December 2, 2022

Human and General Microbiome

Different Characteristics in Gut Microbiome between Advanced Adenoma Patients and Colorectal Cancer Patients by Metagenomic Analysis – Shuwen Han – Microbiology Spectrum

The Spatial Features and Temporal Changes in the Gut Microbiota of a Healthy Chinese Population – Wen Zhang – Microbiology Spectrum

The Gut Microbiota is Important for the Maintenance of Blood-Cerebrospinal Fluid Barrier Integrity – Emily G Knox – The European Journal of Neuroscience

Evaluation of co-circulating pathogens and microbiome from COVID-19 infections – James B Thissen – PloS One

A Clinical Study Provides the First Direct Evidence That Interindividual Variations in Fecal β-Lactamase Activity Affect the Gut Mycobiota Dynamics in Response to β-Lactam Antibiotics – Margot Delavy – mBio

Clostridia isolated from helminth-colonized humans promote the life cycle of Trichuris species – Shushan Sargsian – Cell Reports

Genome Watch: Zooming into the structure of the microbiome – Gemma G R Murray – Nature Reviews. Microbiology

Beneficial Microbes and Compounds

Saussurea involucrata oral liquid regulates gut microbiota and serum metabolism during alleviation of collagen-induced arthritis in rats – Shan Cong – Phytotherapy Research

Prebiotic oligofructose protects against high-fat diet-induced obesity by changing the gut microbiota, intestinal mucus production, glycosylation and secretion – Paola Paone – Gut Microbes

Review: Predicting Personalized Responses to Dietary Fiber Interventions: Opportunities for Modulation of the Gut Microbiome to Improve Health – Car Reen Kok – Annual Review of Food Science and Technology

Animal Microbiome

Gut dysbiosis induces the development of mastitis through a reduction in host anti-inflammatory enzyme activity by endotoxemia – Caijun Zhao – Microbiome

Chronic clinical signs of upper respiratory tract disease associate with gut and respiratory microbiomes in a cohort of domestic felines – Holly Kristin Arnold – PloS One

Plant and Soil Microbiome

Bio-Organic Fertilizer Promotes Pear Yield by Shaping the Rhizosphere Microbiome Composition and Functions – Zhonghua Wang – Microbiology Spectrum

Impacts of maize hybrids with different nitrogen use efficiency on root-associated microbiota based on distinct rhizosphere soil metabolites – Keke Li – Environmental Microbiology

Environmental Microbiome

Coupled C, H, N, S and Fe biogeochemical cycles operating in the continental deep subsurface of the Iberian Pyrite Belt – Ricardo Amils – Environmental Microbiology

Long-Read Sequencing Improves Recovery of Picoeukaryotic Genomes and Zooplankton Marker Genes from Marine Metagenomes – N V Patin – mSystems

Bioinformatics and Microbiome Analysis

The Application of Spearman Partial Correlation for Screening Predictors of Weight Loss in a Multiomics Dataset – Joel Correa da Rosa – Omics

Sampling of Human Microbiomes to Screen for Antibiotic-Producing Commensals – Benjamin Torres Salazar – Methods in Molecular Biology

November 26, 2022

Human and General Microbiome

Essay: Autobiography of a gut bacterium – Florian Schmidt – Science

Untargeted Fecal Metabolomic Analyses across an Industrialization Gradient Reveal Shared Metabolites and Impact of Industrialization on Fecal Microbiome-Metabolome Interactions – Jacob J Haffner – mSystems

Diet standardization reduces intra-individual microbiome variation – Clara Delaroque – Gut Microbes

Investigation of the gut microbiome, bile acid composition and host immunoinflammatory response in a model of azoxymethane-induced colon cancer at discrete timepoints – J M Keane – British Journal of Cancer

A comparative study to determine the association of gut microbiome with schizophrenia in Zhejiang, China – Fuyang Yan – BMC Psychiatry

Review: Gut Microbiome Analysis for Personalized Nutrition: The State of Science – Marie-Christine Simon – Molecular Nutrition & Food Research

Review: The nonindustrialised microbiome in a modern world – Fergus Shanahan – Clinical Science

Beneficial Microbes and Compounds

A gut microbial metabolite of dietary polyphenols reverses obesity-driven hepatic steatosis – Lucas J Osborn – PNAS

Akkermansia muciniphila ameliorates depressive disorders in a murine alcohol-LPS (mALPS) model – Dingming Guo – Food & Function

Animal Microbiome

The Kitty Microbiome Project: Defining the Healthy Fecal Core Microbiome in Pet Domestic Cats – Holly H Ganz – Veterinary Sciences

Bioinformatics and Microbiome Analysis

Bioinformatic Approaches for Describing the Oral Microbiota – Kristi Biswas – Methods in Molecular Biology

Predicting butyrate- and propionate-forming bacteria of gut microbiota from sequencing data – Berenike Kircher – Gut Microbes

Review: Machine learning for data integration in human gut microbiome – Peishun Li – Microbial Cell Factories

More Microbes 

Impact of innovative nanoadditives on biodigesters microbiome – Fatma Y Hassaneen – Microbial Biotechnology

Microbiome analysis in Lascaux Cave in relation to black stain alterations of rock surfaces and collembola – Lise Alonso – Environmental Microbiology Reports

November 21, 2022

Highlights!

The cancer chemotherapeutic 5-fluorouracil is a potent Fusobacterium nucleatum inhibitor and its activity is modified by intratumoral microbiota – Kaitlyn D LaCourse – Cell Reports

Enterococci enhance Clostridioides difficile pathogenesis – Alexander B Smith – Nature

Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species – Jeremiah J Minich – Nature Communications

Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave – Gabriele Scorrano – Communications Biology

Human and General Microbiome

Gut microbiota analysis for prediction of clinical relapse in Crohn’s disease – Sylvie Buffet-Bataillon – Scientific Reports

Implications of oral streptococcal bacteriophages in autism spectrum disorder – Zhan Tong – NPJ Biofilms and Microbiomes

Reproducible changes in the anorexia nervosa gut microbiota following inpatient therapy remain distinct from non-eating disorder controls – Farnaz Fouladi – Gut Microbes

Nasal microbiome disruption and recovery after mupirocin treatment in Staphylococcus aureus carriers and noncarriers – Valérie O Baede – Scientific Reports

BlpC-mediated selfish program leads to rapid loss of Streptococcus pneumoniae clonal diversity during infection – Surya D Aggarwal – Cell host & Microbe

Treasures from trash in cancer research – Fabiano Cordeiro Moreira – Oncotarget

Human Gut Metagenomes Encode Diverse GH156 Sialidases – Evan Mann – Applied and Environmental Microbiology

Species-Specific Patterns of Gut Metabolic Modules in Dutch Individuals with Different Dietary Habits – Sudarshan A Shetty – mSphere

Effect of the intratumoral microbiota on spatial and cellular heterogeneity in cancer – Jorge Luis Galeano Niño – Nature

Broad-spectrum antibiotics associated gut microbiome disturbance impairs T cell immunity and promotes lung cancer metastasis: a retrospective study – Ke Xu – BMC Cancer

Diet-induced modifications to human microbiome reshape colonic homeostasis in irritable bowel syndrome – Hadar Bootz-Maoz – Cell Reports

Review: The dynamic lung microbiome in health and disease – Jake G Natalini – Nature Reviews. Microbiology

Non-model Animal Microbiome 

Modulation of gut microbiota, blood metabolites, and disease resistance by dietary β-glucan in rainbow trout (Oncorhynchus mykiss) – Simon Menanteau-Ledouble – Animal Microbiome

Living in honey: bacterial and fungal communities in honey of sympatric populations of Apis mellifera and the stingless bee Melipona beecheii, in Yucatan, Mexico – Diana Fátima Jacinto-Castillo – Archives of Microbiology

Plant Microbiome

Review: The involvement of organic acids in soil fertility, plant health and environment sustainability – Satyavir S Sindhu – Archives of Microbiology

Bioinformatics and Microbiome Analysis

Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome – Rebecca H Smith – Animal Microbiome

dbCAN-seq update: CAZyme gene clusters and substrates in microbiomes – Jinfang Zheng – Nucleic Acids Research

Gene co-expression network analysis of the human gut commensal bacterium Faecalibacterium prausnitzii in R-Shiny – Sandrine Auger – PloS One

November 14, 2022

Human and General Microbiome

Genetic regulation of serum IgA levels and susceptibility to common immune, infectious, kidney, and cardio-metabolic traits – Lili Liu – Nature Communications

Kidney microbiota dysbiosis contributes to the development of hypertension – Xin-Yu Liu – Gut Microbes

Gut mycobiota dysbiosis in drug-naïve, first-episode schizophrenia – Xiuxia Yuan – Schizophrenia Research

Transcriptomic analysis reveals an association of FCGBP with Parkinson’s disease – Pilar Gómez-Garre – NPJ Parkinson’s Disease

Integration of stool microbiota, proteome and amino acid profiles to discriminate patients with adenomas and colorectal cancer – Sofie Bosch – Gut Microbes

Human gut homeostasis and regeneration: the role of the gut microbiota and its metabolites – Claudia Marcela Arenas-Gómez – Critical Reviews in Microbiology

Colibactin possessing E. coli isolates in association with colorectal cancer and their genetic diversity among Pakistani population – Habiba Tariq – PloS one

Intestinal toxicity to CTLA-4 blockade driven by IL-6 and myeloid infiltration – Yifan Zhou – The Journal of Experimental Medicine

Genome-microbiome interplay provides insight into the determinants of the human blood metabolome – Christian Diener – Nature Metabolism

Vaginal microbiota in women with spontaneous preterm labor versus those with term labor in Kenya: a case control study – Edgar Gulavi – BMC Microbiology

Characteristics of oral microbiome of healthcare workers in different clinical scenarios: a cross-sectional analysis – Zhixia Zhang – BMC Oral Health

Multi-kingdom gut microbiota analyses define COVID-19 severity and post-acute COVID-19 syndrome – Qin Liu – Nature Communications

Characterization of antibiotic-resistance traits in Akkermansia muciniphila strains of human origin – Rossella Filardi – Scientific Reports

Food Microbiome

Causality Verification for the Correlation between the Presence of Nonstarter Bacteria and Flavor Characteristics in Soft-Type Ripened Cheeses – Ryosuke Unno – Microbiology Spectrum

Animal Microbiome

Microbiota of healthy and bleached corals of the species Siderastrea stellata in response to river influx and seasonality in Brazilian northeast – Gustavo Vasconcelos Bastos Paulino – Environmental Science and Pollution Research International

Environmental Microbiome

Exploring structure, microbiota, and metagenome functions of epigean and hypogean black deposits by microscopic, molecular and bioinformatic approaches – Beatrice Farda – Scientific Reports

Plant Microbiome

High throughput method of 16S rRNA gene sequencing library preparation for plant root microbial community profiling – Kie Kumaishi – Scientific Reports

Sugarcane cultivation practices modulate rhizosphere microbial community composition and structure – Ana Paula Corrêa Moneda – Scientific Reports

Effects of Two Bacillus velezensis Microbial Inoculants on the Growth and Rhizosphere Soil Environment of Prunus davidiana – Huimin Shi – International Journal of Molecular Sciences

Review: Climate change and plant pathogens – Muhammad M Raza – Current Opinion in Microbiology

Bioinformatics and Microbiome Analysis

Faecal microbiome-based machine learning for multi-class disease diagnosis – Qi Su – Nature Communications

Wochenende – modular and flexible alignment-based shotgun metagenome analysis – Ilona Rosenboom – BMC Genomics

De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee – Yunxi Liu – Nature Communications

October 3, 2022

Human and General Microbiome

Mucus-degrading Bacteroides link carbapenems to aggravated graft-versus-host disease – Eiko Hayase – Cell

Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions – Lian Narunsky-Haziza – Cell

A pan-cancer mycobiome analysis reveals fungal involvement in gastrointestinal and lung tumors – Anders B Dohlman – Cell

Gut microbiota of hepatitis B virus-infected patients in the immune-tolerant and immune-active phases and their implications in metabolite changes – Ya-Nan Li – World Journal of Gastroenterology

Streptococcus mutans promotes tumor progression in oral squamous cell carcinoma – Ming-Shao Tsai – Journal of Cancer

Short-chain fatty acid concentrations in the incidence and risk-stratification of colorectal cancer: a systematic review and meta-analysis – Ehsan Alvandi – BMC Medicine

Mycobacterium potentiates protection from colorectal cancer by gut microbial alterations – Yu-Mi Kim – Immunology

Nutrition, Immunosenescence, and Infectious Disease: An Overview of the Scientific Evidence on Micronutrients and on Modulation of the Gut Microbiota – Philip C Calder – Advances in Nutrition 

Unfermented β-fructan fibers fuel inflammation in select inflammatory bowel disease patients – Heather K Armstrong – Gastroenterology

Machine-learning algorithms for asthma, COPD, and lung cancer risk assessment using circulating microbial extracellular vesicle data and their application to assess dietary effects – Andrea McDowell – Experimental & Molecular Medicine

Microbiome ethics, guiding principles for microbiome research, use and knowledge management – Lene Lange – Environmental Microbiome

Review: The gut mycobiome in health, disease, and clinical applications in association with the gut bacterial microbiome assembly – Fen Zhang – The Lancet. Microbe

Beneficial Microbes and Compounds

Review: Tailoring gut microbiota with a combination of Vitamin K and probiotics as a possible adjuvant in the treatment of rheumatic arthritis: a systematic review – Luciana Pereira – Clinical Nutrition ESPEN

Dietary Isoflavones Alter Gut Microbiota and Lipopolysaccharide Biosynthesis to Reduce Inflammation – Sudeep Ghimire – Gut Microbes

Bacteroides thetaiotaomicron rough-type lipopolysaccharide: The chemical structure and the immunological activity – Molly Dorothy Pither – Carbohydrate Polymers

Animal Microbiome

Study of cattle microbiota in different regions of Kazakhstan using 16S metabarcoding analysis – Aida Daugaliyeva – Scientific Reports

Microscopic marine invertebrates are reservoirs for cryptic and diverse protists and fungi – Corey C Holt – Microbiome

Plant Microbiome

Review: Microbiomes in agroecosystem: Diversity, function and assembly mechanisms – Chao Xiong – Environmental Microbiology Reports

Bioinformatics and Microbiome Analysis

Integrating Phylogenetic and Functional Data in Microbiome Studies – Gavin M Douglas – Bioinformatics 

Higher off-target amplicon detection rate in MiSeq v3 compared to v2 reagent kits in the context of 16S-rRNA-sequencing – Mari-Lee Odendaal – Scientific Reports

September 24, 2022

Human and General Microbiome

Systemic antibody responses against human microbiota flagellins are overrepresented in chronic fatigue syndrome patients – Thomas Vogl – Science Advances

Strain-level resolution and pneumococcal carriage dynamics by single-molecule real-time (SMRT) sequencing of the plyNCR marker: a longitudinal study in Swiss infants – Oluwaseun Rume-Abiola Oyewole – Microbiome

Longitudinal disease-associated gut microbiome differences in infants with food protein-induced allergic proctocolitis – Victoria M Martin – Microbiome

Host and gut bacteria share metabolic pathways for anti-cancer drug metabolism – Peter Spanogiannopoulos – Nature Microbiology

Diet-driven microbial ecology underpins associations between cancer immunotherapy outcomes and the gut microbiome – Rebecca C Simpson – Nature Medicine

Advances in the gut microbiome and mood disorders – Sabrina Mörkl – Current Opinion in Psychiatry

Review: Modulation of the intestinal microbiota impacts the efficacy of immunotherapy in cancer patients – A recent literature survey – Stella Ziegler – European Journal of Microbiology & Immunology

Animal Microbiome

Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome – Tina Keller-Costa – Microbiome

Intestinal microbiome-mediated resistance against vibriosis for Cynoglossus semilaevis – Qian Zhou – Microbiome

Plant Microbiome

Response of soil microecology to different cropping practice under Bupleurum chinense cultivation – Li Liu – BMC Microbiology

Community Assembly of Fungi and Bacteria along Soil-Plant Continuum Differs in a Zoige Wetland – Jie Li – Microbiology Spectrum

Review: Investigating plant-microbe interactions within the root – Yuniar Devi Utami – Archives of Microbiology

Food Microbiome

Geographically Associated Fungus-Bacterium Interactions Contribute to the Formation of Geography-Dependent Flavor during High-Complexity Spontaneous Fermentation – Yuwei Tan – Microbiology Spectrum

More Microbes

A meta-analysis of acetogenic and methanogenic microbiomes in microbial electrosynthesis – Simon Mills – NPJ Biofilms and Microbiomes

Bioinformatics and Microbiome Analysis

MicrobiomeCensus estimates human population sizes from wastewater samples based on inter-individual variability in gut microbiomes – Lin Zhang – PLoS Computational Biology

September 18, 2022

Human and General Microbiome

Neisseria species as pathobionts in bronchiectasis – Liang Li – Cell Host & Microbe

The gut microbiome molecular complex in human health and disease – Paul Wilmes – Cell Host & Microbe

Codiversification of gut microbiota with humans – Taichi A Suzuki – Science

Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course – The iMSMS Consortium – Cell

Composition and diverse differences of intestinal microbiota in ulcerative colitis patients – Siying Zhu – Frontiers in Cellular and Infection Microbiology

A systematic review on omics data (metagenomics, metatranscriptomics, and metabolomics) in the role of microbiome in gallbladder disease – Paola Di Carlo – Frontiers in Physiology

Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases – Gianluca Ianiro – Nature Medicine

Drivers and determinants of strain dynamics following fecal microbiota transplantation – Thomas S B Schmidt – Nature Medicine

Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects – Jonathan T L Kang – Nature Microbiology

Structural and functional dysbiosis of gut microbiota in Tibetan subjects with coronary heart disease – Qi Cheng – Genomics

Growth of succinate consumer Dialister hominis is supported by Bacteroides thetaiotaomicron – Mitsuo Sakamoto – Anaerobe

RhoB affects colitis through modulating cell signaling and intestinal microbiome – Jianming Yang – Microbiome

Review: Diet fuelling inflammatory bowel diseases: preclinical and clinical concepts – Timon E Adolph – Gut

Review: Recent findings in Akkermansia muciniphila-regulated metabolism and its role in intestinal diseases – Meng-Jie Liu – Clinical Nutrition

Beneficial Microbes and Compounds

Comprehensive analysis of microbiome, metabolome and transcriptome revealed the mechanisms of Moringa oleifera polysaccharide on preventing ulcerative colitis – Hanchen Tian – International Journal of Biological Macromolecules

Probiotics ameliorates pulmonary inflammation via modulating gut microbiota and rectifying Th17/Treg imbalance in a rat model of PM2.5 induced lung injury – Yongcan Wu – Ecotoxicology and Environmental Safety

Short-term supplementation with ω-3 polyunsaturated fatty acids modulates primarily mucolytic species from the gut luminal mucin niche in a human fermentation system – Charlène Roussel – Gut Microbes

Model Animal Microbiome

Interactive Effect of Combined Intermittent and Sustained Hypoxia and High-Fat Diet on the Colonic Mucosal Microbiome and Host Gene Expression in Mice – Saif Mashaqi – Nature and Science of Sleep

Non-Model Animal Microbiome

Fungi are more transient than bacteria in caterpillar gut microbiomes – Martin Šigut – Scientific Reports

Adapting to climate with limited genetic diversity: Nucleotide, DNA methylation and microbiome variation among populations of the social spider Stegodyphus dumicola – Anne Aagaard – Molecular Ecology

Bioinformatics and Microbiome Analysis

Filtering ASVs/OTUs via mutual information-based microbiome network analysis – Elham Bayat Mokhtari – BMC Bioinformatics

Batch effects removal for microbiome data via conditional quantile regression – Wodan Ling – Nature Communications

Phylogenetic Analysis of Anti-CRISPR and Member Addition in the Families – Sweta Nidhi – Molecular Biotechnology

Shallow shotgun sequencing of the microbiome recapitulates 16S amplicon results and provides functional insights – Mason R Stothart – Molecular Ecology Resources

SnapShot: The Expobiome Map – Velma T E Aho – Cell Host & Microbe

September 10, 2022

Human and General Microbiome

Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life – Conner L Jackson – mBio

Gastrointestinal microbiota profile and clinical correlations in advanced EGFR-WT and EGFR-mutant non-small cell lung cancer – Woraseth Saifon – BMC Cancer

Hybrid metagenome assemblies link carbohydrate structure with function in the human gut microbiome – Anuradha Ravi – Communications Biology

Genetic Determinants of Hydrogen Sulfide Biosynthesis in Fusobacterium nucleatum Are Required for Bacterial Fitness, Antibiotic Sensitivity, and Virulence – Yi-Wei Chen – mBio

Preprint: Genomic and ecologic characteristics of the airway microbial-mucosal complex – Leah Cuthbertson – BioXriv 

Beneficial Microbes and Compounds

Lactiplantibacillus plantarum Regulated Intestinal Microbial Community and Cytokines to Inhibit Salmonella typhimurium Infection – Rui-Han Liu – Probiotics and Antimicrobial Proteins

Animal Microbiome

Exploration of rumen microbial and carbohydrate-active enzyme profiles in cattle fed coir a lignin-rich diet using a metagenomic approach – Munni Khatoon – Gene

Plant Microbiome

The core bacterial microbiome of banana (Musa spp.) – Henry W G Birt – Environmental Microbiome

Higher pH is associated with enhanced co-occurrence network complexity, stability and nutrient cycling functions in the rice rhizosphere microbiome – Yaping Guo – Environmental Microbiology

Environmental Microbiology

Virome analysis in lakes of the South Shetland Islands, Antarctica – 2020 – Tatiana Prado – The Science of the Total Environment

Bioinformatics and Microbiome Analysis

Investigating differential abundance methods in microbiome data: A benchmark study – Marco Cappellato – PLoS Computational Biology

A rapid and standardized workflow for functional assessment of bacterial biosensors in fecal samples – Ana Zúñiga – Frontiers in Bioengineering and Biotechnology

August 27, 2022

Highlights!

Capturing the antibiotic resistome of preterm infants reveals new benefits of probiotic supplementation – Allison K Guitor – Microbiome → A survey of the microbiome from preterm infants showed that probiotics use during hospitalization of these infants reduced the diversity and prevented the persistence of antibiotic resistance genes in the gut microbiome. The authors used a targeted capture approach involving lower costs.

Human gut microbiota after bariatric surgery alters intestinal morphology and glucose absorption in mice independently of obesity – Fernando F Anhê – Gut → The exposition of mice to human gut microbiota after restrictive or malabsorptive bariatric surgery could improve glycaemic control, involving, for example, the inhibition of host sodium-glucose cotransporter (Sglt)-1.

Human and General Microbiome

Temporal dynamics of oropharyngeal microbiome among SARS-CoV-2 patients reveals continued dysbiosis even after Viral Clearance – Suman Kalyan Paine – NPJ Biofilms and Microbiomes

Comparison of Metagenomic Sequencing and the NanoString nCounter Analysis System for the Characterization of Bacterial and Viral Communities in Vaginal Samples – Todd N Wylie – mSphere

Oral Microbiota from Periodontitis Promote Oral Squamous Cell Carcinoma Development via γδ T Cell Activation – Wei Wei – mSystems

Gut Microbiota and Coronary Plaque Characteristics – Akihiro Nakajima – Journal of the American Heart Association

Toward FAIR Representations of Microbial Interactions – Alan R Pacheco – mSystems

Review: Gut microbiome-mediated mechanisms for reducing cholesterol levels: implications for ameliorating cardiovascular disease – Baolei Jia – Trends in Microbiology

Review: Type 2 diabetes, gut microbiome, and systems biology: A novel perspective for a new era – Yoscelina Estrella Martínez-López – Gut Microbes

Beneficial Microbes and Compounds

Human gut bifidobacteria inhibit the growth of the opportunistic fungal pathogen Candida albicans – Liviana Ricci – FEMS Microbiology Ecology

Animal Model Microbiome

Orally administered Odoribacter laneus improves glucose control and inflammatory profile in obese mice by depleting circulating succinate – Isabel Huber-Ruano – Microbiome

Experimental methods modestly impact interpretation of the effect of environmental exposures on the larval zebrafish gut microbiome – Keaton Stagaman – Scientific Reports

A Metabologenomic approach reveals alterations in the gut microbiota of a mouse model of Alzheimer’s disease – Francesco Favero – PloS ONE

Non-Model Animal Microbiome

Intraintestinal Analysis of the Functional Activity of Microbiomes and Its Application to the Common Marmoset Intestine – Mika Uehara – mSystems

A comprehensive comparison of fecal microbiota in three ecological bird groups of raptors, waders, and waterfowl – Caiquan Zhao – Frontiers in Microbiology

IHNV Infection Induces Strong Mucosal Immunity and Changes of Microbiota in Trout Intestine – Zhenyu Huang – Viruses

Fungi and Soil Microbiome

Wildfire-dependent changes in soil microbiome diversity and function – Amelia R Nelson – Nature Microbiology

Fungal succession on the decomposition of three plant species from a Brazilian mangrove – Marta A Moitinho – Scientific Reports

Fungi-on-a-Chip: microfluidic platforms for single-cell studies on fungi – Felix Richter – FEMS Microbiology Reviews

Environmental Microbiome

Climate-Endangered Arctic Epishelf Lake Harbors Viral Assemblages with Distinct Genetic Repertoires – Myriam Labbé – Applied and Environmental Microbiology

Food Microbiome

Profiling of the microbiota in the remaining sports drink and orange juice in plastic bottles after direct drinking – Miho Kawachi – Journal of Oral Biosciences

Bioinformatic Tools and Microbiome Analysis Techniques

K-Clique Multiomics Framework: A Novel Protocol to Decipher the Role of Gut Microbiota Communities in Nutritional Intervention Trials – Carlo Mengucci – Metabolites

Principal microbial groups: compositional alternative to phylogenetic grouping of microbiome data – Aslı Boyraz – Briefings in Bioinformatics

Analysis of Gut Microbiome Using Fecal Samples – Ahmed Gamal – Methods in Molecular Biology 

August 22, 2022

Highlights!!

Personalized microbiome-driven effects of non-nutritive sweeteners on human glucose tolerance – Jotham Suez – Cell a randomized-controlled trial (120 healthy adults) observed the effects of saccharin, sucralose, aspartame, and stevia on the human microbiome showed person-specific, microbiome-dependent glycemic alterations. Saccharin and sucralose significantly impaired glycemic responses.

A comprehensive evaluation of microbial differential abundance analysis methods: current status and potential solutions – Lu Yang – Microbiome → assessment of several differential abundance analysis (DAA) tools, using real data-based simulations, suggests that “none of the evaluated methods is simultaneously robust, powerful, and flexible, which makes the selection of the best DAA tool difficult”. These findings suggest that the application of a DAA method depends of data context.  

Systematic Review: Probiotics and Synbiotics Supplementation Improve Glycemic Control Parameters in Subjects with Prediabetes and Type 2 Diabetes Mellitus: A GRADE-assessed systematic review, meta-analysis, and meta-regression of randomized clinical trials – Kaveh Naseri – Pharmacological Research → “Our findings suggest that probiotic and synbiotic intake has favorable effects on glycemic profile in patients with prediabetes and T2DM.”

Human and General Microbiome

The diversity and abundance of gut microbiota are associated with the pain sensation threshold in the Japanese population – Yuki Takeuchi – Neurobiology of Disease

Oral microbiota associated with gingiva of healthy, gingivitis and periodontitis cases – Nemmat A Hussein – Microbial Pathogenesis

Effects of extracellular vesicles derived from oral bacteria on osteoclast differentiation and activation – Hyun Young Kim – Scientific Reports

Porphyromonas gingivalis is a risk factor for the development of nonalcoholic fatty liver disease via ferroptosis – Chao Yao – Microbes and Infection

Review: The Role of a Gut Microbial-Derived Metabolite, Trimethylamine N-Oxide (TMAO), in Neurological Disorders – Sankar Simla Praveenraj – Molecular Neurobiology

Review: The association between early-life gut microbiota and childhood respiratory diseases: a systematic review – Cristina Garcia-Maurino Alcazar – The Lancet. Microbe

Beneficial Microbes and Compounds

Effect of Bifidobacterium animalis subsp. lactis SF on enhancing the tumor suppression of irinotecan by regulating the intestinal flora – Zhongyue Ren – Pharmacological Research

Effect of probiotic supplementation on plasma metabolite profile after Roux-Y gastric bypass: a prospective, randomized, double-blind, placebo-controlled clinical trial – Marília Rizzon Zaparolli Ramos – International Journal of Obesity 

Faecalibaculum rodentium remodels retinoic acid signaling to govern eosinophil-dependent intestinal epithelial homeostasis – Y Grace Cao – Cell Host & Microbe

Human milk nutrient fortifiers alter the developing gastrointestinal microbiota of very-low-birth-weight infants – Michelle R Asbury – Cell Host & Microbe

More Microbes

Diversity of ethanolamine utilization by human commensal Escherichia coli – Maria Ines Moreira de Gouveia – Research in Microbiology

Review: Archaea from the gut microbiota of humans: Could be linked to chronic diseases? – Denise Mafra – Anaerobe

Animal Microbiome

Genomic insights into the phylogeny and biomass-degrading enzymes of rumen ciliates – Zongjun Li – The ISME Journal

Environmental Microbiome

Microbiota and mobile genetic elements influence antibiotic resistance genes in dust from dense urban public places – Tianshu Feng – Environmental Pollution 

Review: Synergy between microalgae and microbiome in polluted waters – Noreen Ashraf – Trends in Microbiology

Bioinformatic Tools and Microbiome Analysis Techniques

Review: Molecular tools for probing the microbiome – Marcelo Der Torossian Torres – Current Opinion in Structural Biology