Tag Archives: Animal microbiome

October 23, 2023

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Human and General Microbiome

Secretory IgA impacts the microbiota density in the human nose – Rob van Dalen – Microbiome

Disease-specific loss of microbial cross-feeding interactions in the human gut – Vanessa R Marcelino – Nature Communications

Feasibility of a dietary intervention to modify gut microbial metabolism in patients with hematopoietic stem cell transplantation – Mary M Riwes – Nature Medicine

Four functional profiles for fibre and mucin metabolism in the human gut microbiome – Simon Labarthe – Microbiome

The airway microbiota of neonates colonized with asthma-associated pathogenic bacteria – Jonathan Thorsen – Nature Communications

Multiomic profiling of cutaneous leishmaniasis infections reveals microbiota-driven mechanisms underlying disease severity – Camila Farias Amorim – Science Translational Medicine

Tumor-resident Lactobacillus iners confer chemoradiation resistance through lactate-induced metabolic rewiring – Lauren E Colbert – Cancer Cell

Analysis of the influence of host lifestyle (coffee consumption, drinking, and smoking) on Korean oral microbiome – Kyeong-Min Yu – Forensic Science International. Genetics

Potential roles of gut microbiota in metal mixture and bone mineral density and osteoporosis risk association: an epidemiologic study in Wuhan – Jianli Zhang – Environmental Science and Pollution Research International

Characteristics of gut microbiota and metabolic phenotype in patients with major depressive disorder based on multi-omics analysis – Xianpeng Zu – Journal of Affective Disorders

The role of microbial interactions in dental caries: Dental plaque microbiota analysis – Qingyi Shao – Microbial Pathogenesis

A distinctive subgingival microbiome in patients with periodontitis and Alzheimer’s disease compared with cognitively unimpaired periodontitis patients – Hee Sam Na – Journal of Clinical Periodontology

Review: On developmental programming of the immune system – Jun Young Hong – Trends in Immunology

Review: Regulation of pain perception by microbiota in Parkinson’s Disease – Zulmary Manjarres – Pharmacological Reviews

Review: Single-cell analysis and spatial resolution of the gut microbiome – Bhoomi Madhu – Frontiers in Cellular and Infection Microbiology

Beneficial Microbes and Compounds

Synbiotic Sapota-do-Solimões (Quararibea cordata Vischer) Juice Improves Gut Microbiota and Short-Chain Fatty Acid Production in an In Vitro Model – Rhonyele Maciel da Silva – Probiotics and Antimicrobial Proteins

Limosilactobacillus fermentum HF06-derived paraprobiotic and postbiotic alleviate intestinal barrier damage and gut microbiota disruption in mice with ulcerative colitis – Chunhong Liu – Journal of the Science of Food and Agriculture

Animal Microbiome (including Animal Models)

A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs – Mirja Thomsen – Microbiome

High soluble fiber promotes colorectal tumorigenesis through modulating gut microbiota and metabolites in mice – Jia Yang – Gastroenterology

Gut bacterial consortium enriched in a biofloc system protects shrimp against Vibrio parahaemolyticus infection – Haipeng Guo – Microbiome

Environmental Microbiome

Prokaryotic communities inhabiting a high-radon subterranean ecosystem (Castañar Cave, Spain): Environmental and substrate-driven controls – Tamara Martin-Pozas – Microbiological Research

Review: The interplay between microbial communities and soil properties – Laurent Philippot – Nature Reviews. Microbiology

Plant Microbiome

Insights into accumulation of active ingredients and rhizosphere microorganisms between Salvia miltiorrhiza and S. castanea – Zishu Xu – FEMS Microbiology Letters

Microbiome and Evolution

Review: Hierarchical eco-evo dynamics mediated by the gut microbiome – Ellen Decaestecker – Trends in Ecology & Evolution

October 16, 2023

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Human and General Microbiome

A Sedentary Lifestyle Changes the Composition and Predicted Functions of the Gut Bacterial and Fungal Microbiota of Subjects from the Same Company – Longwei Xu – Current Microbiology

Animal Microbiome

Effect of urbanization and parasitism on the gut microbiota of Darwin’s finch nestlings – Gabrielle Solomon – Molecular Ecology

Metabarcoding using nanopore long-read sequencing for the unbiased characterization of apicomplexan haemoparasites – Lucas G Huggins – Molecular Ecology Resources

Bacterial networks in Atlantic salmon with Piscirickettsiosis – Yoandy Coca – Scientific Reports

Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions that respond to ovulation regulation in the mouse endometrium – Sisi Pu – BMC Genomics

Beneficial Microbes, Foods and Compounds

Probiotic-fermented tomato alleviates high-fat diet-induced obesity in mice: Insights from microbiome and metabolomics – Benliang Wei – Food Chemistry

Lactobacillus rhamnosus Modulates Lung Inflammation and Mitigates Gut Dysbiosis in a Murine Model of Asthma-COPD Overlap Syndrome – Jéssica Aparecida Vasconcelos – Probiotics and Antimicrobial Proteins

Fermented Goat’s Milk Contributes to the Recovery of Iron Deficiency Anemia via Modulation of the Gut Microbiome – Ana Soriano-Lerma – Journal of Agricultural and Food Chemistry

Environmental Microbiome

Coexistence of specialist and generalist species within mixed plastic derivative-utilizing microbial communities – Laura Schaerer – Microbiome

Review: A critical review of the recent trends in source tracing of microplastics in the environment – Kiruthika K M – Environmental Research

Keystone taxa of phoD-harboring bacteria mediate alkaline phosphatase activity during biochar remediation of Cd-contaminated soil – Qiang Wang – The Science of the Total Environment

Plant Microbiome

Maintaining beneficial alga-associated bacterial communities under heat stress: Insights from controlled co-culture experiments using antibiotic-resistant bacterial strains – Elham Karimi – FEMS Microbiology Ecology

Review: Deep discovery informs difficult deployment in plant microbiome science – Dor Russ – Cell

Highlights: Plant cell wall component induced bacterial development – Ákos T Kovács – Trends in Microbiology

Microbiome Analysis: Tools, Techniques and Resources

MGS2AMR: a gene-centric mining of metagenomic sequencing data for pathogens and their antimicrobial resistance profile – Pieter-Jan Van Camp – Microbiome

Subgroup Identification Using Virtual Twins for Human Microbiome Studies – Hyunwook Koh – IEEE/ACM Transactions on Computational Biology and Bioinformatics

October 9, 2023

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Human and General Microbiome

Mitochondrial dysfunction promotes microbial composition that negatively impacts on ulcerative colitis development and progression – Ainize Peña-Cearra – NPJ Biofilms and Microbiomes

The recovery of the microbial community after plaque removal depends on periodontal health status – Xiaoqing Li – NPJ Biofilms and Microbiomes

Uncover a microbiota signature of upper respiratory tract in patients with SARS-CoV-2 +  – Massimo Bellato – Scientific Reports

COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition – Shilin Zhao – NPJ Vaccines

Spatial diversity of the skin bacteriome – Marcos Pérez-Losada – Frontiers in Microbiology

Microbiota-gut-brain axis drives overeating disorders – Sijia Fan – Cell Metabolism

Review: Human-gut bacterial protein-protein interactions: understudied but impactful to human health – Diana Balint – Trends in Microbiology

Review: Progress of linking gut microbiota and musculoskeletal health: casualty, mechanisms, and translational values – Yu Wang – Gut Microbes

Review: The microbial landscape of colorectal cancer – Maxwell T White – Nature Reviews. Microbiology

Beneficial Microbes and Compounds

Probiogenomics of Leuconostoc Mesenteroides Strains F-21 and F-22 Isolated from Human Breast Milk Reveal Beneficial Properties – Juan Carlos Ariute – Probiotics and Antimicrobial Proteins

Faecalibacterium prausnitzii, Bacteroides faecis and Roseburia intestinalis attenuate clinical symptoms of experimental colitis by regulating Treg/Th17 cell balance and intestinal barrier integrity – Nooshin Mohebali – Biomedicine & Pharmacotherapy 

Simulated gastrointestinal digestion of beer using the simgi® model. Investigation of colonic phenolic metabolism and impact on human gut microbiota – Magaly Rodriquez-Saavedra – Food Research International

Animal Microbiome (Model and Non-model organisms)

High temperatures augment inhibition of parasites by a honey bee gut symbiont – Evan C Palmer-Young – Applied and Environmental Microbiology

The maternal microbiome promotes placental development in mice – Geoffrey N Pronovost – Science Advances

Omics-Based Mathematical Modeling Unveils Pathogenesis of Periodontitis in an Experimental Murine Model – C Fujihara – Journal of Dental Research

Environmental Microbiome

Compost, plants and endophytes versus metal contamination: choice of a restoration strategy steers the microbiome in polymetallic mine waste – Martina Kracmarova-Farren – Environmental Microbiome

Litter decomposition and nutrient release are faster under secondary forests than under Chinese fir plantations with forest development – Shuaijun Li – Scientific Reports

Microbiome Analysis: Tools, Techniques and Resources

PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation – Guangping Huang – Microbiome

The newest Oxford Nanopore R10.4.1 full-length 16S rRNA sequencing enables the accurate resolution of species-level microbial community profiling – Tianyuan Zhang – Applied and Environmental Microbiology

October 2, 2023

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Highlights!

Review: A relational framework for microbiome research with Indigenous communities – Alyssa C Bader – Nature Microbiology

Review: Microbiome ownership for Indigenous peoples – Matilda Handsley-Davis – Nature Microbiology

Human and General Microbiome

Expanded microbiome niches of RAG-deficient patients – Ryan A Blaustein – Cell Reports Medicine

Low dietary fiber intake impairs small intestinal Th17 and intraepithelial T cell development over generations – Charlotte J Royer – Cell Reports

Iron acquisition by a commensal bacterium modifies host nutritional immunity during Salmonella infection – Luisella Spiga – Cell Host & Microbe

Microbiome profile and calprotectin levels as markers of risk of recurrent Clostridioides difficile infection – Silvia Vázquez-Cuesta – Frontiers in Cellular and Infection Microbiology

Safety and tolerability of frozen, capsulized autologous faecal microbiota transplantation. A randomized double blinded phase I clinical trial – Måns Stefansson – PloS One

Metabolism of azo food dyes by bacterial members of the human gut microbiome – Riley Elder – Anaerobe

Genetic risk score in multiple sclerosis is associated with unique gut microbiome – Noha S Elsayed – Scientific Reports

Antisense inhibition of RNA polymerase α subunit of Clostridioides difficile – Rusha Pal – Microbiology Spectrum

Review: Metabolic signature for a dysbiotic microbiome in the female genital tract: A systematic review and meta-analysis – Biban Gill – American Journal of Reproductive Immunology

Review: Influence of Plant-Based Diet on the Cardiovascular System: A Narrative Review – Gurusha Jangid – Cardiology in Review

Review: Bile acid and its bidirectional interactions with gut microbiota: a review – Shuqi He – Critical Reviews in Microbiology

Animal Microbiome

Population mixing mediates the intestinal flora composition and facilitates invasiveness in a globally invasive fruit fly – Yidan Wang – Microbiome

Diet-related factors strongly shaped the gut microbiota of Japanese macaques – Wanyi Lee – American Journal of Primatology

Skin and gut microbiomes of tadpoles vary differently with host and water environment: a short-term experiment using 16S metabarcoding – Bárbara Santos – Scientific Reports

Multi-omics revealed the long-term effect of ruminal keystone bacteria and the microbial metabolome on lactation performance in adult dairy goats – Dangdang Wang – Microbiome

The multi-kingdom microbiome of the goat gastrointestinal tract – Yanhong Cao – Microbiome

Multi-breed host rumen epithelium transcriptome and microbiome associations and their relationship with beef cattle feed efficiency – P A S Fonseca – Scientific Reports

Animal Model Microbiome

Select symbionts drive high IgA levels in the mouse intestine – Shanshan Zhang – Cell Host & Microbe

Blocked conversion of Lactobacillus johnsonii derived acetate to butyrate mediates copper-induced epithelial barrier damage in a pig model – Yang Wen – Microbiome

Laboratory mice with a wild microbiota generate strong allergic immune responses – Junjie Ma – Science Immunology

Plant Microbiome

Host genetic variation drives the differentiation in the ecological role of the native Miscanthus root-associated microbiome – Niuniu Ji – Microbiome

Changes in structure and assembly of a species-rich soil natural community with contrasting nutrient availability upon establishment of a plant-beneficial Pseudomonas in the wheat rhizosphere – Daniel Garrido-Sanz – Microbiome

Microbially produced fertilizer provides rhizobacteria to hydroponic tomato roots by forming beneficial biofilms – Yuya Sato – Applied Microbiology and Biotechnology

Terpenes modulate bacterial and fungal growth and sorghum rhizobiome communities – Ming-Yi Chou – Microbiology Spectrum 

Rhizosphere and detritusphere habitats modulate expression of soil N-cycling genes during plant development – Ella T Sieradzki – mSystems

Environmental Microbiome

The presence of benzene ring activating CoA ligases for aromatics degradation in the ANaerobic MEthanotrophic (ANME) archaea – Wei-Wei Liu – Microbiology Spectrum

Microbial biogeography of pit mud from an artificial brewing ecosystem on a large time scale: all roads lead to Rome – Jun-Lan Mei – mSystems

Stable microbial community in compacted bentonite after 5 years of exposure to natural granitic groundwater – Katja Engel – mSphere

Microbiome Analysis Tools, Techniques and Resources

Impact of Experimental Bias on Compositional Analysis of Microbiome Data – Yingtian Hu – Genes

happi: a hierarchical approach to pangenomics inference – Pauline Trinh – Genome Biology

Integrating a tailored recurrent neural network with Bayesian experimental design to optimize microbial community functions – Jaron C Thompson – PLoS Computational Biology

Review: Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics – Koji Arikawa – Computational and Structural Biotechnology Journal

September 25, 2023

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Highlights!

Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide – Petros Andrikopoulos – Nature Communications

A blood-based metabolomic signature predictive of risk for pancreatic cancer – Ehsan Irajizad – Cell Reports. Medicine

Enterobacteriaceae growth promotion by intestinal acylcarnitines, a biomarker of dysbiosis in Inflammatory Bowel Disease – Johanna M S Lemons – Cellular and Molecular Gastroenterology and Hepatology

Inducible CRISPR-targeted knockdown of human gut Bacteroides in gnotobiotic mice discloses glycan utilization strategies – Zachary W Beller – PNAS

Review: The gut microbiota and its biogeography – Giselle McCallum – Nature Reviews. Microbiology

Human and General Microbiome

The role of the gut-microbiota-brain axis via the subdiaphragmatic vagus nerve in chronic inflammatory pain and comorbid spatial working memory impairment in complete Freund’s adjuvant mice – Caibao Yue – Journal of Psychiatric Research

Disentangling the interactions between nasopharyngeal and gut microbiome and their involvement in the modulation of COVID-19 infection – Leonardo Mancabelli – Microbiology Spectrum

Changes in salivary microbiota due to gastric cancer resection and its relation to gastric fluid microbiota – Eri Komori – Scientific Reports

Metagenomic sequencing reveals altered gut microbial compositions and gene functions in patients with non-segmental vitiligo – Mei Luan – BMC Microbiology

Review: The role of the glycome in symbiotic host-microbe interactions – Rustam Aminov – Glycobiology

Review: Microbiome-targeted interventions for the control of oral-gut dysbiosis and chronic systemic inflammation – Juan Pacheco-Yanes – Trends in Molecular Medicine

Review: The link between the gut microbiome, inflammation, and Parkinson’s disease – Shiqing Nie – Applied Microbiology and Biotechnology

Food Microbiome

The edible plant microbiome: evidence for the occurrence of fruit and vegetable bacteria in the human gut – Wisnu Adi Wicaksono – Gut Microbes

Animal Microbiome

Reducing gut microbiome-driven adipose tissue inflammation alleviates metabolic syndrome – N K Newman – Microbiome

Combined effect of a neonicotinoid insecticide and a fungicide on honeybee gut epithelium and microbiota, adult survival, colony strength and foraging preferences – Riccardo Favaro – The Science of the Total Environment

Glyphosate decreases survival, increases fecundity, and alters the microbiome of the natural predator Harmonia axyridis (ladybird beetle) – Xueke Gao – Environmental Research

Unfolding the secrets of microbiome (Symbiodiniaceae and bacteria) in cold-water coral – Sanqiang Gong – Microbiology Spectrum

Combined oral intake of short and long fructans alters the gut microbiota in food allergy model mice and contributes to food allergy prevention – Hideaki Takahashi – BMC Microbiology

Review: The pivotal roles of gut microbiota in insect plant interactions for sustainable pest management – Yuxin Zhang – NPJ Biofilms and Microbiomes

Plant Microbiome

Review: Endophytes Modulate Plant Genes: Present Status and Future Perspectives – Vivek Kumar – Current Microbiology

Environmental Microbiome

Planktonic and epilithic prokaryota community compositions in a large temperate river reflect climate change related seasonal shifts – Attila I Engloner – PloS One

Thiothrix and Sulfurovum genera dominate bacterial mats in Slovak cold sulfur springs – Lea Nosalova – Environmental Microbiome

Built Environment Microbiome

Innovative strategy for the conservation of a millennial mausoleum from biodeterioration through artificial light management – Yuanyuan Bao – NPJ Biofilms and Microbiomes

More Microbes

In vitro and in silico evaluation of the serrapeptase effect on biofilm and amyloids of Pseudomonas aeruginosa – Georgios Katsipis – Applied Microbiology and Biotechnology

Microbiome Analysis: Tools, Techniques and Resources

Comprehensive evaluation of methods for differential expression analysis of metatranscriptomics data – Hunyong Cho – Briefings in Bioinformatics

Review: Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data – Ostaizka Aizpurua – Critical Reviews in Biotechnology

September 18, 2023

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Human and General Microbiome

Ocular microbiome evaluation in dry eye disease and meibomian gland dysfunction: Values of variables – Davide Borroni – Experimental Eye Research

Regulation of psoriasis, colitis, and the intestinal microbiota by clusterin – Yu Kyung Jun – Scientific Reports

Bridging of host-microbiota tryptophan partitioning by the serotonin pathway in fungal pneumonia – Giorgia Renga – Nature Communications

High-throughput sequencing analysis of the characteristics of the gut microbiota in aged patients with sarcopenia – Yiyi Zhang – Experimental Gerontology

Draft genome sequence of a Fusobacterium nucleatum strain isolated from a patient in Kazakhstan with colorectal cancer – Gulmira Kulmambetova – Microbiology Resource Announcements

Review: The impacts of oral and gut microbiota on alveolar bone loss in periodontitis – Nannan Han – Journal of Periodontal Research

Control of Helicobacter pylori with engineered probiotics secreting selective guided antimicrobial peptides – Ankan Choudhury – Microbiology Spectrum

Animal Microbiome

The synthetic food dye, Red 40, causes DNA damage, causes colonic inflammation, and impacts the microbiome in mice – Qi Zhang – Toxicology Reports

Disruption of the microbiota-gut-brain axis is a defining characteristic of the α-Gal A (-/0) mouse model of Fabry disease – C Delprete – Gut Microbes

Review: Neuroactive metabolites modulated by the gut microbiota in honey bees – Amélie Cabirol – Molecular Microbiology

Microbiome and Evolution

Insights into early evolutionary adaptations of the Akkermansia genus to the vertebrate gut – Dámariz González – Frontiers in Microbiology

Food Microbiome

Review: Microbiome Assembly in Fermented Foods – Nicolas L Louw – Annual Review of Microbiology

Plant Microbiome

Engineering the Maize Root Microbiome: A Rapid MoClo Toolkit and Identification of Potential Bacterial Chassis for Studying Plant-Microbe Interactions – John van Schaik – ACS Synthetic Biology

Environmental Microbiome

Effects of Fe(III) (hydr)oxide mineralogy on the development of microbial communities originating from soil, surface water, groundwater, and aerosols – Yidan Zhang – The Science of the Total Environment

Combination of sequencing batch reactor activated sludge process with sludge lysis using thermophilic bacterial community for minimizing excess sludge – Baoyan Chi – Journal of Environmental Management

September 11, 2023

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Human and General Microbiome

Obesity is the main driver of altered gut microbiome functions in the metabolically unhealthy – Jacobo de la Cuesta-Zuluaga – Gut Microbes

Elucidating the Role of the Microbiome in Ocular Diseases – Wendy Luo – The American Journal of Pathology

A binary module for microbiota-mediated regulation of γδ17 cells, hallmarked by microbiota-driven expression of programmed cell death protein 1 – Hsin-I Huang – Cell Reports

Resistant starch decreases intrahepatic triglycerides in patients with NAFLD via gut microbiome alterations – Yueqiong Ni – Cell Metabolism

Microbial signature of plaque and gut in acute coronary syndrome – Eugenia Pisano – Scientific Reports

Impact of the lipase inhibitor orlistat on the human gut microbiota – Yudai Uehira – Obesity Research & Clinical Practice

Metabolic network construction reveals probiotic-specific alterations in the metabolic activity of a synthetic small intestinal community – Jack Jansma – mSystems

Colonic phosphocholine is correlated with Candida tropicalis and promotes diarrhea and pathogen clearance – Xihong Zhou – NPJ Biofilms and Microbiomes

Differential dependence on microbiota of IL-23/IL-22-dependent gene expression between the small- and large-intestinal epithelia – Ayaka Nakatani – Genes to Cells

Identification of microbial markers associated with lung cancer based on multi-cohort 16 s rRNA analyses: A systematic review and meta-analysis – Wenjie Han – Cancer Medicine

Review: Targeting microbial quorum sensing: the next frontier to hinder bacterial driven gastrointestinal infections – Ying Su – Gut Microbes

Review: Illuminating the oral microbiome and its host interactions: recent Advancements in omics and bioinformatics technologies in the context of oral microbiome research – Jonathon L Baker – FEMS Microbiology Reviews

Review: Association between primary Sjögren’s syndrome and gut microbiota disruption: a systematic review and meta-analysis – Yue Shen – Clinical Rheumatology

Beneficial Microbes and Compounds

Washed microbiota transplantation for Clostridioides difficile infection: a national multi-center real-world study – Xia Wu – Journal of Digestive Diseases

Lactobacillus johnsonii N6.2 phospholipids induce immature-like dendritic cells with a migratory-regulatory-like transcriptional signature – Alexandra E Cuaycal – Gut Microbes

Akkermansia muciniphila supplementation prevents cognitive impairment in sleep-deprived mice by modulating microglial engulfment of synapses – Na Li – Gut Microbes

Food Microbiome

Metagenomics and metabolomics of Toddy, an Indian fermented date palm beverage – Souvik Das – Food Research International

Animal Microbiome

Gut microbiota from patients with COVID-19 cause alterations in mice that resemble post-COVID symptoms – Viviani Mendes de Almeida – Gut Microbes

Ingestion and biodegradation of disposable surgical masks by yellow mealworms Tenebrio molitor larvae: Differences in mask layers and effects on the larval gut microbiome – Jiaming Wang – The Science of the Total Environment

Assessment of beneficial effects and identification of host adaptation-associated genes of Ligilactobacillus salivarius isolated from badgers – Yu Wang – BMC Genomics

Microbiota-mediated competition between Drosophila species – Antoine Rombaut – Microbiome

Microbial signature profiles of Penaeus vannamei larvae in low-survival hatchery tanks affected by vibriosis – Guillermo Reyes – PeerJ

Fiber deprivation and microbiome-borne curli shift gut bacterial populations and accelerate disease in a mouse model of Parkinson’s disease – Kristopher J Schmit – Cell Reports

Plant Microbiome

Microbial communities associated with resin canal discoloration in mango fruit – Muhammad Umar – Letters in Applied Microbiology

Studying the microbiome of suppressive soils against vascular wilt, caused by Fusarium oxysporum in cape gooseberry (Physalis peruviana) – Daniel Bautista – Environmental Microbiology Reports

Environmental Microbiome

Antarctic snow algae: unraveling the processes underlying microbial community assembly during blooms formation – Daniela F Soto – Microbiome

Understanding how various forms of phosphorus stress affect microbiome functions and boost plant disease resistance: Insights from metagenomic analysis – Jie Kang – The Science of the Total Environment

Reductive soil disinfestation and Fe amendment improve soil microbial composition and Fritillaria production – Yue Yin – Applied Microbiology and Biotechnology

How Benthic Sediment Microbial Communities Respond to Glyphosate and Its Metabolite: a Microcosm Experiment – Christine M Cornish – Microbial Ecology

Functional conservation of microbial communities determines composition predictability in anaerobic digestion – Qiang Lin – The ISME Journal

Microbiome Research Tools

Development of an antibody fused with an antimicrobial peptide targeting Pseudomonas aeruginosa: A new approach to prevent and treat bacterial infections – Kenneth Johnson – PLoS Pathogens

Clustering microbiome data using mixtures of logistic normal multinomial models – Yuan Fang – Scientific Reports

A new spike-in-based method for quantitative metabarcoding of soil fungi and bacteria – Miguel Camacho-Sanchez – International Microbiology

Research Highlight: Microbiome screening platform finds drugs for bugs – Katie Kingwell – Nature Reviews. Drug Discovery

September 4, 2023

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Human and General Microbiome

Gut microbial carbohydrate metabolism contributes to insulin resistance – Tadashi Takeuchi – Nature

Gut Microbiome in Patients With Early-Stage and Late-Stage Melanoma – Russell G Witt – JAMA Dermatology

The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children – A Cristina Paulo – Microbiome

Salivary microbiome of healthy women of reproductive age – Eline Cauwenberghs – mBio

Microbiome characteristics description of COVID-19 patients based on bulk RNA-seq and scRNA-Seq data – Sainan Zhang – Computers in Biology and Medicine

Parkinson’s disease alters the composition of subgingival microbiome – Ekin Yay – Journal of Oral Microbiology

Cervicovaginal Gardnerella sialidase-encoding gene in persistent human papillomavirus infection – Juliano Novak – Scientific Reports

Human milk oligosaccharides modulate the intestinal microbiome of healthy adults – Jonathan P Jacobs – Scientific Reports

Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease – Prabha Chandrasekaran – The Journal of Allergy and Clinical Immunology

Review: The curious case of Prevotella copri – Nehal Adel Abdelsalam – Gut Microbes

Review: Gut microbiota and microbiota-derived metabolites in colorectal cancer: enemy or friend – Xinyi Wang – World Journal of Microbiology & Biotechnology

Beneficial Microbes and Compounds

N-Acetylglucosamine and its dimer ameliorate inflammation in murine colitis by strengthening the gut barrier function – Sung-In Choi – Food & Function

Omega-3 nanoemulgel in prevention of radiation-induced oral mucositis and its associated effect on microbiome: a randomized clinical trial – Basma M Morsy – BMC Oral Health

Lactiplantibacillus plantarum ELF051 Alleviates Antibiotic-Associated Diarrhea by Regulating Intestinal Inflammation and Gut Microbiota – Wei Liang – Probiotics and Antimicrobial Proteins

Animal Microbiome

Microbiomes and metabolomes of dominant coral reef primary producers illustrate a potential role for immunolipids in marine symbioses – Helena Mannochio-Russo – Communications Biology

Alteration of diet microbiota limits the experimentally evolved immune priming response in flour beetles, but not pathogen resistance – Arun Prakash – Journal of Evolutionary Biology

Mammals show distinct functional gut microbiome dynamics to identical series of environmental stressors – Adam Koziol – mBio

Microbiome and Evolution

The hologenome of Daphnia magna reveals possible DNA methylation and microbiome-mediated evolution of the host genome – Anurag Chaturvedi – Nucleic Acids Research

Review: Impact of intraspecific variation in insect microbiomes on host phenotype and evolution – Claudia Lange – The ISME Journal

Review: Why do hosts malfunction without microbes? Missing benefits versus evolutionary addiction – Tobin J Hammer – Trends in Microbiology

Environmental Microbiome

Different microbial assemblage colonized on microplastics and clay particles in aerobic sludge treatment – Zixuan Zhang – The Science of the Total Environment

More Microbes

Metagenomic insights into the microbiota involved in lactate and butyrate production and manipulating their synthesis in alfalfa silage – Rongrong Li – Journal of Applied Microbiology

Microbiome Research Tools

RSim: A reference-based normalization method via rank similarity – Bo Yuan – PLoS Computational Biology

Review: Computation-aided studies related to the induction of specialized metabolite biosynthesis in microbial co-cultures: An introductory overview – Tomasz Boruta – Computational and Structural Biotechnology Journal

Preprint: Analyzing microbial evolution through gene and genome phylogenies – Sarah Teichman – bioRxiv

August 28, 2023

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Human and General Microbiome

The respiratory tract microbiome, the pathogen load, and clinical interventions define severity of bacterial pneumonia – Ana Elena Pérez-Cobas – Cell Reports. Medicine

A phenome-wide association study (PheWAS) to identify the health impacts of 4-cresol sulfate in the Nagahama Study – Huiting Ou – Scientific Reports

A meta-analysis of tissue microbial biomarkers for recurrence and metastasis in multiple cancer types – Xuebo Li – Journal of Medical Microbiology 

Microbe Profile: Ruminococcus gnavus: the yin and yang of human gut symbionts – Nathalie Juge – Microbiology

Oral Porphyromonas gingivalis infection affects intestinal microbiota and promotes atherosclerosis – Sowon Park – Journal of Clinical Periodontology

Gut microbiota and fecal short chain fatty acids differ with adiposity and country of origin: the METS-microbiome study – Gertrude Ecklu-Mensah – Nature Communications

Very early life microbiome and metabolome correlates with primary vaccination variability in children – Michael Shaffer – mSystems

Carbohydrate quality, fecal microbiota and cardiometabolic health in older adults: a cohort study – Alessandro Atzeni – Gut Microbes

Multi-omics analysis revealing the interplay between gut microbiome and the host following opioid use – Udhghatri Kolli – Gut Microbes

The gut microbiota reprograms intestinal lipid metabolism through long noncoding RNA Snhg9 – Yuhao Wang – Science

Staphylococcus epidermidis activates keratinocyte cytokine expression and promotes skin inflammation through the production of phenol-soluble modulins – Michael R Williams – Cell Reports

Review: Targeting nonalcoholic fatty liver disease via gut microbiome-centered therapies – Mijra Koning – Gut Microbes

Review: Intracellular Fusobacterium nucleatum infection increases METTL3-mediated m6A methylation to promote the metastasis of esophageal squamous cell carcinoma – Songhe Guo – Journal of Advanced Research

Beneficial Microbes and Compounds

Characteristics of gut microbiota determine effects of specific probiotics strains in patients with functional constipation – Haohao Zhang – Chinese Medical Journal

Lacticaseibacillus rhamnosus TF318 prevents depressive behavior in rats by inhibiting HPA-axis hyperactivity and upregulating BDNF expression – Yujuan Zhao – Neuroscience Letters

Animal Model Microbiome

Role of mucin glycosylation in the gut microbiota-brain axis of core 3 O-glycan deficient mice – Erika Coletto – Scientific Reports

Non-Model Animal Microbiome

Outer membrane vesicles from a mosquito commensal mediate targeted killing of Plasmodium parasites via the phosphatidylcholine scavenging pathway – Han Gao – Nature Communications

Whole genome analyses of toxicants tolerance genes of Apis mellifera gut-derived Enterococcus faecium strains – Heba A H Zaghloul – BMC Genomics

Fungal Microbiome

The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research – Julia M Kelliher – Microbiome

Plant Microbiome

Microbiome dataset of bacterial and fungal communities in anthosphere of twelve different wild plants in South Korea – Jihoon Kim – Data in Brief 

Environmental and Soil Microbiome

Anthropogenic activities mediate stratification and stability of microbial communities in freshwater sediments – Xiaotian Zhou – Microbiome

Long-term agro-management strategies shape soil bacterial community structure in dryland wheat systems – Shikha Singh – Scientific Reports

Microbial community structure and functional prediction in five full-scale industrial park wastewater treatment plants – Tujun Tong – The Science of the Total Environment

Deterministic Development of Soil Microbial Communities in Disturbed Soils Depends on Microbial Biomass of the Bioinoculum – Yuri Pinheiro Alves de Souza – Microbial Ecology

Microbial communities related to the sulfur cycle in the Sansha Yongle Blue Hole – Kai Sun – Microbiology Spectrum

A study of microbial diversity in a biofertilizer consortium – Cristóbal Hernández-Álvarez – PloS One

Microbiome Research: Resources, Tools and Techniques

Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data – Aubrey R Odom – Scientific Reports

Amplicon-Based Microbiome Profiling: From Second- to Third-Generation Sequencing for Higher Taxonomic Resolution – Elisabetta Notario – Genes

A flexible quasi-likelihood model for microbiome abundance count data – Yiming Shi – Statistics in Medicine

Identification of multivariable Boolean patterns in microbiome and microbial gene composition data – George Golovko – Bio Systems

Machine learning classification by fitting amplicon sequences to existing OTUs – Courtney R Armour – mSphere

Review: Statistical normalization methods in microbiome data with application to microbiome cancer research – Yinglin Xia – Gut Microbes

Book Chapter: Elucidating the role of microbes in celiac disease through gnotobiotic modeling – Alberto Caminero – Methods in Cell Biology

August 20, 2023

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Highlights!

Human microbiome variation associated with race and ethnicity emerges as early as 3 months of age – Elizabeth K Mallott – PLoS Biology

Mapping the T cell repertoire to a complex gut bacterial community – Kazuki Nagashima – Nature

Comparison of the relative impacts of acute consumption of an inulin-enriched diet, milk kefir or a commercial probiotic product on the human gut microbiome and metabolome – Liam H. Walsh – npj Science of Food 

High-resolution strain-level microbiome composition analysis from short reads – Herui Liao – Microbiome

Preprint: Profiling novel lateral gene transfer events in the human microbiome –  Tiffany Y. Hsu – bioRxiv

Human and General Microbiome

Preprint: Major data analysis errors invalidate cancer microbiome findings –  Abraham Gihawi – bioRxiv

Microdiversity of the vaginal microbiome is associated with preterm birth – Jingqiu Liao – Nature Communications

Dysbiosis of gut microbiota during fecal stream diversion in patients with colorectal cancer – Soo Young Lee – Gut Pathogens

The gut microbiome contributes to somatic morphine withdrawal behavior and implicates a TLR2 mediated mechanism – Bridget Truitt – Gut Microbes

Association of the human gut microbiota with vascular stiffness – Rafael R C Cuadrat – Scientific Reports

Gut microbiota and intervertebral disc degeneration: a bidirectional two-sample Mendelian randomization study – Ziming Geng – Journal of Orthopaedic Surgery and Research

News & Views: Microbiome alterations in autism spectrum disorder – Elena J Coley-O’Rourke – Nature Microbiology

Beneficial Microbes and Compounds

Rosmarinic acid alleviates intestinal inflammatory damage and inhibits endoplasmic reticulum stress and smooth muscle contraction abnormalities in intestinal tissues by regulating gut microbiota – Kan Li – Microbiology Spectrum

Prevotella copri alleviates sarcopenia via attenuating muscle mass loss and function decline – Xiaolei Liu – Journal of Cachexia, Sarcopenia and Muscle

The Influence of Protein Secretomes of Enterococcus durans on ex vivo Human Gut Microbiome – Carolina Baldisserotto Comerlato – Probiotics and Antimicrobial Proteins

Kombucha tea as an anti-hyperglycemic agent in humans with diabetes – a randomized controlled pilot investigation – Chagai Mendelson – Frontiers in Nutrition 

Animal Microbiome

The unique gut microbiome of giant pandas involved in protein metabolism contributes to the host’s dietary adaption to bamboo – Feilong Deng – Microbiome

Systematic review of cnidarian microbiomes reveals insights into the structure, specificity, and fidelity of marine associations – M McCauley – Nature Communications

Review: Toward an Integrated Understanding of the Lepidoptera Microbiome – Yongqi Shao – Annual Review of Entomology

Plant Microbiome

Characterization of bacterial community in tobacco leaves at flue-curing and redrying processing stages – Yue Yang – Scientific Reports

Environmental Microbiome

Inter-comparison of marine microbiome sampling protocols – Francisco Pascoal – ISME Communications

Discovery of a novel bacterial class with the capacity to drive sulfur cycling and microbiome structure in a paleo-ocean analog – Adrien Vigneron – ISME Communications

Microbiome Research: Resources, Tools and Techniques

MT-MAG: Accurate and interpretable machine learning for complete or partial taxonomic assignments of metagenome assembled genomes – Wanxin Li – PloS one

BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes – Michael J Pavia – Microbiome

Detection of viable commensal bacteria in murine melanoma tumors by culturomics – Catherine M Phelps – STAR Protocols