October 27, 2024

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Human and General Microbiome

Gut

A human gut Faecalibacterium prausnitzii fatty acid amide hydrolase – Jiye Cheng – Science

A ubiquitous mobile genetic element changes the antagonistic weaponry of a human gut symbiont – Madeline L Sheahan – Science

Exploring alterations of gut/blood microbes in addressing iron overload-induced gut dysbiosis and cognitive impairment in thalassemia patients – Kanokphong Suparan – Scientific Reports

Effects of bile acids on the growth, composition and metabolism of gut bacteria – Yi-Lei Peng – NPJ Biofilms and Microbiomes

Gut-first Parkinson’s disease is encoded by gut dysbiome – Mário F Munoz-Pinto – Molecular Neurodegeneration

Metaproteomics reveals diet-induced changes in gut microbiome function according to Crohn’s disease location – Stefano Levi Mortera – Microbiome

Review: Examining the healthy human microbiome concept – Raphaela Joos – Nature Reviews Microbiology

Review: Host-pathobiont interactions in Crohn’s disease – Roberta Caruso – Nature Reviews Gastroenterology & Hepatology

Early Microbiome

Species- and subspecies-level characterization of health-associated bacterial consortia that colonize the human gut during infancy – Samuel S Minot – Gut Microbes

Metal availability shapes early life microbial ecology and community succession – Joshua Soto Ocaña – mBio

Virome

Oral reovirus reshapes the gut microbiome and enhances antitumor immunity in colon cancer – Won Suk Lee – Nature Communications

Oral Cavity

Pooled analysis of oral microbiome profiles defines robust signatures associated with periodontitis – Assem Soueidan – mSystems

Animal Microbiome (Model and Non-Model Organisms)

Type VI secretion systems promote intraspecific competition and host interactions in a bee gut symbiont – Erick V S Motta – PNAS

Gut bacteria facilitate leaf beetles in adapting to dietary specialization by enhancing larval fitness – Meiqi Ma – NPJ Biofilms and Microbiomes

The dietary effects of two strain probiotics (Leuconostoc mesenteroides, Lactococcus lactis) on growth performance, immune response and gut microbiota in Nile tilapia (Oreochromis niloticus) – Assel Paritova – PloS One

Effects of Lactiplantibacillus plantarum CBT LP3 and Bifidobacterium breve CBT BR3 supplementation on weight loss and gut microbiota of overweight dogs – Jihee Choi – Scientific Reports

Maternal gastrointestinal microbiome shapes gut microbial function and resistome of newborns in a cow-to-calf model – Yimin Zhuang – Microbiome

Integrated analysis of metabolome and microbiome in a rat model of perimenopausal syndrome – Yanqiu Wei – mSystems

Maternal dysbiosis produces long-lasting behavioral changes in offspring – Jacob Hudobenko – Molecular Psychiatry

DNA metabarcoding analyses reveal fine-scale microbiome structures on Western Canadian bat wings – Chadabhorn Insuk – Microbiology Spectrum

Plant and Environmental Microbiome

Aquificae overcomes competition by archaeal thermophiles, and crowding by bacterial mesophiles, to dominate the boiling vent-water of a Trans-Himalayan sulfur-borax spring – Nibendu Mondal – PloS One

Metagenome-assembled genomes of Macrocystis-associated bacteria – Emily G Aguirre – Microbiology Resource Announcements

Metagenomic time-series reveals a western English Channel viral community dominated by members with strong seasonal signals – Luis M Bolaños – The ISME Journal

Volatile-mediated interspecific plant interaction promotes root colonization by beneficial bacteria via induced shifts in root exudation – Xingang Zhou – Microbiome

Other Microbes

Microbial community acclimation during anaerobic digestion of high-oil food waste – Yangqing Hu – Scientific Reports

The choice of 16S rRNA gene sequence analysis impacted characterization of highly variable surface microbiota in dairy processing environments – Sarah E Daly – mSystems

Microbiome Analysis: Tools, Techniques and Resources

A single-stranded based library preparation method for virome characterization – Xichuan Zhai – Microbiome

Microbiome-based correction for random errors in nutrient profiles derived from self-reported dietary assessments – Tong Wang – Nature Communications

Fecal samples and rectal swabs adequately reflect the human colonic luminal microbiota – Julia Rode – Gut Microbes

Optimal 16S rRNA gene amplicon sequencing analysis for oral microbiota to avoid the potential bias introduced by trimming length, primer, and database – Takahiko Nagai – Microbiology Spectrum

Moving Toward Metaproteogenomics: A Computational Perspective on Analyzing Microbial Samples via Proteogenomics – Franziska Singer – Methods in Molecular Biology

October 20, 2024

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Human and General Microbiome

Fecal glycoprotein 2 is a marker of gut microbiota dysbiosis and systemic inflammation – Fabian Frost – Gut Pathogens

Detrimental effect of an early exposure to antibiotics on the outcomes of immunotherapy in a multi-tumor cohort of patients – Patricia Guerrero – The Oncologist

Upper respiratory microbial communities of healthy populations are shaped by niche and age – Susan Zelasko – Microbiome

Dysbiosis of the initial stool microbiota increases the risk of developing necrotizing enterocolitis or feeding intolerance in newborns – Hyojin Chae – Scientific Reports

Resource sharing of an infant gut microbiota synthetic community in combinations of human milk oligosaccharides – Athanasia Ioannou – The ISME Journal

Aging-induced dysbiosis worsens sepsis severity but is attenuated by probiotics in D-galactose-administered mice with cecal ligation and puncture model – Chalisa Pinitchun – PloS One

Multi-omics analysis reveals the interplay between pulmonary microbiome and host in immunocompromised patients with sepsis-induced acute lung injury – Fan Lu – Microbiology Spectrum

A Blautia producta specific gFET-based aptasensor for quantitative monitoring of microbiome quality – Hu Xing – Nanoscale Horizons

Alterations of the gut microbiome in HIV infection highlight human anelloviruses as potential predictors of immune recovery – Celia Boukadida – Microbiome

Review: Gut microbiota determines the fate of dietary fiber-targeted interventions in host health – Wenjing Wang – Gut Microbes

Beneficial Microbes and Compounds

Vaginal lactobacilli produce anti-inflammatory β-carboline compounds – Virginia J Glick – Cell host & Microbe

EphA2 blockage ALW-II-41-27 alleviates atherosclerosis by remodeling gut microbiota to regulate bile acid metabolism – Cong Lu – NPJ Biofilms and Microbiomes

Lactobacillus rhamnosus GG and Bifidobacterium animalis subsp. lactis BB-12 promote infected wound healing via regulation of the wound microenvironment – Zhe Yin – Microbial Biotechnology

Ameliorative effects of Akkermansia muciniphila on anxiety-like behavior and cognitive deficits in a rat model of Alzheimer’s disease – Hamideh Maftoon – Brain Research

Animal Microbiome

Bacterial and Symbiodiniaceae communities’ variation in corals with distinct traits and geographical distribution – Livia Bonetti Villela – Scientific Reports

The Role of Geography, Diet, and Host Phylogeny on the Gut Microbiome in the Hawaiian Honeycreeper Radiation – Maria S Costantini – Ecology and Evolution

New insights into the enteric methane production based on the archaeal genome map of ruminant gastrointestinal tract – Yifan Tang – Journal of Advanced Research

Plant and Soil Microbiome

A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plants – Alon Avraham Ginatt – eLife

Unravelling the microbiome of wild flowering plants: a comparative study of leaves and flowers in alpine ecosystems – Dinesh Kumar Ramakrishnan – BMC Microbiology

Algae-fungi symbioses and bacteria-fungi co-exclusion drive tree species-specific differences in canopy bark microbiomes – Jule Freudenthal – The ISME Journal

Agricultural practices influence soil microbiome assembly and interactions at different depths identified by machine learning – Yujie Mo – Communications Biology

More Microbes

Community successional patterns and inter-kingdom interactions during granular biofilm development – Miguel de Celis – NPJ Biofilms and Microbiomes

Metagenome-based microbial community analysis of urine-derived fertilizer – Nebiyat N Woldeyohannis – BMC Microbiology

Metabolic cross-feeding interactions modulate the dynamic community structure in microbial fuel cell under variable organic loading wastewaters – Natchapon Srinak – PLoS Computational Biology

Microbiome Analysis: Tools, Techniques and Resources

Evaluation of inter- and intra-variability in gut health markers in healthy adults using an optimised faecal sampling and processing method – Kirsten Kruger – Scientific Reports

LineageFilter: Improved Proteotyping of Complex Samples Using Metaproteomics and Machine Learning – Hamid Hachemi – Journal of Proteome Research

October 18, 2024

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Human microbiome

Alterations of the gut microbiome in HIV infection highlight human anelloviruses as potential predictors of immune recovery  – Boukadida et al  – Microbiome 

Vaginal lactobacilli produce anti-inflammatory β-carboline compounds – Glick et al – Cell Host & Microbe

An ancient ecospecies of Helicobacter pylori  – Tourrette et al – Nature

Review – Intestinal fungal-host interactions in promoting and maintaining health – Hill & Round – Cell Host & Microbe

Review – Gut microbiome and health: mechanistic insights – de Vos et al – Gut

Animal microbiome

Genomic and functional characterization of the Atlantic salmon gut microbiome in relation to nutrition and health – de Leon et al – Nature Microbiology

Stress triggers irritable bowel syndrome with diarrhea through a spermidine-mediated decline in type I interferon – Zhang et al – Cell Metabolism

Built environment

Diverse and specialized metabolic capabilities of microbes in oligotrophic built environments  – Tong et al – Microbiome 

Plant microbiome

Multi-omics framework to reveal the molecular determinants of fermentation performance in wine yeast populations  – de Celis et al – Microbiome

Viruses

Using artificial intelligence to document the hidden RNA virosphere – Cell – Hou et al.

Rapid design of bacteriophage cocktails to suppress the burden and virulence of gut-resident carbapenem-resistant Klebsiella pneumoniae – Rotman et al – Cell Host & Microbe

Bioinformatics

SurvBal: Compositional microbiome balances for survival outcomes – Li et al – Bioinformatics

q2-metnet: QIIME2 package to analyze 16S rRNA data via high-quality metabolic reconstructions of the human gut microbiota – Balzerani et al – Bioinformatics 

Non-microbiome

News feature – Your diet can change your immune system — here’s how – Nature

October 13, 2024

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Human and General Microbiome

Aggregatibacter is inversely associated with inflammatory mediators in sputa of patients with chronic airway diseases and reduces inflammation in vitro – Ellen Goeteyn – Respiratory Research

Oral Microbiota Development in the First 60 Months: A Longitudinal Study – K Yama – Journal of Dental Research

Microbiome-derived metabolites in early to mid-pregnancy and risk of gestational diabetes: a metabolome-wide association study – Sita Manasa Susarla – BMC Medicine

Unique Gut Microbiome and Metabolic Profiles in Chinese Workers Exposed to Dust: Insights from a Case-Control Study – Xiaojun Qian – Journal of Occupational and Environmental Medicine

Dysbiotic signatures and diagnostic potential of gut microbial markers for inflammatory bowel disease in Korean population – Hyun Sik Kim – Scientific Reports

A search for bacteria identified from cerebrospinal fluid shunt infections in previous surgical events – Paul Hodor – PloS One

Microbiome and metabolome patterns after lung transplantation reflect underlying disease and chronic lung allograft dysfunction – Christian Martin – Microbiome

Review: Reexamining the role of Fusobacterium nucleatum subspecies in clinical and experimental studies – Madeline Krieger – Gut Microbes

Review: Host-microbe interaction paradigms in acute and recurrent vulvovaginal candidiasis – Jessie MacAlpine – Cell Host & Microbe

Review: Balancing act: counteracting adverse drug effects on the microbiome – Jacobo de la Cuesta-Zuluaga – Trends in Microbiology

Cancer Research

Preview: Gut microbiome and bladder cancer: A new link through nitrosamine metabolism – Sridhar Mani – Cell Host & Microbe

Review: Prostate cancer microenvironment: multidimensional regulation of immune cells, vascular system, stromal cells, and microbiota – Lin Chen – Molecular Cancer

Review: Gut and oral microbiota in gynecological cancers: interaction, mechanism, and therapeutic value – Jian Wu – NPJ Biofilms and Microbiomes

Beneficial Microbes and Compounds

Effects of complex probiotics on intestinal function and its regulatory mechanism in patients with constipation – X Zhang – Beneficial Microbes

Lactiplantibacillus plantarum P101 Alleviated Alcohol-Induced Hepatic Lipid Accumulation in Mice via AMPK Signaling Pathway: Gut Microbiota and Metabolomics Analysis – Xiaoyan Feng – Probiotics and Antimicrobial Proteins

Preview: Unlocking the genetic influence on milk variation and its potential implication for infant health – Claudia Nussbaum – Cell Genomics

Review: The gut microbiome and dietary fibres: implications in obesity, cardiometabolic diseases and cancer – Nathalie M Delzenne – Nature Reviews. Microbiology

Review: Microbiome-based therapeutics for Parkinson’s disease – Adam M Hamilton – Neurotherapeutics

Animal Microbiome

Gut bacteria of lepidopteran herbivores facilitate digestion of plant toxins – Nan Zhang – PNAS

Sea cucumbers and their symbiotic microbiome have evolved to feed on seabed sediments – Wenjie Pan – Nature Communications

Comprehensive profile of the companion animal gut microbiome integrating reference-based and reference-free methods – Tobyn Branck – The ISME Journal

Review: Quantitative Synthesis of Microbe-Driven Acclimation and Adaptation in Wild Vertebrates – Garazi Martin Bideguren – Evolutionary Applications

Plant Microbiome

The role of foraging pollinators in assembling the flower microbiota and transmitting the fire blight pathogen Erwinia amylovora – Salma Mukhtar – Environmental Microbiology

Environmental Microbiome

Distinct microbial communities supported by iron oxidation – Kateřina Burkartová – Environmental Microbiology

Microbiome Analysis: Tools, Techniques and Resources

Normalization of short-chain fatty acid concentration by bacterial count of stool samples improves discrimination between eubiotic and dysbiotic gut microbiota caused by Clostridioides difficile infection – Anna Sayol-Altarriba – Gut Microbes

SmT/SHM-seq: simultaneously capturing spatial transcriptome and microbiome information in plants – Peng Mu – Trends in Plant Science

High accuracy meets high throughput for near full-length 16S ribosomal RNA amplicon sequencing on the Nanopore platform – Xuan Lin – PNAS Nexus

A deployable film method to enable replicable sampling of low-abundance environmental microbiomes – Phoebe Mankiewicz Ledins – Scientific Reports

October 10, 2024

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Pregnancy and early life

Maternal and infant microbiome and birth anthropometry – Padiyar et al. – iScience

Human oral microbiome

Tumor-colonized Streptococcus mutans metabolically reprograms tumor microenvironment and promotes oral squamous cell carcinoma – Zhou et al. – Microbiome

Human skin microbiome

Causal relationship between 150 skin microbiomes and prostate cancer: insights from bidirectional mendelian randomization and meta-analysis – Chen et al. – Frontiers in Immunology

Human respiratory microbiome

Microbiome and metabolome patterns after lung transplantation reflect underlying disease and chronic lung allograft dysfunction – Martin et al. – Microbiome

Human gut microbiome

Visceral adiposity in postmenopausal women is associated with a pro-inflammatory gut microbiome and immunogenic metabolic endotoxemia – Gaber et al. – Microbiome

[REVIEW]From gut to bone: deciphering the impact of gut microbiota on osteoporosis pathogenesis and management – Hao et al. – Frontiers in Cellular and Infection Microbiology

[PREPRINT]Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome – Lopez et al. – bioRxiv

[REVIEW]The role of gut microbiota in prostate inflammation and benign prostatic hyperplasia and its therapeutic implications – Chen et al. – Heliyon

Unveiling the gut microbiota blueprint of schizophrenia: a multilevel omics approach – Qi et al. – Frontiers in Psychiatry

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

[PREPRINT]Failure of colonization following gut microbiota transfer exacerbates DSS-induced colitis – Gustafson et al. – bioRxiv

Animal microbiome (for animals in the wild)

Gut microbiome in two high-altitude bird populations showed heterogeneity in sex and life stage – Sun et al. – FEMS Microbes

Plant, root, and soil microbiome

Analysis of rhizosphere fungal diversity in lavender at different planting years based on high-throughput sequencing technology – Deng et al. – PLOS One

[PREPRINT]Soil microbiome perturbation impedes growth of Bouteloua curtipendula and increases relative abundance of soil microbial pathogens – Hobbs et al. – bioRxiv

Microbes in space

Adaptation to space conditions of novel bacterial species isolated from the International Space Station revealed by functional gene annotations and comparative genome analysis – Szydlowski et al. – Microbiome

Metabolomics

[PREPRINT]Metabolomics survey of uropathogenic bacteria in human urine – Chan et al. – bioRxiv

Bioinformatics/Resources

[PREPRINT]FungAMR: A comprehensive portrait of antimicrobial resistance mutations in fungi – Bedard et al. – bioRxiv

[PREPRINT]argNorm: Normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO) – Perovic et al. – QUT ePrints

[PREPRINT]BEREN: A bioinformatic tool for recovering Giant viruses, Polinton-like Viruses, and Virophages in metagenomic data – Minch & Moniruzzman – bioRxiv

[DATASET]Dataset of 16S rRNA gene sequences of 111 healthy and Newcastle disease infected caecal samples from multiple chicken breeds of Pakistan – Ameer et al. – Data in Brief

Techniques

High accuracy meets high throughput for near full-length 16S ribosomal RNA amplicon sequencing on the Nanopore platform – Lin et al. – PNAS Nexus

October 6, 2024

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Human and General Microbiome

Noninvasive, microbiome-based diagnosis of inflammatory bowel disease – Jiaying Zheng – Nature Medicine

Advancing microbiome research in Māori populations: insights from recent literature exploring the gut microbiomes of underrepresented and Indigenous peoples – Ella T Silk – mSystems

Salivary microbiota reflecting changes in subgingival microbiota – Jae-Suk Jung – Microbiology Spectrum

Differences in the human gut microbiota with varying depressive symptom severity scores – Yuka Masamura – Bioscience of Microbiota, Food and Health

Review: Sophorolipid: An Effective Biomolecule for Targeting Microbial Biofilms – Sunidhi Dhadwal – Current Microbiology

News: Microbiome-based treatment helps ease severe malnutrition – Elizabeth Pennisi – Science

Beneficial Microbes and Compounds

A multivalent mRNA-LNP vaccine protects against Clostridioides difficile infection – Mohamad-Gabriel Alameh – Science

Safety and Tolerability of CP101, a full spectrum, oral microbiome therapeutic for the prevention of recurrent C. difficile infection: A Phase 2 Randomized Controlled Trial – Jessica R Allegretti – Gastroenterology

Animal Microbiome

Recruitment of complete crAss-like phage genomes reveals their presence in chicken viromes, few human-specific phages, and lack of universal detection – María Dolores Ramos-Barbero – The ISME Journal

Structural and functional differences of gut microbiota in Pomacea canaliculata from different geographical locations and habitats – Miao Fang – Ecology and Evolution

Plant Microbiome

Rhizosphere microbial community structure in high-producing, low-input switchgrass families – Christina Stonoha-Arther – PloS One

Dynamic alterations and ecological implications of rice rhizosphere bacterial communities induced by an insect-transmitted reovirus across space and time – Nan Wu – Microbiome

Microbiome Analysis: Tools, Techniques and Resources 

Microbiome-induced reprogramming in post-transcriptional landscape using nanopore direct RNA sequencing – Zihe Xu – Cell Reports

rRNA operon improves species-level classification of bacteria and microbial community analysis compared to 16S rRNA – Sohyoung Won – Microbiology Spectrum

ASV vs OTUs clustering: Effects on alpha, beta, and gamma diversities in microbiome metabarcoding studies – Andrea Fasolo – PloS One

October 4, 2024

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Happy Friday! And see you next week at MVIF!

Plastisphere microbiome

What harmful microbes are lurking in the world’s 7 billion tonnes of plastic waste? – Changchao Li – Nature

Respiratory microbiome

Integrating respiratory microbiome and host immune response through machine learning for respiratory tract infection diagnosis – Hongbin Chen – npj Biofilms and Microbiomes

Vaginal microbiome

Characterization of vaginal microbiomes in clinician-collected bacterial vaginosis diagnosed samples – Hayden N Brochu – bioRxiv

Oral microbiome

The intensive physical activity causes changes in the composition of gut and oral microbiota – Szymon Urban – Scientific Reports
⚽ “Twenty professional football players and twelve amateurs were invited to the study groups.”

Giant extrachromosomal element “Inocle” potentially expands the adaptive capacity of the human oral microbiome – Yuya Kiguchi – bioRxiv

The association between mode of childbirth delivery and early childhood caries: A comprehensive systematic review and meta-analysis – Li Xiang – PlosOne

Gut microbiome

What’s GABA got to do with it? A potential link between the microbiome, schizophrenia, and the endo-cannabinoid system – Ayala Glinert – Psychiatry Research

Changes in intestinal permeability and gut microbiota following diet-induced weight loss in patients with metabolic dysfunction-associated steatohepatitis and liver fibrosis – Dimitrios A. Koutoukidis – Gut Microbes

Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis – Yan Jia – Scientific Reports

Detailed Analysis of Prebiotic Fructo- and Galacto-Oligosaccharides in the Human Small Intestine – Mara P. H. van Trijp – Journal of Agricultural and Food Chemistry

Dietary fibers boost gut microbiota-produced B vitamin pool and alter host immune landscape – Erica T. Grant – Microbiome

Human milk microbiome

Maternal HIV infection and the milk microbiome – Nicole H. Tobin – Microbiome

Viruses and phages

Genomic surveillance as a scalable framework for precision phage therapy against antibiotic-resistant pathogens – Mihály Koncz – Cell

Animals

Differential interactions of Rickettsia species with tick microbiota in Rh. sanguineus and Rh. turanicus – Apolline Maitre – Scientific Reports 

Animal experiments

Disruption of the intestinal clock drives dysbiosis and impaired barrier function in colorectal cancer – Rachel C. Fellows – Science Advances

Photoperiod effects on corticosterone and seasonal clocks in cafeteria-induced obese fischer 344 rats are influenced by gut microbiota – Verónica Arreaza-Gil – Scientific Reports 

Plant, root, soil microbiome

Closing the gap: examining the impact of source habitat proximity on plant and soil microbial communities in post-mining spoil heap succession – Lenka Mészárošová – Frontiers in Microbiology

Bacterial Communities from the Antique Roman City of Carnuntum (Austria):16S r-RNA-Based Comparison of Soil Samples from Different Archaeological Horizons – Johann Michael Köhler – preprints

Microbiome–metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient – Viviana Freire-Zapata – Nature Microbiology

Phosphorus availability influences disease-suppressive soil microbiome through plant-microbe interactions – Yifan Cao – Microbiome

Plant diversity drives positive microbial associations in the rhizosphere enhancing carbon use efficiency in agricultural soils – Luiz A. Domeignoz-Horta – Nature Communications

Bacterial diversity of cantaloupes and soil from Arizona and California commercial fields at the point of harvest – Madison Goforth – Plos One

Drinking water microbiome

Making waves: From tap to gut- exploring the impact of drinking water on gut microbiota – Hanieh Shakeri Moghaddam – Water Research

Bioinformatics

Taxometer: Improving taxonomic classification of metagenomics contigs – Svetlana Kutuzova – Nature Communications

Jaeger: an accurate and fast deep-learning tool to detect bacteriophage sequences – Yasas Wijesekara – bioRxiv

Emergent ecological patterns and modelling of gut microbiomes in health and in disease – Jacopo Pasqualini – Plos Computational Biology

Technique

Comparative evaluation of soil DNA extraction kits for long read metagenomic sequencing – Harry T. Child – Access Microbiology

Microbial community interactions on a chip – Duane S. Juang – PNAS

October 2, 2024

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Gut Microbiome

Gut microbiota wellbeing index predicts overall health in a cohort of 1000 infants – Brandon Hickman et al – Nature Communications

Pangenomes of human gut microbiota uncover links between genetic diversity and stress response – Saar Shoer et al – Cell Host & Microbe

[MINI REVIEW] The human gut microbiome in health and disease: time for a new chapter? – Jee-Yon Lee et al – ASM Infection & Immunity

Metabolic interactions shape emergent biofilm structures in a conceptual model of gut mucosal bacterial communities – Amin Valiei et al – NPJ Biofilms & Microbiomes

A population-scale analysis of 36 gut microbiome studies reveals universal species signatures for common diseases – Wen Sun et al – NPJ Biofilms & Microbiomes

A single amplified genome catalog reveals the dynamics of mobilome and resistome in the human microbiome – Tetsuro Kawano-Sugaya et al – BMC Microbiome

Stratification of human gut microbiomes by succinotype is associated with inflammatory bowel disease status – Laura Anthamatten et al – BMC Microbiome

Impact of complementary feeding on infant gut microbiome, metabolites and early development – Yudong Shi et al – Food & Function

Can longer lifespan be associated with gut microbiota involvement in lipid metabolism? – Sára Šardzíková et al – FEMS Microbiology Ecology

Beneficial microbes & compounds

[REVIEW] Preventive effect of probiotics on oral mucositis induced by anticancer therapy: a systematic review and meta-analysis of randomized controlled trials – Bo Yang et al – BMC Oral Health

Animal Microbiome

Bacteria from the Amycolatopsis genus associated with a toxic bird secrete protective secondary metabolites – Elena Seibel et al – Nature Communications

Impact of virginiamycin on the ruminal microbiota of feedlot cattle – Bruna Parapinski Santos – Canadian Journal of Veterinary Research

Microbiome of death

From carrion to soil: microbial recycling of animal carcasses – Jennifer M. DeBruyn et al – Cell Trends in Microbiology

Water & extremophile microbiome

Microbiome–metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient – Viviana Freire-Zapata et al – Nature Microbiology

Prescribed fire regimes influence responses of fungal and bacterial communities on new litter substrates in a brackish tidal marsh – Viet Q. Dao et al – PLOS One

Plant, root & soil microbiome

The phyllosphere of Nigerian medicinal plants, Euphorbia lateriflora and Ficus thonningii is inhabited by a specific microbiota – Anderson O. Oaikhena et al – Scientific Reports

Water‒soil-air‒plant mutual feedback mechanism under the application of red bed composite polymers – Tianpeng Chen et al – PLOS One

Diversity and community distribution of soil bacterial in the Yellow River irrigation area of Ningxia, China – Xia Wu et al – PLOS One

Bioinformatics & tools

Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs – Annika Jochheim et al – BMC Microbiome

September 29, 2024

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Human and General Microbiome

Gut microbiota drives colon cancer risk associated with diet: a comparative analysis of meat-based and pesco-vegetarian diets – Carlotta De Filippo – Microbiome

Decoding the diagnostic and therapeutic potential of microbiota using pan-body pan-disease microbiomics – Georges P Schmartz – Nature Communications

Deep longitudinal lower respiratory tract microbiome profiling reveals genome-resolved functional and evolutionary dynamics in critical illness – Minghui Cheng – Nature Communications

Small Bowel Microbiome Profiles in Overweight and Obese Humans – Liqi Li – The American Journal of Gastroenterology

Intratumoral microbiota as a novel prognostic indicator in bladder cancer – Yuwei Zhang – Scientific Reports

Research Highlight: Identifying antimicrobials in the human microbiome – Sarah Crunkhorn – Nature Reviews. Drug Discovery

Review: Akkermansia muciniphila as a Potential Guardian against Oral Health Diseases: A Narrative Review – Molly H Anderson – Nutrients

Review: Intratumoral microbiota in colorectal cancer: focus on specific distribution and potential mechanisms – Jing Long – Cell Communication and Signaling

Review: Bacterial extracellular vesicles at the interface of gut microbiota and immunity – Inês Melo-Marques – Gut Microbes

Beneficial Microbes and Compounds

GV-971 prevents severe acute pancreatitis by remodeling the microbiota-metabolic-immune axis – Xi Chen – Nature Communications

Fecal Microbiota Transplantation-Mediated Rebalancing of the Gut-Brain Axis Alleviates Cisplatin-Induced Neuropathic Pain – Mousmi Rani – ACS Chemical Neuroscience

FMT rescues mice from DSS-induced colitis in a STING-dependent manner – Dan Pu – Gut Microbes

Aged garlic oligosaccharides modulate host metabolism and gut microbiota to alleviate high-fat and high-cholesterol diet-induced atherosclerosis in ApoE(-/-) mice – Xiaomin Wang – Food Chemistry

Phytoactives for Obesity Management: Integrating Nanomedicine for Its Effective Delivery – Ashok Kumar Mandal – Nutrition Reviews

Animal Microbiome

Exploring microbial diversity and biosynthetic potential in zoo and wildlife animal microbiomes – Georges P Schmartz – Nature Communications

Fur microbiome as a putative source of symbiotic bacteria in sucking lice – Jana Martin Říhová – Scientific Reports

Fecal microbiota transplantation from patients with polycystic ovary syndrome induces metabolic disorders and ovarian dysfunction in germ-free mice – Feiling Huang – BMC Microbiology

Dietary fiber intake impacts gut bacterial and viral populations in a hypertensive mouse model – Laura Avellaneda-Franco – Gut Microbes

Effect of shipping on the microbiome of donor mice used to reconstitute germ-free recipients – Zachary L McAdams – Gut Microbes Reports

Bacterial microbiome diversity along poultry slaughtering lines: insights from chicken carcasses and environmental sources – Arife Ezgi Telli – Journal of Veterinary Research

The Gut Microbiome of Two Wild Bumble Bee Species Native of South America: Bombus pauloensis and Bombus bellicosus – Gregorio Fernandez de Landa – Microbial Ecology

Gill-associated ammonia oxidizers are widespread in teleost fish – Wouter Mes – Microbiology Spectrum

Microbiome Analysis: Methods, Tools and Resources

Automated annotation of scientific texts for ML-based keyphrase extraction and validation – Oluwamayowa O Amusat – Database

SpeciateIT and vSpeciateDB: novel, fast, and accurate per sequence 16S rRNA gene taxonomic classification of vaginal microbiota – Johanna B Holm – BMC Bioinformatics

Implementing high-throughput insect barcoding in microbiome studies: impact of non-destructive DNA extraction on microbiome reconstruction – Veronika Andriienko – PeerJ

A Metagenomics Pipeline to Characterize Self-Collected Vaginal Microbiome Samples – Krystal Thomas-White – Diagnostics

Microbe-drug association prediction model based on graph convolution and attention networks – Bo Wang – Scientific Reports

September 26, 2024

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General microbiome

[RESOURCE/COLLECTION]Microbial Primers

Phages reconstitute NAD+ to counter bacterial immunity – Osterman et al. – Nature

The direct inhibitory effects of Lactobacillus acidophilus, a commensal urinary bacterium, on calcium oxalate stone development – Noonin et al. – Microbiome

Pregnancy and early life

Neonatal gut microbiota profile and the association with retinopathy of prematurity in preterm infants – Chang et al. – Clinical & Experimental Ophthalmology

Human skin microbiome

The wound microbiota: microbial mechanisms of impaired wound healing and infection – Uberoi, McCready-Vangi, Grice – Nature Reviews Microbiology

Human oral microbiome

[PREPRINT]Altered oral microbiota of drug-resistant organism carriers exhibit impaired gram-negative pathogen inhibition – Zelasko et al. – bioRxiv

Human gut microbiome

Emergence of community behaviors in the gut microbiota upon drug treatment – Garcia-Santamarina et al. – Cell

Microbial transformation of dietary xenobiotics shapes gut microbiome composition – Culp et al. – Cell

[REVIEW]Microglia and Gut Microbiota: A Double-Edged Sword in Alzheimer’s Disease – Bano et al. – Ageing Research Reviews

[REVIEW]What defines a healthy gut microbiome? – van Hul et al. – Gut

[OUTLOOK]The gut microbiome and chronic pain – Watson – Nature

Acarbose enhances the efficacy of immunotherapy against solid tumours by modulating the gut microbiota – Zhang et al. – Nature Metabolism

Animal microbiome (for animals in the wild)

Trait-based study predicts glycerol/diol dehydratases as a key function of the gut microbiota of hindgut-fermenting carnivores – Li et al. – Microbiome

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

Microbial community storm dynamics signal sources of “old” stream water – URycki et al. – PLOS One

Hyperexpansion of genetic diversity and metabolic capacity of extremophilic bacteria and archaea in ancient Andean lake sediments – Lezcano et al. – Microbiome

Food microbiology

Bronze Age cheese reveals human-Lactobacillus interactions over evolutionary history – Liu et al. – Cell

Bioinformatics

A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies – Wirbel et al. – Genome Biology

[PREPRINT]Quantifying Data Distortion in Bar Graphs in Biological Research – Lin & Landry – bioRxiv