September 13, 2024

Posted on by

Happy Friday!
And, see you next week at the MVIF and African Microbiome Day events!

Human microbiome

Gut Microbiome

Transient colonizing microbes promote gut dysbiosis and functional impairment – Sunjae Lee – npj Biofilms and Microbiomes

Cataloging metagenome-assembled genomes and microbial genes from the athlete gut microbiome – Laura Wosinska – Microbiome Research Reports

Gut microbiome and schizophrenia: insights from two-sample Mendelian randomization – Keer Zhou – Schizophrenia

Disease-associated microbiome signature species in the gut – Junhui Li – PNAS Nexus

Nasal microbiome

E-Cigarette Use, Cigarette Smoking, and Sex Are Associated With Nasal Microbiome Dysbiosis Get access Arrow – Elise Hickman – Nicotine & Tobacco Research

Urinary microbiome

Review: Synthesis of current pediatric urinary microbiome research – Layla M. Jeries – Frontiers in Pediatrics

Skin microbiome

The skin microbiome stratifies patients with cutaneous T cell lymphoma and determines event-free survival – Philipp Licht – npj Biofilms and Microbiomes

Animal microbiome

Antibiotics damage the colonic mucus barrier in a microbiota-independent manner – Jasmin Sawaed – Science Advances

Host diet drives gut microbiome convergence between coral reef fishes and mammals – Samuel Degregori – Molecular Ecology

Functional insights into the effect of feralisation on the gut microbiota of cats worldwide – Ostaizka Aizpurua – bioRxiv

Animal experiments

Diet-microbiome interactions promote enteric nervous system resilience following spinal cord injury – Adam M. Hamilton – npj Biofilms and Microbiomes

Ketogenic interventions restore cognition and modulate peripheral metabolic dysfunctions in Alzheimer’s disease mouse models – Paule E. H. M’Bra – bioRxiv

Plant microbiome

The influence of plant traits on soil microbial communities varies between arid and mesic grasslands – Eleonora Egidi – Plant and Soil

Enrichment of novel entomopathogenic Pseudomonas species enhances willow resistance to leaf beetles – Haitao Wang – Microbiome

Microbial colonisation rewires the composition and content of poplar root exudates, root and shoot metabolomes – F. Fracchia – Microbiome

Built environment

Predicting how varying moisture conditions impact the microbiome of dust collected from the International Space Station – Nicholas Nastasi – Microbiom

The predicted secreted proteome of activated sludge microorganisms indicates distinct nutrient niches – Kenneth Wasmund – Environmental Microbiology

Bioinformatics

Microbial network inference for longitudinal microbiome studies with LUPINE – Saritha Kodikara, Kim-Anh Le Cao – bioRxiv

September 12, 2024

Posted on by

General microbiome

[REVIEW]Emerging roles of intratumor microbiota in cancer: tumorigenesis and management strategies – Shi, Li & Zhang – Journal of Translational Medicine

[REVIEW]Fungal effectors: past, present, and future – Li et al. – Current Opinion in Microbiology

[Voices]Microbes and metabolites in immunity – Elinav et al. – Immunity

Pregnancy and early life

Human milk variation is shaped by maternal genetics and impacts the infant gut microbiome – Johnson et al. – Cell Genomics

Human urinary tract microbiome

[REVIEW]Urinary tract infections: pathogenesis, host susceptibility and emerging therapeutics – Timm, Russell & Hultgren

Human gut microbiome

Dietary-timing-induced gut microbiota diurnal oscillations modulate inflammatory rhythms in rheumatoid arthritis – Ma et al. – Cell Metabolism

Animal microbiome

[PREPRINT]The holobiont’s extracellular microbiome modulates the adaptation of an intracellular endosymbiont – Imchen et al. – bioRxiv

[PREPRINT]Functional insights into the effect of feralisation on the gut microbiota of cats worldwide – Aizpurua et al. – bioRxiv

Microbial community profiling in intestinal tract of indigenous chickens from different villages – Mootane et al. – Scientific Reports

Vitamin B12 ameliorates gut epithelial injury via modulating the HIF-1 pathway and gut microbiota – Feng et al. – Cellular and Molecular Life Sciences

[PREPRINT]Symbiont loss and gain, rather than co-diversification shapes honeybee gut microbiota diversity and function – Prasad et al. – bioRxiv

[PREPRINT]Effects of parental care on skin microbial community composition in poison frogs – Fischer et al. – bioRxiv

Plant, root, and soil microbiome

Metabolome-driven microbiome assembly determining the health of ginger crop (Zingiber officinale L. Roscoe) against rhizome rot – Wang et al. – Microbiome

[REVIEW]Re-Envisioning the Plant Disease Triangle: Full Integration of the Host Microbiota and a Focal Pivot to Health Outcomes – Leveau – Annual Review of Phytopathology

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

Global marine microbial diversity and its potential in bioprospecting – Chen et al. – Nature

Bioinformatics

Stable biomarker discovery in multi-omics data via canonical correlation analysis – Pusa & Rousu – PLOS One

Techniques

Highly accurate and sensitive absolute quantification of bacterial strains in human fecal samples – Li et al. – Microbiome

September 8, 2024

Posted on by

Human and General Microbiome

Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes – Aarthi Ravikrishnan – Nature Communications

Integrated analysis of facial microbiome and skin physio-optical properties unveils cutotype-dependent aging effects – Chuqing Sun – Microbiome

Regulation of Bacteroides acidifaciens by the aryl hydrocarbon receptor in IL-22-producing immune cells has sex-dependent consequential impact on colitis – Chandani Mitchell – Frontiers in Immunology

The role of KLF5 in gut microbiota and lung adenocarcinoma: unveiling programmed cell death pathways and prognostic biomarkers – Qingliang Fang – Discover Oncology

Healthy first-degree relatives from multiplex families versus simplex families have a higher subclinical intestinal inflammation, a distinct fecal microbial signature, and harbor a higher risk of developing Crohn’s disease – Pablo A Olivera – Gastroenterology

Reversions mask the contribution of adaptive evolution in microbiomes – Paul A Torrillo – eLife

Review: The hidden base of the iceberg: gut peptidoglycome dynamics is foundational to its influence on the host – Richard Wheeler – Gut Microbes

Review: Benefits and concerns of probiotics: an overview of the potential genotoxicity of the colibactin-producing Escherichia coli Nissle 1917 strain – Luca Falzone – Gut Microbes

Book Chapter: Microbial Extracellular Vesicles in Host-Microbiota Interactions – Sarah Abubaker – Results and Problems in Cell Differentiation

Beneficial Microbes and Compounds

A probiotic Limosilactobacillus fermentum GR-3 mitigates colitis-associated tumorigenesis in mice via modulating gut microbiome – Tuoyu Zhou – NPJ Science of Food

Review: Pathophysiological and Clinical Potential of Human Microbiome: Microbe-based Therapeutic Insights – Somali Sanyal – Current Pharmaceutical Biotechnology

Plant Microbiome

Soil volatilomics uncovers tight linkage between soybean presence and soil omics profiles in agricultural fields – Hikari Kuchikata – Scientific Report

Review: Meddling with the microbiota: Fungal tricks to infect plant hosts – Fantin Mesny – Current Opinion in Plant Biology

Environmental Microbiome

A comprehensive catalog encompassing 1376 species-level genomes reveals the core community and functional diversity of anammox microbiota – Depeng Wang – Water Research

Revealing the intricate temporal dynamics and adaptive responses of prokaryotic and eukaryotic microbes in the coastal South China Sea – Wenqian Xu – The Science of the Total Environment

Biodegradation of low-density polyethylene by mixed fungi composed of Alternaria sp. and Trametes sp. isolated from landfill sites – Wei-Kang Yang – BMC Microbiology

Using patterns of shared taxa to infer bacterial dispersal in human living environment in urban and rural areas – M Grönroos – Applied and Environmental Microbiology

Annotation-free prediction of microbial dioxygen utilization – Avi I Flamholz – mSystem

Microbiome Analysis: Tools, Techniques and Resources

MRGM: an enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes – Nayeon Kim – Gut Microbes

A unified web cloud computing platform MiMedSurv for microbiome causal mediation analysis with survival responses – Hyojung Jang – Scientific Reports

A quantitative approach to measure and predict microbiome response to antibiotics – Vincent Tu – mSphere

Metagenomic functional profiling: to sketch or not to sketch? – Mahmudur Rahman Hera – Bioinformatics

TolRad, a model for predicting radiation tolerance using Pfam annotations, identifies novel radiosensitive bacterial species from reference genomes and MAGs – Philip Sweet – Microbiology Spectrum

Review: Improving viral annotation with artificial intelligence – Zachary N Flamholz – mBio

Additionally, the Cold Spring Harbor Protocols Journal released a set of protocols covering the study of Maize Microbiome:

Sampling the Maize (Zea mays) Leaf Microbiome – Jason G Wallace – Cold Spring Harbor Protocols

Sampling Root-Associated Microbiome Communities of Maize (Zea mays) – Alonso Favela – Cold Spring Harbor Protocols

Sampling and Analysis of the Maize Microbiome – Jason G Wallace – Cold Spring Harbor Protocols

Manipulating the Maize (Zea mays) Microbiome – Sierra S Raglin – Cold Spring Harbor Protocols

September 4, 2024

Posted on by

Good morning (or afternoon, or evening, wherever you are in the world reading this,) Microbiome Digesters! Today’s post features a piece from Nature highlighting the ethical dilemmas and evolving approaches in Indigenous microbiome research. Indigenous peoples have historically faced exploitation through extraction of their lands, biological samples, and genetic data without proper consent. Researchers are re-evaluating their methods, shifting towards more respectful and collaborative practices that involve Indigenous communities in designing studies and ensuring they benefit from the findings. Check out the piece by Sam Jones for Nature to learn more.

An ethical way forward for Indigenous microbiome research – Sam Jones – Nature Outlook: The human microbiome

Human gut microbiome

Interplay between particle size and microbial ecology in the gut microbiome – Jeffrey Letourneau et al – ISME Journal

Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome – Niccolò Carlino – Cell

A streamlined culturomics case study for the human gut microbiota research – Hyunjoon Park et al – Scientific Reports

Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia – Getnet Tesfaw et al – Nature Communications

Association of maternal gut microbial metabolites with gestational diabetes mellitus: evidence from an original case-control study, meta-analysis, and Mendelian randomization – Mengxin Yao et al – European Journal of Clinical Nutrition

The Microleaks study: 16S community profile and metagenomic shotgun sequencing signatures associated with anastomotic leak – Emily C. Hoedt et al – NPJ Gut & Liver

Targeted isolation of Methanobrevibacter strains from fecal samples expands the cultivated human archaeome – Stefanie Duller et al – Nature Communications

Characterization of gut microbiota in the Uyghur osteopenia population – Kunchen Teng et al – Scientific Reports

Spaceflight alters host-gut microbiota interactions – E. Gonzalez et al – NPJ Biofilms & Microbiomes

Other human microbiome

Bacterial association with metals enables in vivo monitoring of urogenital microbiota using magnetic resonance imaging – Sarah C. Donnelly et al – Communications Biology

Urine metabolomic profiles of autism and autistic traits – A twin study – Abishek Arora et al – PLOS One

Animal microbiome

Massive expansion of the pig gut virome based on global metagenomic mining – Jiandui Mi et al – NPJ Biofilms & Microbiomes

Marine sponge microbe provides insights into evolution and virulence of the tubercle bacillus – Sacha J. Pidot et al – PLOS Pathogens

Exploring the interactions between Nosema ceranae infection and the honey bee gut microbiome – Edmund Lau et al – Scientific Reports

Metagenomic characterisation of canine skin reveals a core healthy skin microbiome – Michaella J. Whittle et al – Scientific Reports

CHIKV infection drives shifts in the gastrointestinal microbiome and metabolites in rhesus monkeys – Hongyu Chen et al – BMC Microbiome

Effects of dietary restriction and one-carbon metabolite supplementation during the first 63 days of gestation on the maternal gut, vaginal, and blood microbiota in cattle – Sarah M. Luecke et al – BMC Animal Microbiome

Aloe arborescens supplementation in drying-off dairy cows: influence on rumen, rectum and milk microbiomes – Paola Cremonesi et al – BMC Animal Microbiome

Comparative genomics identifies key adaptive traits of sponge-associated microbial symbionts – Paul A. O’Brien et al – Environmental Microbiology

Plant, root & soil microbiome

Deciphering the role of rhizosphere microbiota in modulating disease resistance in cabbage varieties – Xingxing Ping et al – BMC Microbiome

Oak seedling microbiome assembly under climate warming and drought – Daniel Hoefle et al – BMC Environmental Microbiome

The ancestral environment of teosinte populations shapes their root microbiome – Christopher J. Barnes et al – BMC Environmental Microbiome

Water & marine microbiome

Prokaryotic-virus-encoded auxiliary metabolic genes throughout the global oceans – Funing Tian et al – BMC Microbiome

Global distribution, diversity, and ecological niche of Picozoa, a widespread and enigmatic marine protist lineage – BMC Microbiome

Microbial core communities in activated sludge plants are strongly affected by immigration and geography – Sofie Zacho Vertergaard et al – BMC Environmental Microbiome

The eukaryome of modern microbialites reveals distinct colonization across aquatic ecosystems – Anthony M. Bonacolta et al – NPJ Biofilms & Microbiomes

Methods & techniques

[PREPRINT] Domestic freezer storage: a solution for preserving stool microbiota integrity for at-home collection – Paula Momo Cabrera et al – bioRxiv

COVID-19 prevention behaviors and dietary habits among undergraduate students: A health belief model approach – Doreen Liou – PLOS One

A catalog of small proteins from the global microbiome – Yiqian Duan et al – Nature Communications

August 28, 2024

Posted on by

Human gut microbiome

[REVIEW] Feeding gut microbes to nourish the brain: unravelling the diet–microbiota–gut–brain axis – Elizabeth Schneider et al – Nature Metabolism

Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes – Jordy Evan Sulaiman et al – Nature Communications

Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients – Anna K. Hartikainen et al – NPJ Biofilms & Microbiomes

Impact of probiotics on gut microbiome of extremely preterm or extremely low birthweight infants – Lauren C. Beck et al – Nature Pediatric Research

Effect of Helicobacter pylori on sleeve gastrectomy and gastric microbiome differences in patients with obesity and diabetes – Yong Suk Park et al – International Journal of Obesity

Mining human microbiomes reveals an untapped source of peptide antibiotics – Marcelo D.T. Torres et al – Cell

Both pathogen and host dynamically adapt pH responses along the intestinal tract during enteric bacterial infection – Sarah E. Woodward et al – PLOS Biology

Examination of sex-specific interactions between gut microbiota and host metabolism after 12-week combined polyphenol supplementation in individuals with overweight or obesity – Kelly M. Jardon et al – Gut Microbes

Human vaginal microbiome

The potential of residual clinical Group B Streptococcus swabs for assessing the vaginorectal microbiome in late pregnancy – Laura K. Boelsen et al – Scientific Reports

Animal models

Sex-dependent effects of a high fat diet on metabolic disorders, intestinal barrier function and gut microbiota in mouse – Candice Lefebvre et al – Scientific Reports

Animal microbiome

16S rRNA metabarcoding for the identification of tick-borne bacteria in ticks in the Republic of Korea – Badriah Alkathiri et al – Scientific Reports

The bacterial microbiome and resistome of house dust mites in Irish homes – Amal Aljohani et al – Scientific Reports

Social environment influences microbiota and potentially pathogenic bacterial communities on the skin of developing birds – Ester Martínez-Renau – BMC Animal Microbiome

16S amplicon-based microbiome biomapping of a commercial broiler hatchery – Michael J. Rothrock Jr. et al – BMC Animal Microbiome

Phages & viruses

[REVIEW] Renewed insights into Ackermannviridae phage biology and applications – Anders Nørgaard Sørensen & Lone Brøndsted – NPJ Viruses

Adaptation strategies of giant viruses to low-temperature marine ecosystems – Marianne Buscaglia et al – ISME Journal

Targeted viromes and total metagenomes capture distinct components of bee gut phage communities – Dino Lorenzo Sbardellati et al – BMC Microbiome

Plant, root & soil microbiome

Soil health is associated with higher primary productivity across Europe – Ferran Romero et al – Nature Ecology & Evolution

Pathogen-driven Pseudomonas reshaped the phyllosphere microbiome in combination with Pseudostellaria heterophylla foliar disease resistance via the release of volatile organic compounds – Qing-Song Yuan et al – BMC Environmental Microbiome

Water & extremophile microbiome

Impact of temperature and water source on drinking water microbiome during distribution in a pilot-scale study – Fien Waegenaar et al – NPJ Clean Water

Metagenomics analysis of sewage for surveillance of antimicrobial resistance in South Africa – Anthony M. Smith et al – PLOS One

Nitrite-oxidizing bacteria adapted to low oxygen conditions dominate nitrite oxidation in marine oxygen minimum zones – Samantha G Fortin et al – ISME Journal

Niche separation in bacterial communities and activities in porewater, loosely attached, and firmly attached fractions in permeable surface sediments – Chyrene Moncada et al – ISME Journal

Microbial assemblages and associated biogeochemical processes in Lake Bonney, a permanently ice-covered lake in the McMurdo Dry Valleys, Antarctica – Hanbyul Lee et al – BMC Environmental Microbiome

Tools & methods

Intestinal organ chips for disease modelling and personalized medicine – Alican Özkan et al – Nature Reviews Gastroenterology & Hepatology

MICROPHERRET: MICRObial PHEnotypic tRait ClassifieR using Machine lEarning Techniques – Edoardo Bizzotto et al – BMC Environmental Microbiome

refMLST: reference-based multilocus sequence typing enables universal bacterial typing – Mondher Khdhiri et al – BMC Bioinformatics

Smccnet 2.0: a comprehensive tool for multi-omics network inference with shiny visualization – Weixian Liu et al – BMC Bioinformatics

August 18, 2024

Posted on by

Human and General Microbiome

Maternal antibiotic prophylaxis during cesarean section has a limited impact on the infant gut microbiome – Trishla Sinha – Cell Host & Microbe

Microbial assimilatory sulfate reduction-mediated H(2)S: an overlooked role in Crohn’s disease development – Wanrong Luo – Microbiome (BMC)

Characterization of the vaginal microbiota in Italian women with endometriosis: preliminary study – Rosa Sessa – Archives of Gynecology and Obstetrics

Profiles and interactions of gut microbiome and intestinal microRNAs in pediatric Crohn’s disease – Yao Lv – mSystems

Regional variation and adaptive evolution in Bifidobacterium pseudocatenulatum: Insights into genomic and functional diversity in human gut – Qiong Wu – Food Research International

Review: Effects of physical exercise on Akkermansia muciniphila: a systematic review of human and animal studies – S S Aguiar – Beneficial Microbes

Beneficial Microbes and Compounds

Commentary: Microbiome modification for personalized treatment of dysbiotic diseases – R Balfour Sartor – Cell Host & Microbe

Combining Gut Microbiota Modulation and Enzymatic-Triggered Colonic Delivery by Prebiotic Nanoparticles Improves Mouse Colitis Therapy – Hui Li – Biomaterials Research

Animal Microbiome

Effect of chronic alcohol consumption on oral microbiota in rats with periodontitis – Zirui Zhao – PeerJ

Fecal microbiota transplantation accelerates restoration of florfenicol-disturbed intestinal microbiota in a fish model – Zhuoran Han – Communications Biology

Structural, Biochemical, and Phylogenetic Analysis of Bacterial and Fungal Carbohydrate Esterase Family 15 Glucuronoyl Esterases in the Rumen – Robert J Gruninger – The Protein Journal

Plant Microbiome

Review: Harnessing the plant microbiome for sustainable crop production – Stéphane Compant – Nature Reviews Microbiology

Review: The impact of filamentous plant pathogens on the host microbiota – Victor M Flores-Nunez – BMC Biology

Environmental Microbiome

Metagenomic insights into the prokaryotic communities of heavy metal-contaminated hypersaline soils – Cristina Galisteo – The Science of the Total Environment

Ecological phage therapy: Can bacteriophages help rapidly restore the soil microbiome? – Tarryn Davies – Ecology and Evolution

Do restoration strategies in mangroves recover microbial diversity? A case study in the Yucatan peninsula – Daniel Esguerra-Rodríguez – PloS One

Metagenome sequencing and 107 microbial genomes from seamount sediments along the Yap and Mariana trenches – Yue Zhang – Scientific Data

Microbiome Analysis: Tools, Techniques and Resources

Metrological evaluation of DNA extraction method effects on the bacterial microbiome and resistome in sputum – Aleksander Benčič – mSystems

Commentary: AI in microbiome research: Where have we been, where are we going? – Georg K Gerber – Cell Host & Microbe

Review: Modeling Microbial Communities: Perspective and Challenges – Lavanya Raajaraam – ACS Synthetic Biology

August 14, 2024

Posted on by

Human microbiome

Major depletion of insulin sensitivity-associated taxa in the gut microbiome of persons living with HIV controlled by antiretroviral drugs – Eugeni Belda et al – BMC Medical Genomics

The impact of breastfeeding on the preterm infant’s microbiome and metabolome: a pilot study – Keriann Schulkers Escalante et al – Nature Pediatric Research

[REVIEW] The human microbiome in space: parallels between Earth-based dysbiosis, implications for long-duration spaceflight, and possible mitigation strategies – Sofia Etlin et al – Clinical Microbiology Reviews

MASS cohort: Multicenter, longitudinal, and prospective study of the role of microbiome in severe pneumonia and host susceptibility – Xin Wei et al – iMeta

Distinctive duodenal microbiomes and bile acid profiles in duodenal tumor patients revealed by prospective observational study – Yoko Kubosawa et al – Nature Scientific Reports

Elucidating the dynamics and impact of the gut microbiome on maternal nutritional status during pregnancy, effect on pregnancy outcomes and infant health in rural Pakistan: study protocol for a prospective, longitudinal observational study – Yaqub Wassan et al – BMJ Open

Time-varying ambient air pollution exposure is associated with gut microbiome variation in the first 2 years of life – Tianlai Qiu et al – Environmental Pollution

Animal experiments

Gut Microbiota-Induced Modulation of the Central Nervous System Function in Parkinson’s Disease Through the Gut-Brain Axis and Short-Chain Fatty Acids – Yiting Ni et al – Molecular Neurobiology

Animal microbiome

Synergistic pectin deconstruction is a prerequisite for mutualistic interactions between honeybee gut bacteria – Junbo Tang et al – Nature Communications

Environmentally acquired gut-associated bacteria are not critical for growth and survival in a solitary bee, Megachile rotundata – Gagandeep Brar et al – Applied & Environmental Microbiology

Duck gut metagenome reveals the microbiome signatures linked to intestinal regional, temporal development, and rearing condition – Lingyan Ma & Wentao Lyu et al – iMeta

Meconium microbiota in naturally delivered canine puppies – Alessia Bertero et al – BMC Veterinary Research

Gut microbiome perturbation and its correlation with tylosin pharmacokinetics in healthy and infected pigs – Eon-Bee Lee et al – Nature Scientific Reports

Beneficial microbes, compounds, & foods

Restriction of growth and biofilm formation of ESKAPE pathogens by caprine gut-derived probiotic bacteria – Prerna Saini et al – Frontiers in Microbiology

[REVIEW] Polyphenols improve non-alcoholic fatty liver disease via gut microbiota: A comprehensive review – Kimia Mohammadhasani et al – Food Science & Nutrition

[REVIEW] Exploring the Potential of Postbiotics for Food Safety and Human Health Improvement – Folayemi Janet Isaac-Bamgboye et al – Journal of Nutrition & Metabolism

Transcriptomics and gut microbiome analysis of the edible herb Bidens pilosa as a functional feed additive to promote growth and metabolism in tilapia (Oreochromis spp.) – Che-Chun Chen et al – BMC Genomics

[REVIEW] A comprehensive review of the characterization, host interactions, and stabilization advancements on probiotics: Addressing the challenges in functional food diversification – Eskindir Getachew Fentie et al – Comp. Rev. in Food Science & Safety

Effects of kefir consumption on gut microbiota and health outcomes in women with polycystic ovary syndrome – Merve Esra Çıtar Dazıroğlu – Food Science & Nutrition

Plant, root, & soil microbiome

Decrease due to pollution in the rhizosphere microbial diversity can be amended by supplementation from adapted plants of another species – Anastasiia Fetsiukh et al – Nature Scientific Reports

Differences in the constituents of bacterial microbiota of soils collected from two fields of diverse potato blackleg and soft rot diseases incidences, a case study – Weronika Babinska-Wensierska et al – Nature Scientific Reports

Variations of soil metal content, soil enzyme activity and soil bacterial community in Rhododendron delavayi natural shrub forest at different elevations – Li Wang et al – BMC Microbiology

Effective microorganism combinations improve the quality of compost-bedded pack products in heifer barns: exploring pack bacteria-fungi interaction mechanisms – Zhenbin Zhang et al – BMC Microbiology

Global patterns in the growth potential of soil bacterial communities – Ernest D. Osburn et al – Nature Communications

Microplastic-contamination can reshape plant community by affecting soil properties – Mengzuan He et al – Ecotoxicology & Environmental Safety

Water & extremophile microbiome

Microbial Succession on Microplastics in Wastewater Treatment Plants: Exploring the Complexities of Microplastic-Microbiome Interactions – Klaudia Kwiatkowska & Paulina Ormaniec – Microbial Ecology

Microbial ecology

Higher-order interactions and emergent properties of microbial communities: The power of synthetic ecology – Oscar Gallardo-Navarro et a – Heliyon

Antibiotic resistance

[NEWS FEATURE] Five ways science is tackling the antibiotic resistance crisis – Amber Dance – Nature

Antibiotic resistance gene dynamics in the commensal infant gut microbiome over the first year of life – Pål Trosvik et al – Nature Scientific Reports

Bioinformatics tools

MetaBakery: a Singularity implementation of bioBakery tools as a skeleton application for efficient HPC deconvolution of microbiome metagenomic sequencing data to machine learning ready information – Boštjan Murovec et al – Frontiers in Microbiology

August 11, 2024

Posted on by

Human and General Microbiome

B cell senescence promotes age-related changes in oral microbiota – Hiroya Mizuno – Aging Cell

Exploring the relationship between gut microbiota and breast cancer risk in European and East Asian populations using Mendelian randomization – Wei Lin – BMC Cancer

Intratumoral microbiome promotes liver metastasis and dampens adjuvant imatinib treatment in gastrointestinal stromal tumor – Yanze Li – Cancer Letters

Comparison of Vaginal microbiota in HPV-negative and HPV-positive pregnant women using a culture-based approach – Podoprigora Irina – Diagnostic Microbiology and Infectious Disease

The gut-microbiome in adult Attention-deficit/hyperactivity disorder – A Meta-analysis – Babette Jakobi – European Neuropsychopharmacology

An Empirical Dietary Pattern Associated with the Gut Microbial Features in Relation to Colorectal Cancer Risk – Kai Wang – Gastroenterology

Species-level characterization of gut microbiota and their metabolic role in kidney stone formation using full-length 16S rRNA sequencing – Bashir Hussain – Urolithiasis

Review: Game of microbes: the battle within – gut microbiota and multiple sclerosis – Ti-Ara Turner – Gut Microbes

Review: The early life exposome and autism risk: a role for the maternal microbiome? – Claudia M Di Gesù – Gut Microbes

Review: Gut mycobiome alterations and implications for liver diseases – Suling Zeng – PLoS Pathogens

Beneficial Microbes and Compounds

A novel intervention of molecular hydrogen on the unbalance of the gut microbiome in opioid addiction: Experimental and human studies – Bing Xie – Biomedicine & Pharmacotherapy

Lower fecal microbiota transplantation ameliorates ulcerative colitis by eliminating oral-derived Fusobacterium nucleatum and virulence factor – Dong-Hao Li – Gut Pathogens

Induction of Cell Death by Bifidobacterium infantis DS1685 in Colorectal and Breast Cancers via SMAD4/TGF-Beta Activation – In Hwan Tae – Journal of Microbiology and Biotechnology

Review: Peptide GLP-1 receptor agonists: From injection to oral delivery strategies – Zhiqiang Ke – Biochemical Pharmacology

Animal Microbiome (including model experiments)

Stress-sensitive neural circuits change the gut microbiome via duodenal glands – Hao Chang – Cell

Effect of Hafnia alvei on Morphophysiologic Parameters and Gut Microbiota of Mice with Inherited Type 2 Diabetes Mellitus – V A Zolotarev – Bulletin of Experimental Biology and Medicine

Spatial analysis of murine microbiota and bile acid metabolism during amoxicillin treatment – Chapman N Beekman – Cell Reports

Evaluating impacts of radiation-induced sterilization on the performance and gut microbiome of mass-reared Mediterranean fruit fly (Ceratitis capitata) in Hawai’i – Charles J Mason – Journal of Economic Entomology

Plant Microbiome

Disease Resistance Correlates with Core Microbiome Diversity in Cotton – Rhea Aqueel – Current Microbiology

Environmental Microbiome

The symbiotic alga Trebouxia fuels a coherent soil ecosystem on the landscape scale in the Atacama Desert – Patrick Jung – Environmental Microbiome

Relationships between radiation, wildfire and the soil microbial communities in the Chornobyl Exclusion Zone – Alexandre Barretto de Menezes – The Science of the Total Environment

The first large scale rDNA amplicon database of soil microbiomes from Pamir Plateau, China – Jing Zhu – Scientific Data

Food and Beverage Microbiome

Changes in the solid-associated bacterial and fungal communities following ruminal in vitro fermentation of winery by-products: aspects of the bioactive compounds and feed safety – Ratchaneewan Khiaosa-Ard – Anaerobe

16S amplicon-based microbiome biomapping of a commercial broiler hatchery – Michael J Jr Rothrock – Animal Microbiome

Analyzing the gut microbiota and microbial-associated metabolites of tomato-based sauces – Alicia Paulina Cárdenas-Castro – Food Chemistry

August 8, 2024

Posted on by

Human respiratory, skin, and gut microbiome

Nurturing futures through the maternal microbiome – Roberta Pala & Katherine Kenny – Sociology of Health & Illness

The skin microbiota of preterm infants and impact of diaper change frequency – Noelle E. Younge et al – PLOS One

Vitamin A carotenoids, but not retinoids, mediate the impact of a healthy diet on gut microbial diversity – Ana M. Valdes et al – BMC Medicine

Gut microbial composition is altered in sarcopenia: A systematic review and meta-analysis of clinical studies – Xiaohong Mai et al – PLOS One

Associations of upper respiratory mucosa microbiota with Rheumatoid arthritis, autoantibodies, and disease activity – Young Bin Joo et al – PLOS One

Effect of β-lactam antibiotics on the gut microbiota of term neonates – Hongdan Gu et al – BMC Annals of Clinical Microbiology & Antimicrobials

Clinical efficacy of a multilamellar cream on skin physiology and microbiome in an epidermal stress model: A controlled double-blinded study – Joachim W Fluhr et al – Int. Journal of Cosmetic Science

Animal experiments

Mouse adaptation of human inflammatory bowel diseases microbiota enhances colonization efficiency and alters microbiome aggressiveness depending on the recipient colonic inflammatory environment – Simon M. Gray et al – BMC Microbiome

Animal microbiome

Gut microbiota composition of the isopod Ligia in South Korea exposed to expanded polystyrene pollution – Young-Mi Lee et al – PLOS One

Effects of a supplemented diet containing 7 probiotic strains (Honeybeeotic) on honeybee physiology and immune response: analysis of hemolymph cytology, phenoloxidase activity, and gut microbiome – Patrizia Robino et al – BMC Biological Research

Survey of antimicrobial and probiotic use practices in wildlife rehabilitation in the United States – Elizabeth A. Miller et al – PLOS One

The impact of management on the fecal microbiome of endangered greater sage-grouse (Centrocercus urophasianus) in a zoo-based conservation program – Emma Vaasjo et al – Conservation Physiology

Water & extremophile microbiome

Microdiversity in marine pelagic ammonia-oxidizing archaeal populations in a Mediterranean long-read metagenome – Pablo Suárez-Moo et al – Environmental Microbiology

Production of structurally diverse sphingolipids by anaerobic marine bacteria in the euxinic Black Sea water column – Su Ding et al – ISME Journal

Plant, root & soil microbiome

Characterization of fungal microbiome structure in leaf litter compost through metagenomic profiling for harnessing the bio-organic fertilizer potential – Sophayo Mahongnao et al – 3Biotech

Plant species influences the composition of root system microbiome and its antibiotic resistance profile in a constructed wetland receiving primary treated wastewater – Valentina Riva et al – Frontiers in Microbiology

DNA stable isotope probing reveals the impact of trophic interactions on bioaugmentation of soils with different pollution histories – Esteban E. Nieto et al – BMC Microbiome

Seed endophytes and rhizosphere microbiome of Imperata cylindrica, a pioneer plant of abandoned mine lands – Wenqin Mao et al – Frontiers in Microbiology

Temperature-dependent trophic associations modulate soil bacterial communities along latitudinal gradients – Xing Huang et al – ISME Journal.

Microbial ecology

[PREPRINT] Models of microbiome evolution incorporating host resource provisioning – Yao Xiao et al – bioRxiv

Beneficial microbes & compounds

Combining Bifidobacterium longum subsp. infantis and human milk oligosaccharides synergistically increases short chain fatty acid production ex vivo – Florac De Bruyn et al – Nature Communications Biology

August 6, 2024

Posted on by

Human Gut Microbiota

Review – The role of the gut microbiota in regulating responses to vaccination: current knowledge and future directions – Rossouw et al. FEBS

Systemic antibody responses against gut microbiota flagellins implicate shared and divergent immune reactivity in Crohn’s disease and chronic fatigue syndrome – Bourgonje et al. – Microbiome

Pregnancy and early life

Diet at birth is critical for healthy growth, independent of effects on the gut microbiota – Lieke et al. – Microbiome

Delivery mode is a larger determinant of infant gut microbiome composition at 6 weeks than exposure to peripartum antibiotics – Leech et al. Microbial Genomics.

Association of breast milk-derived arachidonic acid-induced infant gut dysbiosis with the onset of atopic dermatitis – Jiang et al. – Gut

General Human Microbiota

The potential role of lung microbiota and lauroylcarnitine in T-cell activation associated with checkpoint inhibitor pneumonitis – Yu et al. eBioMedicine

Evidence of Lactobacillus strains shared between the female urinary and vaginal microbiota – Atkins et al. – Microbial Genomics

A human commensal-pathogenic fungus suppresses host immunity via targeting TBK1 – Lou et al. Cell Host & Microbe

Bacteriophage

Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses – Van den Berg et al. – Cell Host & Microbe

Genomic and induction evidence for bacteriophage contributions to sargassum-bacteria symbioses – Stiffler et al. – Microbiome