November 13, 2024

Today we are highlighting a recent call to action by leading scientists and scientific organizations around the globe aimed at drawing attention to the increasingly urgent climate catastrophe. The authors argue for the use of microbe-based solutions that could be promising in addressing the crisis, and yet are not used effectively at scale. Here we’ve included links to the press release and the journals which have jointly published the paper:

[PRESS RELEASE] Scientists issue call to action underlining importance of microbial solutions to tackle climate crisis – Linda Stewart – The Microbiologist by Applied Microbiology International

Microbial solutions must be deployed against climate catastrophe – Raquel Peixoto, Christian R Voolstra, Lisa Y Stein, Philip Hugenholtz, Joana Falcao Salles, Shady A Amin, Max Häggblom, Ann Gregory, Thulani P Makhalanyane, Fengping Wang, Nadège Adoukè Agbodjato, Yinzhao Wang, Nianzhi Jiao, Jay T Lennon, Antonio Ventosa, Patrik M Bavoil, Virginia Miller, Jack A Gilbert – Sustainable Microbiology

The paper can also be found in journals published by FEMS, ISME, ASM, and Nature.

Human gut microbiome

Predictable regulation of gut microbiome in immunotherapeutic efficacy of gastric cancer – Wei Gao et al – Genes & Immunity

Multimodal analysis identifies microbiome changes linked to stem cell transplantation-associated diseases – Alejandro Artacho et al – BMC Microbiome

Human oral microbiome

Large-scale metagenomic analysis of oral microbiomes reveals markers for autismspectrum disorders – Paolo Manghi et al – Nature Communications

[REVIEW] Viral infection and antiviral immunity in the oral cavity – Heather D. Hickman & Niki M. Moutsopoulos – Nature Reviews Immunology

Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized – Eria P. Ryu et al – BMC Microbiome

Human respiratory microbiome

Major alteration of lung microbiome and the host responses in critically ill COVID-19 patients with high viral load – Ingrid G. Bustos et al – Scientific Reports

Human skin microbiome

The healing process of diabetic ulcers correlates with changes in the cutaneous microbiota – Emanuele Bruni et al – Scientific Reports

Soil microbiome

Microplastic diversity increases the abundance of antibiotic resistance genes in soil – Yi-Fei Wang et al – Nature Communications

Built environment microbiome

Moving beyond species: fungal function in house dust provides novel targets for potential indicators of mold growth in homes – Neeraja Balasubrahmaniam et al – BMC Microbiome

Animal microbiome

Reef site and habitat influence effectiveness of Acropora palmata restoration and its microbiome in the Florida Keys – Stephanie M. Rosales et al – Nature Communications Earth & Environment

Melatonin alleviates heat stress-induced spermatogenesis dysfunction in male dairy goats by regulating arachidonic acid metabolism mediated by remodeling the gut microbiota – Xinrui Guo et al – BMC Microbiome

Pathobiont and symbiont contribute to microbiota homeostasis through Malpighian tubules-gut countercurrent flow in Bactrocera dorsalis – Yanning Liu et al – ISME Journal

Medium-chain fatty acid triglycerides improve feed intake and oxidative stress of finishing bulls by regulating ghrelin concentration and gastrointestinal tract microorganisms and rumen metabolites – Jiaming Luan et al – BMC Microbiome

Intestinal commensal bacteria promote Bactrocera dorsalis larval development through the vitamin B6 synthesis pathway – Jian Gu et al – BMC Microbiome

Water & extremophile microbiome

Latitudinal gradients and ocean fronts strongly influence protist communities in the southern Pacific Ocean – Daniela Sturm et al – FEMS Microbial Ecology

Urea assimilation and oxidation support activity of phylogenetically diverse microbial communities of the dark ocean – Nestor Arandia-Gorostidi et al – ISME Journal

Bioinformatics & tools

MAGqual: a stand-alone pipeline to assess the quality of metagenome-assembled genomes – Annabel Cansdale & James P.J. Chong – BMC Microbiome

November 10, 2024

Human and General Microbiome

Novel biomarkers for hepatocellular carcinoma detection and treatment – Hongyuan Yi – Hepatobiliary Surgery and Nutrition

Animal Model Experiments

Gut microbiota modulates depressive-like behaviors induced by chronic ethanol exposure through short-chain fatty acids – Hui Shen – Journal of Neuroinflammation

Host genetics and gut microbiota influence lipid metabolism and inflammation: potential implications for ALS pathophysiology in SOD1(G93A) mice – Elena Niccolai – Acta Neuropathologica Communications

Lactobacillus rhamnosus modulates murine neonatal gut microbiota and inflammation caused by pathogenic Escherichia coli – Hao Xuan – BMC Microbiology

Animal Microbiome

Introduction into natural environments shifts the gut microbiome of captivity-raised filter-feeding bivalves – Stephanie N Vaughn – ISME Communications

A metagenomic catalogue of the ruminant gut archaeome – Jiandui Mi – Nature Communications

Large-scale metagenomic assembly provide new insights into the genetic evolution of gut microbiomes in plateau ungulates – Bo Xu – NPJ Biofilms and Microbiomes

Diet affects reproductive development and microbiota composition in honey bees – Anjali Zumkhawala-Cook – Animal Microbiome

Plant Microbiome

Biological and experimental factors that define the effectiveness of microbial inoculation on plant traits: a meta-analysis – Hamed Azarbad – ISME Communications

Can microbiome adaptations protect crops from pests and climate change? – Carolyn Beans – PNAS

Environmental Microbiome

Ecological roles of nano-picoplankton in stratified waters of an embayment in the southern Benguela – Nicole R Dames – FEMS Microbiology Letters

Metagenomic insights into inhibition of soil microbial carbon metabolism by phosphorus limitation during vegetation succession – Haocai Wang – ISME Communications

Microbiome Analysis

Cross-comparison of gut metagenomic profiling strategies – Gábor Gulyás – Communications Biology

November 3, 2024

Human and General Microbiome

Gut microbiota and metabolic profile changes unveil the deterioration of alveolar bone inflammatory resorption with aging induced by D-galactose – Fangzhou Liu – Scientific Reports

The human gut symbiont Ruminococcus gnavus displays strain-specific exopolysaccharides modulating the host immune response – Victor Laplanche – Carbohydrate Polymers

Stage dependent microbial dynamics in hepatocellular carcinoma and adjacent normal liver tissues – Hee Eun Jo – Scientific Reports

Intestinal microflora and metabolites affect the progression of acute pancreatitis (AP) – Zhenjiang Wang – Gut Pathogens

Longitudinal analysis of the gut microbiota during anti-PD-1 therapy reveals stable microbial features of response in melanoma patients – Angeli D G Macandog – Cell Host & Microbe

Review: A pathophysiologic framework for the overlap of disorders of gut-brain interaction and the role of the gut microbiome – Ayesha Shah – Gut Microbes

Review: AI in microbiome-related healthcare – Niklas Probul – Microbial Biotechnology

Review: The oncomicrobiome: new insights into microorganisms in cancer – Yingying Ma – Microbial Pathogenesis

Viewpoint: Gut microbiome: a biomedical revolution – Maria Carmen Collado – Nature Reviews Gastroenterology & Hepatology

Research Highlight: Microbiome-colonizing RNAs – Andrea Du Toit – Nature Reviews. Microbiology

Beneficial Microbes and Compounds

Effects of Limosilactobacillus reuteri DSM 17938 in neonates exposed to antibiotics: a randomised controlled trial – J Lozar Krivec – Beneficial Microbes

Lactobacillus rhamnosus 1.0320 Postbiotics Ameliorate Dextran Sodium Sulfate-Induced Colonic Inflammation and Oxidative Stress by Regulating the Intestinal Barrier and Gut Microbiota – Jing Zhang – Journal of Agricultural and Food Chemistry

Oral administration of Lactobacillus casei DG® after ileostomy closure in restorative proctocolectomy: a randomized placebo-controlled trial (microbiota and immune microenvironment in pouchitis -MEP1) – Imerio Angriman – Gut Microbes

Development of interleukin-27 recombinant Lactococcus lactis and its efficacy in treating psoriasis and colitis in mice – Shaoju Qian – International Journal of Biological Macromolecules

Animal Models

The gut microbiome in patients with Cushing’s disease affects depression- and anxiety-like behavior in mice – Ding Nie – Microbiome

Alpha-synuclein overexpression and the microbiome shape the gut and brain metabolome in mice – Livia H Morais – NPJ Parkinson’s Disease

Transfer of microbiota from lean donors in combination with prebiotics prevents excessive weight gain and improves gut-brain vagal signaling in obese rats – Dulce M Minaya – Gut Microbes

Animal Microbiome (non-models)

Microbiome divergence of marine gastropod species separated by the Isthmus of Panama – Alexander T Neu – Applied and Environmental Microbiology

Plant and Soil Microbiome

Planting density effect on poplar growth traits and soil nutrient availability, and response of microbial community, assembly and function – Rongye Qiao – BMC Plant Biology

Plant growth-promoting fungi improve tobacco yield and chemical components by reassembling rhizosphere fungal microbiome and recruiting probiotic taxa – Mingzi Shi – Environmental Microbiome

Review: Community standards and future opportunities for synthetic communities in plant-microbiota research – Trent R Northen – Nature Microbiology

Review: Alpine and subalpine plant microbiome mediated plants adapt to the cold environment: A systematic review – Mengyan Hou – Environmental Microbiome

Environmental Microbiome

Arctic’s hidden hydrocarbon degradation microbes: investigating the effects of hydrocarbon contamination, biostimulation, and a surface washing agent on microbial communities and hydrocarbon biodegradation pathways in high-Arctic beaches – Ya-Jou Chen – Environmental Microbiome

SALINITY-Induced Changes in Diversity, Stability, and Functional Profiles of Microbial Communities in Different Saline Lakes in Arid Areas – Lei Gao – Microbial Ecology

Resistome analysis of wastewater treatment plants in Agadir city, Morocco, using a metagenomics approach – Maryem Wardi – Scientific Reports

Comparative genomic analysis and characterization of novel high-quality draft genomes from the coal metagenome – Arunmozhi Bharathi Achudhan – World Journal of Microbiology & Biotechnology

November 1, 2024

General human microbiome

[Review] Examining the healthy human microbiome concept – Joos et a. Nature Reviews Microbiology

Bifidobacteria with indole-3-lactic acid-producing capacity exhibit psychobiotic potential via reducing neuroinflammation – Qian et al. Cell Reports Medicine

Longitudinal analysis of the gut microbiota during anti-PD-1 therapy reveals stable microbial features of response in melanoma patients – Macandog et al. Cell Host & Microbe

Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn’s disease – Hacker et al. Cell Host & Microbe

Identification of gut microbiome features associated with host metabolic health in a large population-based cohort – Keshet & Segal. Nature Communications

Probiotics

Design and reporting of prebiotic and probiotic clinical trials in the context of diet and the gut microbiome – Whelan et al. Nature Microbiology

Virome

Prediction of strain level phage–host interactions across the Escherichia genus using only genomic information – Gaborieau et al. Nature Microbiology

Bioinformatics

BakRep – a searchable large-scale web repository for bacterial genomes, characterizations and metadata – Fenske et al. Microbial Genomics

A long-context language model for deciphering and generating bacteriophage genomes – Shao and Yan. Nature Communications

Non Microbiome Piks

We continue to learn more about the mechanisms underpinning long COVID in recent weeks 

Blood transcriptomic analyses do not support SARS-CoV-2 persistence in patients with post-COVID-19 condition with chronic fatigue syndrome – Rahmati et al. The Lancet Microbe

Post-acute sequelae of SARS-CoV-2 cardiovascular symptoms are associated with trace-level cytokines that affect cardiomyocyte function – Sinclair et al. Nature Microbiology

October 27, 2024

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

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 13, 2024

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 2, 2024

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

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 22, 2024

Human and General Microbiome

Multi-way modelling of oral microbial dynamics and host-microbiome interactions during induced gingivitis – G R van der Ploeg – NPJ Biofilms and Microbiomes

Establishing human microbial observatory programs in low- and middle-income countries – Jeffrey I Gordon – Annals of the New York Academy of Sciences

Vaginal microbiota stability over 18 months in young student women in France – Jeanne Tamarelle – European Journal of Clinical Microbiology & Infectious Diseases

Transfer and persistence of microbiota markers from the human hand to the knife: A preliminary study – Sukriye Karadayı – Journal of Forensic and Legal Medicine

Dental Caries: The Way Forward – D T Kopycka-Kedzierawski – JDR Clinical and Translational Research

Changes in the Firmicutes to Bacteriodetes ratio in the gut microbiome in individuals with anorexia nervosa following inpatient treatment: A systematic review and a case series – Passent Helal – Brain and Behavior

Fusobacterium nucleatum facilitates anti-PD-1 therapy in microsatellite stable colorectal cancer – Xueliang Wang – Cancer Cell

Bacterial Extracellular Vesicles as Potential Promoting Factors for Oral Lichen Planus Pathogenesis – Yu Gyung Kim – Inflammation

Gut microbiota metabolite trimethylamine N-oxide promoted NAFLD progression by exacerbating intestinal barrier disruption and intrahepatic cellular imbalance – Fulin Nian – International Immunopharmacology

Comment: Strengthening the foundation of African microbiome research: strategies for standardized data collection – Soumaya Kouidhi – Nature Reviews: Gastroenterology & Hepatology

Review: Microbiota-gut-brain axis in health and neurological disease: Interactions between gut microbiota and the nervous system – Yuhong He – Journal of Cellular and Molecular Medicine

Review: Effect of Staphylococcus aureus colonization and immune defects on the pathogenesis of atopic dermatitis – Evrim Özdemіr – Archives of Microbiology

Beneficial Microbes and Compounds

Gastrointestinal Self-Adaptive and Nutrient Self-Sufficient Akkermansia muciniphila-Gelatin Porous Microgels for Synergistic Therapy of Ulcerative Colitis – Yujie Zhang – ACS Nano

2′-Fucosyllactose attenuates aging-related metabolic disorders through modulating gut microbiome-T cell axis – Ang Li – Aging Cell

Review: Akkermansia in the gastrointestinal tract as a modifier of human health – Maria E Panzetta – Gut Microbes

Animal Microbiome (including Animal Models)

Dipeptide metabolite, glutamyl-glutamate mediates microbe-host interaction to boost spermatogenesis – Balázs Juhász – Scientific Reports

Intestinal deguelin drives resistance to acetaminophen-induced hepatotoxicity in female mice – Shenhai Gong – Gut Microbes

Metformin reprograms tryptophan metabolism via gut Microbiome-Derived bile acid metabolites to ameliorate Depression-Like behaviors in mice – Xiaoxian Xie – Brain, Behavior, and Immunity

Food Microbiome

Dynamics of the microbiome and volatile organic compounds during fermentation and aging of soy sauce – Yuichi Mizuno – Journal of Bioscience and Bioengineering

Unveiling the Brazilian kefir microbiome: discovery of a novel Lactobacillus kefiranofaciens (LkefirU) genome and in silico prospection of bioactive peptides with potential anti-Alzheimer properties – Matheus H Silva – BMC Genomics

Plant Microbiome

Pseudomonas fluorescens Inoculation Enhances Salix matsudana Growth by Modifying Phyllosphere Microbiomes, Surpassing Nitrogen Fertilization – Qing Li – Plant, cell & Environment

Environmental Microbiome

Deep insights into the assembly mechanisms, co-occurrence patterns, and functional roles of microbial community in wastewater treatment plants – Zi-Yan Wei – Environmental Research

Genomic profiling of Antarctic geothermal microbiomes using long-read, Hi-C, and single-cell techniques – Nu Ri Myeong – Scientific Data