February 26, 2024

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General and Human Microbiome

Fusobacterium nucleatum promotes tumor progression in KRAS p.G12D-mutant colorectal cancer by binding to DHX15 – Huiyuan Zhu – Nature Communications

Gut microbial co-metabolite 2-methylbutyrylcarnitine exacerbates thrombosis via binding to and activating integrin α2β1 – Kan Huang – Cell Metabolism

Robustness of cancer microbiome signals over a broad range of methodological variation – Gregory D Sepich-Poore – Oncogene

A cross-sectional study observing the association of psychosocial stress and dietary intake with gut microbiota genera and alpha diversity among a young adult cohort of black and white women in Birmingham, Alabama – Rachel O Knight – BMC Women’s Health

Faecal hsa-miR-7704 inhibits the growth and adhesion of Bifidobacterium longum by suppressing ProB and aggravates hepatic encephalopathy – Yuchong Wang – NPJ Biofilms and Microbiomes

Beneficial Microbes and Compounds

Review: How probiotics, prebiotics, synbiotics, and postbiotics prevent dental caries: an oral microbiota perspective – Si-Chen Luo – NPJ Biofilms and Microbiomes

Review: Limosilactobacillus fermentum Strains as Novel Probiotic Candidates to Promote Host Health Benefits and Development of Biotherapeutics: A Comprehensive Review – Micaelle Oliveira de Luna Freire – Probiotics and Antimicrobial Proteins

AGA Clinical Practice Guideline on Fecal Microbiota-Based Therapies for Select Gastrointestinal Diseases – Anne F Peery – Gastroenterology

Plant Microbiome

Root endophyte-mediated alteration in plant H2O2 homeostasis regulates symbiosis outcome and reshapes the rhizosphere microbiota – Kai Sun – Journal of Experimental Botany

Micronutrient-microbiome interplay: a critical regulator of soil-plant health – Muhammad Noman – Trends in Microbiology

Dynamic root microbiome sustains soybean productivity under unbalanced fertilization – Mingxing Wang – Nature Communications

Environmental Microbiome

Adaptive response of prokaryotic communities to extreme pollution flooding in a Paleolithic rock art cave (Pindal Cave, northern Spain) – Tamara Martin-Pozas – The Science of the Total Environment

Effects of running time on biological activated carbon filters: water purification performance and microbial community evolution – Shuangjia Shi – Environmental Science and Pollution Research International

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

February 15, 2024

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Human and General Microbiome

Review: Gastrointestinal and brain barriers: unlocking gates of communication across the microbiota-gut-brain axis – María R Aburto – Nature Reviews Gastroenterology & Hepatology

Alterations of gut microbiota in infants with biliary atresia identified by 16S rRNA-sequencing – Fei Liu – BMC Pediatrics

Culture- and non-culture-based approaches reveal unique features of the ocular microbiome in dry eye patients – Maria Naqvi – The Ocular Surface

Animal Microbiome

Herptile gut microbiomes: a natural system to study multi-kingdom interactions between filamentous fungi and bacteria – Lluvia Vargas-Gastélum – mSphere

Beneficial Microbes 

Colonic probiotic insufflation: clinical proposal for an economical game-changer for restoration of the gut microbiome in colorectal cancer and beyond – Ryan Varghese – International Journal of Surgery

Neuroprotective Effect of a Multistrain Probiotic Mixture in SOD1(G93A) Mice by Reducing SOD1 Aggregation and Targeting the Microbiota-Gut-Brain Axis – Zikai Xin – Molecular Neurobiology

Plant Microbiome

Metagenomic and biochemical analyses reveal the potential of silicon to alleviate arsenic toxicity in rice (Oryza sativa L.) – Temoor Ahmed – Environmental Pollution

Mechanisms on salt tolerant of Paenibacillus polymyxa SC2 and its growth-promoting effects on maize seedlings under saline conditions – Chengqiang Wang – Microbiological Research

Environmental Microbiome

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

Biogeography and assembly processes of abundant and rare soil microbial taxa in the southern part of the Qilian Mountain National Park, China – Zhilin Feng – Ecology and Evolution


Microbiome Analysis: Tools, Techniques and Resources

A Clinical Breathomics Dataset – Ping-Hung Kuo – Scientific Data

DeepMPTB: a vaginal microbiome-based deep neural network as artificial intelligence strategy for efficient preterm birth prediction – Oshma Chakoory – Biomarker Research

MicroMPN: methods and software for high-throughput screening of microbe suppression in mixed populations – Karla Franco Meléndez – Microbiology Spectrum

Nanopore sequencing of infectious fluid is a promising supplement for gold-standard culture in real-world clinical scenario – Manna Zhao – Frontiers in Cellular and Infection Microbiology

February 13, 2024

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General microbiome

Model-free prediction of microbiome compositions – Asher & Bashan – Microbiome

Pregnancy and early life

Divergent maturational patterns of the infant bacterial and fungal gut microbiome in the first year of life are associated with inter-kingdom community dynamics and infant nutrition – Mercer et al. – Microbiome

Human airway microbiome

Genomic attributes of airway commensal bacteria and mucosa – Cuthbertson et al. – Communications Biology

Human skin microbiome

[REVIEW]Triggers for the onset and recurrence of psoriasis: a review and update – Liu et al. – Cell Communication and Signaling

Human vaginal microbiome

Uterine fibroids and longitudinal profiles of the vaginal microbiota in a cohort presenting for transvaginal ultrasound – Robbins – PLOS One

Human gut microbiome

Microbial-derived imidazole propionate links the heart failure-associated microbiome alterations to disease severity – Raju et al. – Genome Medicine

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

Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe – Colorado et al. – Microbiome

Gut microbiome signature of metabolically healthy obese individuals according to anthropometric, metabolic and inflammatory parameters – Lee et al. – Scientific Reports

Animal microbiome

Metagenome-assembled genome reveals species and functional composition of Jianghan chicken gut microbiota and isolation of Pediococcus acidilactic with probiotic properties – Shen et al. – Microbiome

Falcon gut microbiota is shaped by diet and enriched in Salmonella – Ahmad et al. – PLOS One

Sex differences in colonic gene expression and fecal microbiota composition in a mouse model of obesity-associated colorectal cancer – Chang et al. – Scientific Reports

Cadaver decomposition microbiome

A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables – Burcham et al. – Nature Microbiology

Bioinformatics

YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample – Koslicki et al. – Bioinformatics

Gut microbiome-metabolome interactions predict host condition – Shtossel et al. – Microbiome

Techniques

Fecal microbiome composition and diversity of cryopreserved canine stool at different duration and storage conditions – Barko et al. – PLOS One

January 31, 2024

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General microbiome

Finding Candida auris in public metagenomic repositories – Mario-Vasquez et al. – PLOS One

Pregnancy and early life

A pilot study of fecal pH and redox as functional markers in the premature infant gut microbiome – Letourneau et al. – PLOS One

[PREPRINT]Assembly, stability, and dynamics of the infant gut microbiome are linked to bacterial strains and functions in mother’s milk – Allert et al. – bioRxiv

Human nasal microbiome

A genome-wide association study reveals the relationship between human genetic variation and the nasal microbiome – Liu et al. – Communications Biology

Human gut microbiome

Differential peripheral immune signatures elicited by vegan versus ketogenic diets in humans – Link et al. – Nature Medicine

Metagenomic analyses of 7000 to 5500 years old coprolites excavated from the Torihama shell-mound site in the Japanese archipelago – Nishimura et al. – PLOS One

[PREPRINT]Unravelling the ancient fungal DNA from the Iceman’s gut – Oskolkov et al. – bioRxiv

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

Streptococcus anginosus promotes gastric inflammation, atrophy, and tumorigenesis in mice – Fu et al. – Cell

Gut complement induced by the microbiota combats pathogens and spares commensals – Wu et al. – Cell

Complement in breast milk modifies offspring gut microbiota to promote infant health – Xu et al. – Cell

Antidiabetic effects and mechanism of γ-polyglutamic acid on type II diabetes mice – Li et al. – International Journal of Biological Macromolecules

Bacterial microbiome associated with cigarette beetle Lasioderma serricorne (F.) and its microbial plasticity in relation to diet sources – Srinivasan et al. – PLOS One

Animal microbiome (for animals in the wild)

Metagenomics reveals the temporal dynamics of the rumen resistome and microbiome in goat kids – Chai et al. – Microbiome

[PREPRINT]Thermal fluctuations independently modulate physiological plasticity and the dynamics of the gut microbiome in a tropical rocky shore oyster – Arromrak et al. – bioRxiv

[PREPRINT]Diversity and structure of the deep-sea sponge microbiome in the equatorial Atlantic Ocean – Williams et al. – bioRxiv

Plant, root, and soil microbiome

[PREPRINT]Temporal and spatial dynamics within the fungal microbiome of grape fermentation – Onetto et al. – bioRxiv

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

Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism – Valentin-Alvarado et al. – Microbiome

Phages and viruses

[PREPRINT]Viroid-like colonists of human microbiomes – Zheludev et al. – bioRxiv

Bioinformatics

[PREPRINT]DeepGOMeta: Predicting functions for microbes – Hoehndorf et al. – bioRxiv

[PREPRINT]Predicting microbial genome-scale metabolic networks directly from 16S rRNA gene sequences – Øyås et al. – bioRxiv

Techniques

[REVIEW]Unraveling metagenomics through long-read sequencing: a comprehensive review – Kim et al. – Journal of Translational Medicine

Microbes in the news

Non-prescription therapeutics for IBS: where are we? – Costantino – Gut Microbiota for Health by ESNM

January 24, 2024

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Human gut microbiome

[REVIEW]Crosstalk between gut microbiome and neuroinflammation in pathogenesis of HIV-associated neurocognitive disorder – Chen et al. – Journal of the Neurological Sciences

Purified diet affects intestinal epithelial proliferation and barrier functions through gut microbial alterations – Shiratori et al. – International Immunology

[PREPRINT]Gut environmental factors explain variations in the gut microbiome composition and metabolism within and between healthy adults – Prochazkova et al. – bioRxiv

Causal relationship between gut microbiota and gastrointestinal diseases: a mendelian randomization study – Wu et al. – Journal of Translational Medicine

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

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

Animal microbiome (for animals in the wild)

[PREPRINT]Effect of composting and storage on the microbiome and resistome of cattle manure from a commercial dairy farm in Poland – Zalewska et al. – bioRxiv

Assessing the microbiota of the snail intermediate host of trematodes, Galba truncatula – McCann et al. – Parasites & Vectors

Plant, root, and soil microbiome

Host genotype, soil composition, and geo-climatic factors shape the fonio seed microbiome – Tabassum et al. – Microbiome

A tripartite bacterial-fungal-plant symbiosis in the mycorrhiza-shaped microbiome drives plant growth and mycorrhization – Zhang et al. – Microbiome

Built environment (subways, indoor surfaces)

[PREPRINT]Identification and classification of the genomes of novel Microviruses in a poultry slaughterhouse – Xie et al. – bioRxiv

Bioinformatics

[PREPRINT]iVirP: An integrative, efficient, and user-friendly pipeline to annotate viral contigs from raw reads of metagenome or VLP sequencing – Li, Jiao and liang – bioRxiv

[PREPRINT]Microbiome-based correction for random errors in nutrient profiles derived from self-reported dietary assessments – Wang et al. – bioRxiv

Techniques

[PREPRINT]MicroFisher: Fungal taxonomic classification for metatranscriptomic and metagenomic data using multiple short hypervariable markers – Wang et al. – bioRxiv

Microbes in the news

How does chronic stress harm the gut? New clues emerge – Kozlov – Nature

January 20, 2024

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Human and General Microbiome

Gut microbiome for predicting immune checkpoint blockade-associated adverse events – Muni Hu – Genome Medicine

The fusion of multi-omics profile and multimodal EEG data contributes to the personalized diagnostic strategy for neurocognitive disorders – Yan Han – Microbiome

Prediction of lung cancer using novel biomarkers based on microbiome profiling of bronchoalveolar lavage fluid – Gihyeon Kim – Scientific Reports

Exploring the intestinal ecosystem: from gut microbiota to associations with subtypes of inflammatory bowel disease – Fan Li – Frontiers in Cellular and Infection Microbiology

Simulated digestions of free oligosaccharides and mucin-type O-glycans reveal a potential role for Clostridium perfringens – Andrew G McDonald – Scientific Reports

Oral microbiome associated with differential ratios of Porphyromonas gingivalis and Streptococcus cristatus – Qingguo Wang – Microbiology Spectrum

Impact of intratumoral microbiome on tumor immunity and prognosis in human pancreatic ductal adenocarcinoma – Shohei Abe – Journal of Gastroenterology

Evaluation of gut microbiota predictive potential associated with phenotypic characteristics to identify multifactorial diseases – Danielle Cristina Fonseca – Gut Microbes

Review: The Gut Microbiome Affects Atherosclerosis by Regulating Reverse Cholesterol Transport – Yangyang Jiang – Journal of Cardiovascular Translational Research

Review: Role of vertical and horizontal microbial transmission of antimicrobial resistance genes in early life: insights from maternal-infant dyads – Manuel Bernabeu – Current Opinion in Microbiology

Beneficial Microbes and Compounds

Complement in breast milk modifies offspring gut microbiota to promote infant health – Dongqing Xu – Cell

An Oral Nanomedicine Elicits In Situ Vaccination Effect against Colorectal Cancer – Menghang Zu – ACS Nano

Model and Non-Model Animal Microbiome 

Oral bacteria accelerate pancreatic cancer development in mice – Elias Saba – Gut

Bacterial community and diversity in the rumen of 11 Mongolian cattle as revealed by 16S rRNA amplicon sequencing – Yijiu Jia – Scientific Reports

Novel taxonomic and functional diversity of eight bacteria from the upper digestive tract of chicken – Bibiana Rios-Galicia – International Journal of Systematic and Evolutionary Microbiology

Plant Microbiome

A tripartite bacterial-fungal-plant symbiosis in the mycorrhiza-shaped microbiome drives plant growth and mycorrhization – Changfeng Zhang – Microbiome

Host genotype, soil composition, and geo-climatic factors shape the fonio seed microbiome – Naheed Tabassum – Microbiome

The role of plants in ironstone evolution: iron and aluminium cycling in the rhizosphere – Anat Paz – The Science of the Total Environment

Consistent effects of independent domestication events on the plant microbiota – Riccardo Soldan – Current Biology 

Inactivation of siderophore iron-chelating moieties by the fungal wheat root symbiont Pyrenophora biseptata – Katie S French – Environmental Microbiology Reports

Environmental Microbiome

New insights into inhibition of high Fe(III) content on anaerobic digestion of waste-activated sludge – Xuepeng Wang – The Science of the Total Environment

Microbiome Analysis: Tools, Techniques and Resources

Drying as an effective method to store soil samples for DNA-based microbial community analyses: a comparative study – Emily Smenderovac – Scientific Reports

Mock community taxonomic classification performance of publicly available shotgun metagenomics pipelines – E Michael Valencia – Scientific Data

Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics – Georgios Marinos – Microbiology Spectrum

Metagenomes and metagenome-assembled genomes from ex vivo fecal incubations of six unique donors – Adrienne B Narrowe – Microbiology Resource Announcements

Bioinformatic Approach to Investigate Larvae Gut Microbiota Cellulosimicrobium protaetiae via Whole-Genome Analysis – Han Le Ho – Molecular Biotechnology





January 17, 2024

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Pregnancy and early life

Human milk cream alters intestinal microbiome of preterm infants: a prospective cohort study – Adeniyi-Ipadeola et al. – Pediatric Research

A bacterial sialidase mediates early-life colonization by a pioneering gut commensal – Buzun et al. – Cell Host & Microbe

Multi-site human microbiome

[DATA]Multi-cohort shotgun metagenomic analysis of oral and gut microbiota overlap in healthy adults – Rashidi et al. – Scientific Data

Human respiratory microbiome

[REVIEW]Positioning the preventive potential of microbiome treatments for cystic fibrosis in the context of current therapies – Cauwenberghs et al. – Cell Reports Medicine

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

The gut microbiota modulate locomotion via vagus-dependent glucagon-like peptide-1 signaling – Lai et al. – npj Biofilms and Microbiomes volume

Nonylphenol induces depressive behavior in rats and affects gut microbiota: A dose–dependent effect – Pan et al. – Environmental Pollution

Animal microbiome (for animals in the wild)

Ocular mucosal homeostasis of teleost fish provides insight into the coevolution between microbiome and mucosal immunity – Kong et al. – Microbiome

Plant, root, and soil microbiome

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

Biogeographic survey of soil bacterial communities across Antarctica – Varliero et al. – Microbiome

Microbes in space

[PREPRINT]Testing microbial biomining from asteroidal material onboard the International Space Station – Santomartino et al. – bioRxiv

Bioinformatics

[PREPRINT]AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods – Wei et al. – bioRxiv

Techniques

Comparison of the DNBSEQ platform and Illumina HiSeq 2000 for bacterial genome assembly – Hu et al. – Scientific Reports

January 14, 2024

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Human and General Microbiome

Linking microbial genes to plasma and stool metabolites uncovers host-microbial interactions underlying ulcerative colitis disease course – Melanie Schirmer – Cell Host & Microbe

Incorporating metabolic activity, taxonomy and community structure to improve microbiome-based predictive models for host phenotype prediction – Mahsa Monshizadeh – Gut Microbes

Microbiota and mucosal gene expression of fecal microbiota transplantation or placebo treated patients with chronic pouchitis – Anna K Hartikainen – Gut Microbes

A robust microbiome signature for autism spectrum disorder across different studies using machine learning – Lucia N Peralta-Marzal – Scientific Reports

Nasal lavage microbiome, but not nasal swab microbiome, correlates with sinonasal inflammation in children with cystic fibrosis – Jaehi Chung – Journal of Cystic Fibrosis

A Gpr35-tuned gut microbe-brain metabolic axis regulates depressive-like behavior – Lingsha Cheng – Cell Host & Microbe

The salivary microbiota of patients with acute lower respiratory tract infection-A multicenter cohort study – Matthew B Rogers – PloS One

The endometrial microbiota and early pregnancy loss – Joshua Odendaal – Human Reproduction

Multi-omics of the gut microbial ecosystem in patients with microsatellite-instability-high gastrointestinal cancer resistant to immunotherapy – Siyuan Cheng – Cell Reports. Medicine

The microbial metabolite urolithin A reduces Clostridioides difficile toxin expression and toxin-induced epithelial damage – Sweta Ghosh – mSystems

Impact of Periodontitis on the Leakage of Oral Bacteria to the Gut – E Buetas – Journal of Dental Research 

Review: Changes in the fecal microbiota of breast cancer patients based on 16S rRNA gene sequencing: a systematic review and meta-analysis – Biqing Luan – Clinical & Translational Oncology

Review: Bacteroides and related species: The keystone taxa of the human gut microbiota – Jae Hyun Shin – Anaerobe

Review: Enhancing microbiome research in sub-Saharan Africa – Kolawole I Ayeni – Trends in Microbiology

Animal Microbiome (Model and non-model organisms)

Early microbial intervention reshapes phenotypes of newborn Bos taurus through metabolic regulations – Yizhao Shen – GigaScience

Gut microbiota variations in wild yellow baboons (Papio cynocephalus) are associated with sex and habitat disturbance – Marina Bambi – Scientific Reports

Genetic mutation in Escherichia coli genome during adaptation to the murine intestine is optimized for the host diet – Tomoya Tsukimi – mSystems

Candidatus Methanosphaera massiliense sp. nov., a methanogenic archaeal species found in a human fecal sample and prevalent in pigs and red kangaroos – Virginie Pilliol – Microbiology Spectrum

Plant and Soil Microbiome

A novel plant growth-promoting rhizobacterium, Rhizosphaericola mali gen. nov., sp. nov., isolated from healthy apple tree soil – Han Sol Kim – Scientific Reports

Manipulation of the seagrass-associated microbiome reduces disease severity – Olivia J Graham – Environmental Microbiology

Microbiome Analysis: Tools, Techniques and Resources

Assessment of DNA extraction methods for human gut mycobiome analysis – Piyapat Rintarhat – Royal Society Open Science

NanoDeep: a deep learning framework for nanopore adaptive sampling on microbial sequencing – Yusen Lin – Briefings in Bioinformatics

BactInt: A domain driven transfer learning approach for extracting inter-bacterial associations from biomedical text – Krishanu Das Baksi – Computational Biology and Chemistry

The African Human Microbiome Portal: a public web portal of curated metagenomic metadata – Anmol Kiran – Database 

MK-BMC: a Multi-Kernel framework with Boosted distance metrics for Microbiome data for Classification – Huang Xu – Bioinformatics