Tag Archives: Microbiome Digest

December 23, 2022

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Happy Holidays from the Microbiome Digest Team!

Human and General Microbiome

Analysis of the oral microbiome during hormonal cycle and its alterations in menopausal women: the AMICA project – A Tramice – Scientific Reports

Diversity and Prevalence of Clostridium innocuum in the Human Gut Microbiota – Disha Bhattacharjee – mSphere

A multiomics analysis of direct interkingdom dynamics between influenza A virus and Streptococcus pneumoniae uncovers host-independent changes to bacterial virulence fitness – Maryann P Platt – PLoS Pathogens

Butyrate Ameliorates Insufficient Sleep-Induced Intestinal Mucosal Damage in Humans and Mice – Ting Gao – Microbiology Spectrum

Prediction model of poorly differentiated colorectal cancer (CRC) based on gut bacteria – Zhang Qi – BMC Microbiology

Multidisciplinary Perinatal Care in IBD – Lihi Godny – Journal of Crohn’s & Colitis

Review: A multi-omic brain gut microbiome signature differs between IBS subjects with different bowel habits – Rachel P Sarnoff – Neuropharmacology

Review: From fecal microbiota transplantation toward next-generation beneficial microbes: The case of Anaerobutyricum soehngenii – Koen Wortelboer – Frontiers in Medicine

Beneficial Microbes and Compounds

Final Results from a Phase 2b Randomized, Placebo-Controlled Clinical Trial of RBX2660: A Microbiota-Based Drug for the Prevention of Recurrent Clostridioides difficile Infection – Erik R Dubberke – Infectious Diseases and Therapy

Systematic Review: The effect of probiotic and synbiotic supplementation on appetite-regulating hormones and desire to eat: a systematic review and meta-analysis of clinical trials – Morvarid Noormohammadi – Pharmacological Research

Animal Microbiome

Experimental Infection with Mycoplasma hyopneumoniae Strain 232 in Swine Influences the Lower Respiratory Microbiota – Henrique Meiroz de Souza Almeida – Veterinary Sciences

Functional Diversification of Oyster Big Defensins Generates Antimicrobial Specificity and Synergy against Members of the Microbiota – Noémie De San Nicolas – Marine Drugs

Gut microbiota modulates lung fibrosis severity following acute lung injury in mice – Ozioma S Chioma – Communications Biology

Effects of enhanced insect feeding on the faecal microbiota and transcriptome of a family of captive common marmosets (Callithrix jacchus) – Yumiko Yamazaki – PloS ONE

Review: The Mechanism of Important Components in Canine Fecal Microbiota Transplantation – Kerong Li – Veterinary Sciences

Food Microbiome

In vitro selection and characterization of probiotic properties in eight Lactobacillus strains isolated from cocoa fermentation – Milena E DE Almeida – Anais da Academia Brasileira de Ciencias

Microbiome Analysis Techniques

RIAM: A Universal Accessible Protocol for the Isolation of High Purity DNA from Various Soils and Other Humic Substances – Alexander G Pinaev – Methods and Protocols

Review: Compositionality, sparsity, spurious heterogeneity, and other data-driven challenges for machine learning algorithms within plant microbiome studies – Sebastiano Busato – Current Opinion in Plant Biology

December 19, 2022

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Highlights!

Multi-omic interactions in the gut of children at the onset of islet autoimmunity – Patrick G Gavin – Microbiome

“Here, we apply an integrative approach to combine comprehensive fecal virome, microbiome, and metaproteome data sampled before and at the onset of islet autoimmunity in 40 children at increased risk of T1D […] We show a functional remodeling of the gut microbiota accompanies both islet autoimmunity and viral infection with a switch in function in Faecalibacterium occurring at the onset of islet autoimmunity.”

Human and General Microbiome

Review: The microbiota-gut-brain axis in pathogenesis of depression: a narrative review – Hui Yao – Physiology & Behavior

Review: Environmental enteric dysfunction: gut and microbiota adaptation in pregnancy and infancy – Carrie A Cowardin – Nature Reviews. Gastroenterology & Hepatology

Review: Gastrointestinal Tract, Microbiota and Multiple Sclerosis (MS) and the Link Between Gut Microbiota and CNS – Bahman Yousefi – Current Microbiology

Effect of proton pump inhibitors in infants with esophageal atresia on the gut microbiome: a pilot cohort – Nele Brusselaers – Gut Pathogens

Endodontic microbial communities in apical periodontitis – Alessio Buonavoglia – Journal of Endodontics

Gut Microbiota-Generated Phenylacetylglutamine and Heart Failure – Kymberleigh A Romano – Circulation. Heart Failure

Animal Microbiome

Midgut Bacterial Microbiota of 12 Fish Species from a Marine Protected Area in the Aegean Sea (Greece) – Konstantinos Kormas – Microbial Ecology

Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host – Ankur Midha – Microbiome

Plant Microbiome

Multifaceted roles of flavonoids mediating plant-microbe interactions – Lanxiang Wang – Microbiome

Microbiome Analysis and Techniques

An economic and robust TMT labeling approach for high throughput proteomic and metaproteomic analysis – Marybeth Creskey – Proteomics

Machine learning-derived gut microbiome signature predicts fatty liver disease in the presence of insulin resistance – Baeki E Kang – Scientific Reports

Pseudomonas-specific 16S rRNA insect gut-microbiome profiling using next-generation sequencing – Ayushi Gupta – STAR Protocols

December 16, 2022

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Highlights!

A microbiome-dependent gut-brain pathway regulates motivation for exercise – Lenka Dohnalová – Nature 

Here, we report on the discovery of a gut–brain connection in mice that enhances exercise performance by augmenting dopamine signalling during physical activity. We find that microbiome-dependent production of endocannabinoid metabolites in the gut stimulates the activity of TRPV1-expressing sensory neurons and thereby elevates dopamine levels in the ventral striatum during exercise.

Gut microbiota in the early stage of Crohn’s disease has unique characteristics – Xianzong Ma – Gut Pathogens

The present study aimed to identify dysbacteriosis in patients with early Crohn’s Disease (CD) and explore specific gut bacteria related to the progression of CD.

Human and General Microbiome

Longitudinal multi-omics analyses of the gut-liver axis reveals metabolic dysregulation in hepatitis C infection and cirrhosis – Rabab O Ali – Nature Microbiology

Impact of HIV infection and integrase strand transfer inhibitors-based treatment on the gut virome – Pablo Villoslada-Blanco – Scientific Reports

Consequences of collagen induced inflammatory arthritis on circadian regulation of the gut microbiome – Devin Amanda Simpkins – FASEB Journal

Isolation and characterization of a novel choline degrading Citrobacter amalonaticus strain from the human gut – Jyoti Kashyap – Current Research in Microbial Sciences

HIV-Positive Patients on Antiretroviral Therapy Have an Altered Mucosal Intestinal but Not Oral Microbiome – Jingjing Meng – Microbiology Spectrum

Gut dysbiosis and bacterial translocation in the aneurysmal wall and blood in patients with abdominal aortic aneurysm – Ken Nakayama – PloS One

Review: Female reproductive tract microbiome and early miscarriages – Olga Lebedeva – APMIS

Review: Emerging roles of intratumor microbiota in cancer metastasis – Aikun Fu – Trends in Cell Biology

In Brief: Urine microbiota differ in bladder cancer – Louise Stone – Nature Reviews. Urology

Animal Microbiome

Characterization of the bacterial microbiome of Amblyomma scalpturatum and Amblyomma ovale collected from Tapirus terrestris and Amblyomma sabanerae collected from Chelonoidis denticulata, Madre de Dios- Peru – Jesús Rojas-Jaimes – BMC Microbiology

Increased Proportion of Fiber-Degrading Microbes and Enhanced Cecum Development Jointly Promote Host To Digest Appropriate High-Fiber Diets – Guang Pu – mSystems

Review: Involvement of Microbiota in Insect Physiology: Focus on B Vitamins – Javier Serrato-Salas – mBio

Plant Microbiome

The Endophytic Root Microbiome Is Different in Healthy and Ralstonia solanacearum-Infected Plants and Is Regulated by a Consortium Containing Beneficial Endophytic Bacteria – Yiting Li – Microbiology Spectrum

Microbiome Analysis and Methods

Interpreting tree ensemble machine learning models with endoR – Albane Ruaud – PLoS Computational Biology

Analysis of Ancient Microbial DNA – Olivier Gorgé – Methods in Molecular Biology (Book)

Confocal Laser Scanning Microscopy Approach to Investigate Plant-Fungal Interactions – F Fracchia – Methods in Molecular Biology (Book)

December 12, 2022

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Human and General Microbiome

Dental calculus microbiome correlates with dietary intake – Gabriel Innocenti – Molecular Oral Microbiology

Ruminococcus gnavus plays a pathogenic role in diarrhea-predominant irritable bowel syndrome by increasing serotonin biosynthesis – Lixiang Zhai – Cell Host & Microbe

The gut microbiome and child mental health: a population-based study – Robert Kraaij – Brain, Behavior, and Immunity

Gut microbiota profile of COVID-19 patients: Prognosis and risk stratification (MicroCOVID-19 study) – José Guilherme Nobre – Frontiers in Microbiology

Systematic Review: Gut microbiota diversity and composition in predicting immunotherapy response and immunotherapy-related colitis in melanoma patients: A systematic review – Oliver Oey – World Journal of Clinical Oncology

Review: Scientometric analysis of kidney disease and gut microbiota from 2001 to 2020 based on Web of Science – Ran Zhang – Medicine

Review: Crosstalk between liver macrophages and gut microbiota: An important component of inflammation-associated liver diseases – Ziyuan Zhou – Frontiers in Cell and Developmental Biology

Review: Dental calculus – oral health, forensic studies and archaeology: a review – Roger Forshaw – British Dental Journal

Animal Microbiome

Inputs don’t equal outputs: Bacterial microbiomes of the ingesta, gut, and feces of the keystone deposit feeder Ilyanassa obsoleta – Craig J Plante – FEMS Microbiology Ecology

Urinary neopterin reflects immunological variation associated with age, helminth parasitism, and the microbiome in a wild primate – India A Schneider-Crease – Scientific Reports

Dark-purple rice extract modulates gut microbiota composition in acetic acid- and indomethacin-induced inflammatory bowel disease in rats – Kornsuda Thipart – International Microbiology

Review: Nasonia-microbiome associations: a model for evolutionary hologenomics research – Zhengyu Zhu – Trends in Parasitology

Microbiome Analysis

Rapid separation of bacteria from primary nasal samples using inertial microfluidics – Jesus Shrestha – Lab on a Chip

December 2, 2022

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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 28, 2022

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Human and General Microbiome

Vaginal microbiome-host interactions modeled in a human vagina-on-a-chip – Gautam Mahajan – Microbiome

Colonocyte-derived lactate promotes E. coli fitness in the context of inflammation-associated gut microbiota dysbiosis – Savannah J Taylor – Microbiome

Review: The immunomodulatory roles of the gut microbiome in autoimmune diseases of the central nervous system: Multiple sclerosis as a model – Kristina Hoffman – Journal of Autoimmunity

Review: The role of NOD2 in intestinal immune response and microbiota modulation: A therapeutic target in inflammatory bowel disease – Ziyue Liu – International Immunopharmacology

Review: Strategizing the human microbiome for small molecules: approaches and perspectives – Aehtesham Hussain – Drug Discovery Today

Animal Microbiome

Timing matters: age-dependent impacts of the social environment and host selection on the avian gut microbiota – Öncü Maraci – Microbiome

Honeybees affect floral microbiome composition in a central food source for wild pollinators in boreal ecosystems – Elsi Hietaranta – Oecologia

A longitudinal census of the bacterial community in raw milk correlated with Staphylococcus aureus clinical mastitis infections in dairy cattle – Soyoun Park – Animal Microbiome

Hypomagnetic Field Exposure Affecting Gut Microbiota, Reactive Oxygen Species Levels, and Colonic Cell Proliferation in Mice – Aisheng Zhan – Bioelectromagnetics

Environmental Microbiome

Metagenomic insights into feasibility of agricultural wastes on optimizing water quality and natural bait by regulating microbial loop – Lingling Wan – Environmental Research

November 21, 2022

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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

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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

November 7, 2022

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Human and General Microbiome

Immunomodulatory fecal metabolites are associated with mortality in COVID-19 patients with respiratory failure – Matthew R Stutz – Nature Communications

Taxonomic Abundance in Primary and Secondary Root Canal Infections – Ronald Ordinola-Zapata – International Endodontic Journal

Review: The intestinal barrier in disorders of the central nervous system – Carolina Pellegrini – The Lancet. Gastroenterology & Hepatology

Review: Resistance is futile? Mucosal immune mechanisms in the context of microbial ecology and evolution – Emma Slack – Mucosal Immunology

Correspondence: A critical analysis of eating disorders and the gut microbiome – Sydney M Terry – Journal of Eating Disorders

Beneficial Microbes and Compounds

Bifidobacterial carbohydrate/nucleoside metabolism enhances oxidative phosphorylation in white adipose tissue to protect against diet-induced obesity – Gihyeon Kim – Microbiome

Lactobacillus rhamnosus GG supernatant promotes intestinal mucin production through regulating 5-HT4R and gut microbiota – Yu Gu – Food & Function

Animal Model Microbiome

Genetic and environmental circadian disruption induce weight gain through changes in the gut microbiome – Baraa Altaha – Molecular Metabolism

Strains producing different short-chain fatty acids alleviate DSS-induced ulcerative colitis by regulating intestinal microecology – Shuo Yang – Food & Function

Non-Model Animal Microbiome

Microbiome assembly and maintenance across the lifespan of bumble bee workers – Tobin J Hammer – Molecular Ecology

The gut microbiome reflects ancestry despite dietary shifts across a hybrid zone – Danny P Nielsen – Ecology Letters

Characterization of the core gut microbiota of Nile tilapia (Oreochromis niloticus): indication of a putative novel Cetobacterium species and analysis of its potential function on nutrition – Ziyue Zhang – Archives of Microbiology

Forensic Microbiome

Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes – Thomas Clarke – Scientific Reports

Plant Microbiome

Insights into the potential for mutualistic and harmful host-microbe interactions affecting brown alga freshwater acclimation – Hetty KleinJan – Molecular Ecology

Built Environment Microbiome

Review: Microplastics in urban waters and its effects on microbial communities: a critical review – Saber Entezari – Environmental Science and Pollution Research International

Microbiome Analysis and Techniques

Assessing the Dark Field of Metaproteome – Haonan Duan – Analytical Chemistry

October 24, 2022

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Human and General Microbiome

The Association Between Microplastics and Microbiota in Placentas and Meconium: The First Evidence in Humans – Shaojie Liu – Environmental Science & Technology

The salivary microbiome shows a high prevalence of core bacterial members yet variability across human populations – Xinwei Ruan – NPJ Biofilms and Microbiomes

Role of mucus-bacteria interactions in Enterotoxigenic Escherichia coli (ETEC) H10407 virulence and interplay with human microbiome – Thomas Sauvaitre – NPJ Biofilms and Microbiomes

Commensal oral microbiota impacts ulcerative oral mucositis clinical course in allogeneic stem cell transplant recipients – Julia S Bruno – Scientific Reports

Review: Gut microbiota in COVID-19: key microbial changes, potential mechanisms and clinical applications – Raphaela I Lau – Nature Reviews. Gastroenterology & Hepatology

Review: The microbiota and aging microenvironment in pancreatic cancer: Cell origin and fate – Zhou Chen – Biochimica et Biophysica Acta

Review: New perspectives into the vaginal microbiome with systems biology – Christina Y Lee – Trends in Microbiology

Beneficial Microbes and Compounds

Oral supplementation with selected Lactobacillus acidophilus triggers IL-17-dependent innate defense response, activation of innate lymphoid cells type 3 and improves colitis – Jiří Hrdý – Scientific Reports

Animal Model Microbiome

The Benefits of Switching to a Healthy Diet on Metabolic, Cognitive and Gut Microbiome Parameters are Preserved in Adult Rat Offspring of Mothers Fed a High-Fat, High-Sugar Diet – Michael D Kendig – Molecular Nutrition & Food Research

Jatrorrhizine alleviates ulcerative colitis via regulating gut microbiota and NOS2 expression – Jia Ling Zhang – Gut Pathogens

Non-Model Animal Microbiome

Identification of 146 Metagenome-assembled Genomes from the Rumen Microbiome of Cattle in Japan – Yoshiaki Sato – Microbes and Environments

Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium – Yui Sato – Microbiome

Effects of heat stress on 16S rDNA, metagenome and metabolome in Holstein cows at different growth stages – Lei Feng – Scientific data

Screening Salamanders for Symbionts – Elli Vickers – Methods in Molecular Biology

Gut microbiota differs between two cold-climate lizards distributed in thermally different regions – Jun-Qiong Chen – BMC Ecology and Evolution

Microbial community in resistant and susceptible Churra sheep infected by Teladorsagia circumcincta – Verónica Castilla Gómez de Agüero – Scientific Reports

Genome Evolution of a Symbiont Population for Pathogen Defence in Honeybees – Karl Dyrhage – Genome Biology and Evolution

Plant Microbiome

Diverse MarR bacterial regulators of auxin catabolism in the plant microbiome – Jonathan M Conway – Nature Microbiology

Phytohormones producing rhizobacteria alleviate heavy metals stress in soybean through multilayered response –  Husna – Microbiological Research

Review: Linking plant functional genes to rhizosphere microbes: a review – Qi Liu – Plant Biotechnology Journal

Bioinformatics and Microbiome Analysis Techniques 

Resampling-based inferences for compositional regression with application to beef cattle microbiomes – Sujin Lee – Statistical Methods in Medical Research

Review: Methods used for the study of endophytic fungi: a review on methodologies and challenges, and associated tips – Jefferson Brendon Almeida Dos Reis – Archives of Microbiology