Tag Archives: bioinformatics

Septiembre 15, 2024

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Human and General Microbiome

Correlation of gut microbial diversity to sight-threatening diabetic retinopathy – Rehana Khan – BMC Microbiology

Multiomics reveals microbial metabolites as key actors in intestinal fibrosis in Crohn’s disease – Xuehua Li – EMBO Molecular Medicine

Inflammation mediated by gut microbiome alterations promotes lung cancer development and an immunosuppressed tumor microenvironment – Zahraa Rahal – Cancer Immunology Research

Microbial interactions impact stress tolerance in a model oral community – Gina R Lewin – Microbiology Spectrum

The use of metagenomic and untargeted metabolomics in the analysis of the effects of the Lycium barbarum glycopeptide on allergic airway inflammation induced by Artemesia annua pollen – Min Bai – Journal of Ethnopharmacology

Enteric-coated cerium dioxide nanoparticles for effective inflammatory bowel disease treatment by regulating the redox balance and gut microbiome – Yubiao Huang – Biomaterials

Review: Micro- and nano-plastics, intestinal inflammation, and inflammatory bowel disease: A review of the literature – Manasi Agrawal – The Science of the Total Environment

Commentary:  The 3 Ds: Depression, Dysbiosis, and Clostridiodes difficile – Antoine Boustany – Advances in Therapy

Research Highlight: Targeting fatty acid metabolism promotes a healthy vaginal microbiome – Iris Marchal – Nature Biotechnology

Animal Microbiome

Metagenomic analysis of the gut microbiota of hooded cranes (Grus monacha) on the Izumi plain in Japan – Kosuke Takada – FEBS Open Bio

From Skin to Gut: Understanding Microbial Diversity in Rana amurensis and R. dybowskii – Ming-He Yang – Current Microbiology

Plant and Soil Microbiome

Ridge planting increases the rhizosphere microbiome diversity and improves the yield of Pinellia ternata (Thunb.) Breit in North China – Yaofa Li – PloS One

Microbiome Analysis

Forum: Bioinformatics challenges for profiling the microbiome in cancer: pitfalls and opportunities – Nicholas A Bokulich – Trends in Microbiology

September 8, 2024

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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

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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

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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

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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

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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 4, 2024

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Human Gut Microbiome

Exploring the interplay between antiretroviral therapy and the gut-oral microbiome axis in people living with HIV – Aswathy Narayanan – Scientific Reports

Human Gut Microbiota Composition Associated with International Travels – D Henares – Travel Medicine and Infectious Disease

Respiratory microbiome and clinical course of carbapenem-resistant Acinetobacter baumannii pneumonia in critically Ill patients – Jin Gu Yoon – Medicine

Review: Gut Microbiota and Autism Spectrum Disorder: A Neuroinflammatory Mediated Mechanism of Pathogenesis? – Fatemeh Zarimeidani – Inflammation

Review: Gut microbiota and eating behaviour in circadian syndrome – Jorge R Soliz-Rueda – Trends in Endocrinology and Metabolism

Beneficial Microbes and Compounds

Staphylococcus aureus/Staphylococcus epidermidis from skin microbiota are balanced by Pomegranate peel extract: An eco-sustainable approach – Sara D’Arcangelo – PloS One

Microbiome mapping in dairy industry reveals new species and genes for probiotic and bioprotective activities – Francesca De Filippis – NPJ Biofilms and Microbiomes

Bugs as drugs: Extended clinical applications and potential translational trends of Akkermansia muciniphila in oncology and comprehensive clinical investigation panorama of therapeutic microbiome modulators in gastric cancer treatment – Yuning Wang – Pharmacological Research

Polyphenols: potent protectors against chronic diseases – Geetha Shanmugam – Natural Product Research

Animal Microbiome

Effects of berberine hydrochloride on antioxidant response and gut microflora in the Charybdis japonica infected with Aeromonas hydrophila – Mingming Han – BMC Microbiology

Design of an agro-industrial by-products-based media for the production of probiotic bacteria for fish nutrition – Marcelo Fernando Valle Vargas – Scientific Reports

Association of microbial community structure with gill disease in marine-stage farmed Atlantic salmon (Salmo salar); a yearlong study – Morag Clinton – BMC Veterinary Research

Selection for stress tolerance and longevity in Drosophila melanogaster have strong impacts on microbiome profiles – Torsten Nygaard Kristensen – Scientific Reports

Novel insights on microbiome dynamics during a gill disease outbreak in farmed rainbow trout (Oncorhynchus mykiss) – Samuele Zamparo – Scientific Reports

Gut Microbiome-Driven metabolites influence skin pigmentation in TYRP1 mutant Oujiang color common carp – Roland Nathan Mandal – Gene

Plant and Soil Microbiome

From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology – Winston E Anthony – Environmental Microbiome

An acidophilic fungus promotes prey digestion in a carnivorous plant – Pei-Feng Sun – Nature Microbiology

A novel strategy of artificially regulating plant rhizosphere microbial community to promote plant tolerance to cold stress – Jianfeng Zhang – The Science of the Total Environment

A bud’s life: Metabarcoding analysis to characterise hazelnut big buds microbiome biodiversity – Silvia Turco – Microbiological Research

Perspective: Integrating viruses into soil food web biogeochemistry – Cátia Carreira – Nature Microbiology

Review: Rhizosphere microbiome assembly, drivers and functions in perennial ligneous plant health – Morgane Duret – Microbiological Research

Environmental Microbiome

Genomic and induction evidence for bacteriophage contributions to sargassum-bacteria symbioses – Alexandra K Stiffler – Microbiome

July 31, 2024

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Human gut microbiome

The gut mycobiome signatures in long-lived populations – Lixia Pu et al – Cell iScience

Viral metagenomics combined with non-targeted serum metabolomics reveals the role of enteroviruses in a mouse model of coronary heart disease – Xiang Li et al – BMC Virology

Core microbiome-associated proteins associated with ulcerative colitis interact with cytokines for synergistic or antagonistic effects on gut bacteria – Ting Zhang et al – ISME Journal

Comparison between 16S rRNA and shotgun sequencing in colorectal cancer, advanced colorectal lesions, and healthy human gut microbiota – David Bars-Cortina et al – BMC Genomics

Effect of different delivery modes on intestinal microbiota and immune function of neonates – Chunhui Lai et al – Scientific Reports

Animal experiments

Effects of Akkermansia muciniphila on Gut Morphology, Antioxidant Indices, and Gut Microbiome of Mice Under Heat Stress – Caiyu Luo et al – Foodborne Pathogens and Disease

Gut microbiota mediates the anti-inflammatory effects of supplemental infrared irradiation in mice – Shijing Wang et al – Photochemistry and Photobiology

Short-chain fatty acids ameliorate imiquimod-induced skin thickening and IL-17 levels and alter gut microbiota in mice: a metagenomic association analysis – Yi-Ju Chen et al – Scientific Reports

Animal microbiome

Facultative endosymbiosis between cellulolytic protists and methanogenic archaea in the gut of the Formosan termite Coptotermes formosanus – Masayuki Kaneko et al – ISME Communications

Rodents consuming the same toxic diet harbor a unique functional core microbiome – Tess E. Stapleton et al – BMC Animal Microbiome

The plant-sucking insect selects assembly of the gut microbiota from environment to enhance host reproduction – Hong-Wei Shan et al – NPJ Biofilms and Microbiomes

Alterations in captive Alexandrine parakeet (Palaeornis eupatria) gut microbiome and metabolome in response to dietary change – Xin Feng et al – Comparative Biochemistry and Physiology

Link between bacterial communities and contrasted loads in ectoparasitic monogeneans from the external mucus of two wild sparid species (Teleostei) – Judith Revault et al – BMC Animal Microbiome

Beneficial microbes and compounds

Unearthing Lactococcus lactis and Scheffersomyeces symbionts from edible wood-boring beetle larvae as a bio-resource for industrial applications – Shadrick Kibet et al – BMC Microbiology

Plant, root, and soil microbiome

[OPINION] Microbiome Bioprospecting for Sustainable Agrobiome and Circular Bioeconomy – Dhananjaya Pratap Singh – Anthropocene Science

Host genetic variation and specialized metabolites from wheat leaves enriches for phyllosphere Pseudomonas spp. with enriched antibiotic resistomes – Qian Xiang et al – ISME Journal

Rhizosphere microbiome assembly, drivers and functions in perennial ligneous plant health – Morgane Duret et al – Microbiological Research

Diversity, composition and potential roles of sedimentary microbial communities in different coastal substrates around subtropical Okinawa Island, Japan – Kohei Hamamoto et al – BMC Environmental Microbiome

July 28, 2024

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Human and General Microbiome

Shaping Microbiota During the First 1000 Days of Life – Anna Samarra – Advances in Experimental Medicine and Biology

Role of sulfidogenic members of the gut microbiota in human disease – Andreia I Pimenta – Advances in Microbial Physiology

Fecal microbiota transplantation improves anti-PD-1 inhibitor efficacy in unresectable or metastatic solid cancers refractory to anti-PD-1 inhibitor – Yunjae Kim – Cell Host & Microbe

Exploring the genomic traits of infant-associated microbiota members from a Zimbabwean cohort – Taona Emmah Mudhluli – BMC Genomics

Gut microbial features and circulating metabolomic signatures of frailty in older adults – Yanni Pu – Nature Aging

Gut microbiome and metabolome signatures in liver cirrhosis-related complications – Satya Priya Sharma – Clinical and Molecular Hepatology

Detection of Microplastics in Human Breast Milk and Its Association with Changes in Human Milk Bacterial Microbiota – Apisith Saraluck – Journal of Clinical Medicine

Regional Differences in Microbial Infiltration of Brain Tissue from Alzheimer’s Disease Patients and Control Individuals – T Bucky Jones – Brain Sciences

Review: Aggregatibacter actinomycetemcomitans: From the Oral Cavity to the Heart Valves – Jasminka Talapko – Microorganisms

Beneficial Microbes and Compounds

Review: Digesting the complex metabolic effects of diet on the host and microbiome – Rachel N Carmody – Cell

Review: A comprehensive review of synbiotics: an emerging paradigm in health promotion and disease management – Sulhee Lee – World Journal of Microbiology & Biotechnology

Animal Model Microbiome

Desulfovibrio vulgaris caused gut inflammation and aggravated DSS-induced colitis in C57BL/6 mice model – Guoxin Huang – Gut Pathogens

LCN2 regulates the gut microbiota and metabolic profile in mice infected with Mycobacterium bovis – Quntao Huang – mSystems

Non-Model Animal Microbiome

Multiomics of parkinsonism cynomolgus monkeys highlights significance of metabolites in interaction between host and microbiota – Jiang-Mei Gao – NPJ Biofilms and Microbiomes

Vaginal and Uterine Microbiota of Healthy Maiden Mares during Estrus – Ana Gil-Miranda – Veterinary Sciences

Review: Reproductive Tract Microbiota of Mares – Ana Gil-Miranda – Veterinary Sciences

Environmental Microbiology

Soils of two Antarctic Dry Valleys exhibit unique microbial community structures in response to similar environmental disturbances – Mafalda S Baptista – Environmental Microbiome

Plant Microbiome

Thermal sensitivity of soil microbial carbon use efficiency across forest biomes – Chengjie Ren – Nature Communications

Miscanthus sp. root exudate alters rhizosphere microbial community to drive soil aggregation for heavy metal immobilization – Bohan Wu – The Science of the Total Environment

Soil conditions modify species diversity effects on tree functional trait expression – Andréa Davrinche – Scientific Reports

Microbiome Analysis

A novel system to culture human intestinal organoids under physiological oxygen content to study microbial-host interaction – Tatiana Y Fofanova – PloS ONE

Compositional Data and Microbiota Analysis: Imagination and Reality – Tatsuki Itagaki – Microorganisms

Thanos: An R Package for the Gene-Centric Analysis of Functional Potential in Metagenomic Samples – Zhe Zhao – Microorganisms

July 24, 2024

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Human microbiome

Gut virome-wide association analysis identifies cross-population viral signatures for inflammatory bowel disease – Xiangge Tian et al – BMC Microbiome

The Role of Gut Microbiota in the Neuroprotective Effects of Selenium in Alzheimer’s Disease – Anatoly V. Skalny et al – Molecular Neurobiology

[REVIEW] The oral–gut microbiome axis in health and disease – Benoit J. Kunath – Nature Reviews Microbiology

Enhancing gut microbiota and microbial function with inulin supplementation in children with obesity – Chonnikant Visuthranukul et al – International Journal of Obesity

Core antibiotic resistance genes mediate gut microbiota to intervene in the treatment of major depressive disorder – Zaiquan Dong et al – Journal of Affective Disorders

Temporal dynamics and species-level complexity of Prevotella spp. in the human gut microbiota: implications for enterotypes and health – Na Han et al – Frontiers in Microbiology

Skin locations inference and body fluid identification from skin microbial patterns for forensic applications – Litao Huang et al – Forensic Science International

Animal experiments

Improving insulin resistance by sulforaphane via activating the Bacteroides and Lactobacillus SCFAs–GPR–GLP1 signal axis – Sicong Tian et al – Food & Function

Gastroprotective and microbiome-modulating effects of ubiquinol in rats with radiation-induced enteropathy – Walaa A. Eraqi et al – BMC Animal Microbiome

Animal microbiome

Methanogenic patterns in the gut microbiome are associated with survival in a population of feral horses – Mason R. Stothart et al – Nature Communications

Viral Communities Suppress the Earthworm Gut Antibiotic Resistome by Lysing Bacteria on a National Scale – Shuai Du et al – Environmental Science & Technology

Modulation of gut microbiota composition and predicted metabolic capacity after nutritional programming with a plant-rich diet in Atlantic salmon (Salmo salar): insights across developmental stages – Marwa Mamdouh Tawfik et al – BMC Animal Microbiome

Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia – Laura Glendinning et al – BMC Microbiome

Water & extremophile microbiome

Genomic representativeness and chimerism in large collections of SAGs and MAGs of marine prokaryoplankton – Tianyi Chang et al – BMC Microbiome

Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake – Arianna I. Krinos et al – BMC Microbiome

Built environment microbiome

[PREPRINT] Utilizing the biosimulator to analyze the environmental microbiome within the intensive care units of a hospital – Sunil Thomas et al – ResearchSquare

Distributions, interactions, and dynamics of prokaryotes and phages in a hybrid biological wastewater treatment system – Dou Wang et al – BMC Microbiome

Plant, root, & soil microbiome

Unraveling the habitat preferences, ecological drivers, potential hosts, and auxiliary metabolism of soil giant viruses across China – Jie-Liang Liang et al – BMC Microbiome

Bioinformatics tools

MIDASim: a fast and simple simulator for realistic microbiome data – Mengyu He et al – BMC Microbiome