, and host-related factors – Janina N Zünd et al – ISME Communications

Animal experiments

Intact lung tissue and bronchoalveolar lavage fluid are both suitable for the evaluation of murine lung microbiome in acute lung injury – Lijun Zheng et al – BMC Microbiome

Microbiota-derived indoles alleviate intestinal inflammation and modulate microbiome by microbial cross-feeding – Gang Wang et al – BMC Microbiome

Plant, soil, and environmental microbiome

Microbial species pool-mediated diazotrophic community assembly in crop microbiomes during plant development – Chao Xiong et al – mSystems

Bacterial communities associated with an island radiation of lichen-forming fungi – Miguel Blázquez et al – PLOS ONE

Built environment microbiome

Early assessment of fungal and oomycete pathogens in greenhouse irrigation water using Oxford nanopore amplicon sequencing – Enoch Narh Kudjordjie et al – PLOS One

The composition of the bacterial communities collected from the PM10 samples inside the Seoul subway and railway station – Shambhavi Sharma et al – Nature Scientific Reports

Bioinformatics

Differential network connectivity analysis for microbiome data adjusted for clinical covariates using jackknife pseudo-values – Seungjun Ahn & Somnath Datta – BMC Bioinformatics

Beneficial microbes & microbial metabolites
Natural intestinal metabolite xylitol reduces BRD4 levels to mitigate renal fibrosis – Zhouke Tan et al – Clinical and Translational Science

Probiotics supplementation during pregnancy or infancy on multiple food allergies and gut microbiota: a systematic review and meta-analysis – Lan Jiang et al – Nutrition Reviews

Non-Microbiome Microbiology

Koch’s curse: How models of extreme pathology bias studies of host–pathogen interactions – Kalyan K. Dewan & Eric T. Harvill – PLOS Pathogens

March 18, 2024

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Today’s digest features the human gut microbiome atlas of Africa, sociobiome, a large human gut Bacteroidales culture collection, Patescibacteria in global waste water treatment plants, and more.

This month, the May 2024 contribution period of Outreachy started! Outreachy, as an internship program, supports diversity in open source & open science!

See you at #MVIF!

Gut microbiome

Expanding the human gut microbiome atlas of Africa – Dylan G Maghini – bioRxiv

Review: The individual response to antibiotics and diet — insights into gut microbial resilience and host metabolism – Lars M. M. Vliex – Nature Reviews Endocrinology

The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study – Leon Peto – medRxiv

Multi-omics analysis of the gut microbiome and metabolites associated with the psychoneurological symptom cluster in children with cancer receiving chemotherapy – Jinbing Bai – Journal of Translational Medicine

Longitudinal analysis of the gut microbiome in adolescent patients with anorexia nervosa: microbiome-related factors associated with clinical outcome – Nadia Andrea Andreani – Gut Microbes

Healthy microbiome – moving towards functional interpretation – Kinga Zielińska – bioRxiv

Sociobiome – Individual and neighborhood socioeconomic status influence the gut microbiome in a multi-ethnic population in the US – Soyoung Kwak – npj Biofilms and Microbiomes

Cryptic diversity of cellulose-degrading gut bacteria in industrialized humans – Sarah Morais – Science

Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species and strain level diversity and evolution – Zhenrun J. Zhang – bioRxiv

Animal experiment

A history of repeated antibiotic usage leads to microbiota-dependent mucus defects – Kertu Liis Krigul – bioRxiv

Water microbiome

Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants – Huifeng Hu – Microbiome

Bioinformatics

Review: Challenges in computational discovery of bioactive peptides in ’omics data – Luis Pedro Coelho – Proteomics

For long-term sustainable software in bioinformatics – Luis Pedro Coelho – Plos Computational Biology

Data-driven prediction of colonization outcomes for complex microbial communities – Lu Wu – Nature Communications

March 7, 2024

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General microbiome

[OPINION]Toward an integrative framework for microbial community coalescence – Custer, Bresciani & Dini-Andreote – Trends in Microbiology

Studying mixed-species biofilms of Candida albicans and Staphylococcus aureus using evolutionary game theory – Dühring & Schuster – PLOS One

Human oral microbiome

Microbial Communities and Functional Genes in Periodontitis and Healthy Controls – Ma et al. – International Dental Journal

Human gut microbiome

[REVIEW]Unlocking the secrets: exploring the influence of the aryl hydrocarbon receptor and microbiome on cancer development – Rayan et al. – Cellular & Molecular Biology Letters

Short term supplementation with cranberry extract modulates gut microbiota in human and displays a bifidogenic effect – Lessard-Lord et al. – npj Biofilms and Microbiomes

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Fecal microbiota impacts development of Cryptosporidium parvum in the mouse – Widmer & Creasey – Scientific reports

High fat diet is associated with gut microbiota dysbiosis and decreased gut microbial derived metabolites related to metabolic health in young Göttingen Minipigs – Lützhøft et al. – PLOS One

Animal microbiome (for animals in the wild)

Gustatory Responsiveness of Honey Bees Colonized with a Defined or Conventional Gut Microbiota – Suenami, Sato & Miyazaki – Microbes and Environments

[REVIEW]Fungal infection of insects: molecular insights and prospects – Hong et al. – Trends in Microbiology

Plant, root, and soil microbiome

Microbiome sequencing revealed the abundance of uncultured bacteria in the Phatthalung sago palm-growing soil – Nutaratat et al. – PLOS One

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Assigning the unassigned: A signature-based classification of rDNA metabarcodes reveals new deep-sea diversity – Angeles et al. – PLOS One

February 28, 2024

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Human gut microbiome

Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging – Shalini Singh – BMC Microbiome

Safety, feasibility, and impact on the gut microbiome of kefir administration in critically ill adults – Vinod K. Gupta – BMC Medicine

Dissecting Gut-Microbial Community Interactions using a Gut Microbiome-on-a-Chip – Jeeyon Lee – Advanced Science

Animal experiments

CRB1-associated retinal degeneration is dependent on bacterial translocation from the gut – Shanzhen Peng – Cell

Amino acid formula induces microbiota dysbiosis and depressive-like behavior in mice – Ji Hu – Cell Reports

Bacteroides fragilis aggravates high-fat diet-induced non-alcoholic fatty liver disease by regulating lipid metabolism and remodeling gut microbiota – Yumei Huang – Microbiology Spectrum

Animal microbiome

Gut microbiota modulation enhances the immune capacity of lizards under climate warming – Jing Yang – BMC Microbiome

Gut microbiota contribute to variations in honey bee foraging intensity – Cassondra L Vernier – ISME Journal

Virome diversity shaped by genetic evolution and ecological landscape of Haemaphysalis longicornis – Run-Ze Ye – BMC Microbiome

Multi-omics reveal mechanisms of high enteral starch diet mediated colonic dysbiosis via microbiome-host interactions in young ruminant – Chunjia Jin – BMC Microbiome

Plant, root, and soil microbiome

[PREPRINT] Cover Crop Root Exudates Impact Soil Microbiome Functional Trajectories in Agricultural Soils – Valerie A Seitz – Research Square

Stronger compensatory thermal adaptation of soil microbial respiration with higher substrate availability – Lingrui Qu – ISME Journal

Built environment

Effects of operational parameters on bacterial communities in Hong Kong and global wastewater treatment plants – Yulin Zhang – mSystems

Water and extremophile microbiome

Novel functional insights into the microbiome inhabiting marine plastic debris: critical considerations to counteract the challenges of thin biofilms using multi-omics and comparative metaproteomics – Lauren F. Messer – BMC Microbiome

Particle-attached bacteria act as gatekeepers in the decomposition of complex phytoplankton polysaccharides – Feng-Qing Wang – BMC Microbiome

Dynamics of Gut Bacteria Across Different Zooplankton Genera in the Baltic Sea – Tianshuo Zu – Microbial Ecology

Beneficial microbes

[PREPRINT] Enhancing Recovery from Gut Microbiome Dysbiosis and Alleviating DSS-Induced Colitis in Mice with a Consortium of Rare Short-Chain Fatty Acid-Producing Bacteria – Achuthan Ambat – bioRxiv

Neuroprotective Effects of Bifidobacterium animalis subsp. lactis NJ241 in a Mouse Model of Parkinson’s Disease: Implications for Gut Microbiota and PGC-1α – Yuxuan Dong – Molecular Neurobiology

February 23, 2024

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Today’s digest features the MetaPhlAn v4.1 & viral module, early life gut microbiome and diabetes, human milk oligosaccharides study, and more.

NEWS
MVIF has launched their crowdfunding campaign https://www.gofundme.com/f/me-mvif

See you at #MVIF next week!

Oral microbiome

Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases – Davide Bazzani – npj Biofilms and Microbiomes

Nasal microbiome

Nasal commensals reduce Staphylococcus aureus proliferation by restricting siderophore availability – Y Zhao – bioRxiv

Semen microbiome

Characterisation and comparison of semen microbiota and sperm function in men with infertility, recurrent miscarriage, or proven fertility – Shahriar Mowla – bioRxiv

Gut microbiome

CRISPR-Cas-based identification of a sialylated human milk oligosaccharides utilization cluster in the infant gut commensal Bacteroides dorei – Sivan Kijner – Nature Communications

Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study – Kinga Humińska-Lisowska – Plos One

The impact of iron supplementation on the preterm neonatal gut microbiome: A pilot study – Matthew VanOrmer – Plos One

Early-life exposures to specific commensal microbes prevent type 1 diabetes – Jamal Green – bioRxiv

Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing – Philipp Spohr – Scientific Reports

Donor-recipient intermicrobial interactions impact transfer of subspecies and fecal microbiota transplantation outcome – Qiyi Chen – Cell Host & Microbe

Animal experiment

The gut ileal mucosal virome is disturbed in patients with Crohn’s disease and exacerbates intestinal inflammation in mice – Zhirui Cao – Nature Communications

Animal microbiome

Gut microbiome diversity and function during hibernation and spring emergence in an aquatic frog – Ji-Eun Lee – Plos One

Unraveling the gut microbiota of Tibetan chickens: insights into highland adaptation and ecological advantages – Tao Zeng – bioRxiv

Water microbiome

A difficult coexistence: resolving the iron-induced nitrification delay in groundwater filters – Francesc Corbera-Rubio – bioRxiv

Human virome

Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples – Moreno Zolfo – bioRxiv

February 21, 2024

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Human nasal microbiome

[PREPRINT]Nasal commensals reduce Staphylococcus aureus proliferation by restricting siderophore availability – Zhao et al. – bioRxiv

Human oral microbiome

Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases – Bazzani et al. – npj Biofilms and Microbiomes

Human gut microbiome

Horizontal gene transfer after faecal microbiota transplantation in adolescents with obesity – Behling et al. – Microbiome

Animal microbiome

Psychological stress-induced microbial metabolite indole-3-acetate disrupts intestinal cell lineage commitment – Wei et al. – Cell Metabolism

Gut microbiota contributes to bisphenol A-induced maternal intestinal and placental apoptosis, oxidative stress, and fetal growth restriction in pregnant ewe model by regulating gut-placental axis – Zhang et al. – Microbiome

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Novel insights into the rhizosphere and seawater microbiome of Zostera marina in diverse mariculture zones – Sun et al. – Microbiome

Alteration of bacterial community composition in the sediments of an urban artificial river caused by sewage discharge – Li et al. – PeerJ

The exometabolome of microbial communities inhabiting bare ice surfaces on the southern Greenland Ice Sheet – Doting et al. – Environmental Microbiology

Searching for microbial contribution to micritization of shallow marine sediments – Garuglieri et al. – Environmental Microbiology

Food microbiology

Unveiling the microbial communities and metabolic pathways of Keem, a traditional starter culture, through whole-genome sequencing – Rana et al. – Scientific Reports

Phages and viruses

[PREPRINT]Fecal Virome Transplantation (FVT) from healthy humans remodels the gut bacteriome and virome and reduces metabolic syndrome in mice – Cervantes-Echeverría et al. – bioRxiv

[PREPRINT]Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples – Zolfo et al. – bioRxiv

Microbes in the news (popular press, EurekAlert, ScienceDaily, Youtube, NPR, etc)

Why addressing how our brain and our gut talk to each other matter for IBS – Gut microbiota for health

January 8, 2024

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The microbiome digest team, Juan Pablo Cardenas Astudillo, Axel Künstner and Svetlana Ugarcina Perovic (it’s me), wishes you happy and healthy 2024! Also, we wish to have more members in our team in order to cover all daily microbiome science news: if you are interested in reviewing microbiome papers at your convenience (with our support!) and digest them for the community, feel free to contact us. We are happy to welcome you!

And, yes, see you at MVIF #25!

Vaginal microbiome

Vaginal Lactobacillus fatty acid response mechanisms reveal a novel strategy for bacterial vaginosis treatment – Meilin Zhu – bioRxiv

Gut microbiome

BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen – Brantley Hall – Nature Microbiology

Influence of feeding practices in the composition and functionality of infant gut microbiota and its relationship with health – Misael Martínez-Martínez – PlosOne

Mucin-degrading gut bacteria promote anti-parasitic immunity – Mathis Wolter – bioRxiv

Host genetic regulation of human gut microbial structural variation – Daria V. Zhernakova – Nature

Animal microbiome

Deciphering the gut microbiome of grass carp through multi-omics approach – Ming Li – Microbiome

Spotting disease disrupts the microbiome of infected purple sea urchins, Strongylocentrotus purpuratus – Chloe G. Shaw – BMC Microbiology

Animal experiments

Desulfovibrio vulgaris interacts with novel gut epithelial immune receptor LRRC19 and exacerbates colitis – Runxiang Xie – Microbiome

Individualized microbiotas dictate the impact of dietary fiber on colitis sensitivity – Erica Bonazzi – Microbiome

A consortia of clinical E. coli strains with distinct in vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mice – Rachel M. Bleich – Microbiome

Environmental microbiome

A unified compendium of prokaryotic and viral genomes from over 300 anaerobic digestion microbiomes – Victor Borin Centurion – Environmental Microbiome

Plant, root, soil microbiome

Unraveling the interplay between root exudates, microbiota, and rhizosheath formation in pearl millet – Abdelrahman Alahmad – Microbiome

Methods

mEnrich-seq: methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome – Lei Cao – Nature Methods

Bioinformatics

A catalogue of small proteins from the global microbiome – Yiqian Duan – bioRxiv