March 6, 2022

Good morning, everyone! Finally, the microbiome digest is ready after a long break.

In today’s digest, there are several interesting research articles to read specifically from two main sections Gut microbiome and Animal microbiome/Animal experiments. A few of them are highlighted as follows: 1) Use of machine learning approaches to mine functional peptides from metagenomic datasets; 2) An ultimate effort to mine host-microbiome protein-protein interactions which are mostly unexplored to understand mechanistic links with a variety of diseases; 3) Important role of mucosa-associated fungi with host-protective immunity and epithelial barrier function; 4) A fantastic review article summarizes gut microbial regulation of host 5-HT and 5-HT-mediated gut functions and its implications in the microbiota-gut-brain axis; 5) Another study showed; how gut microbiota regulates specific features of microglia from aged mice; 6) A method named MAGISTA to assess intra-bin statistics of metagenome-assembled genomes.

Enjoy reading. Happy Sunday.

General microbiome

Host-microbiome protein-protein interactions capture disease-relevant pathways – Zhou et al. – Genome Biology

Review: Periodontitis, chronic liver diseases, and the emerging oral-gut-liver axis –Albuquerque-Souza et al. – Periodontology 2000

Review: tRNA modification dynamics from individual organisms to metaepitranscriptomics of microbiomes – Zhang et al. – Molecular Cell

Gut microbiome

Socioeconomic disparities and household crowding in association with the fecal microbiome of school-age children – Lapidot et al. – npj biofilms and microbiomes

Oligofructose-Enriched Inulin Intake, Gut Microbiome Characteristics, and the V̇O2 Peak Response to High-Intensity Interval Training in Healthy Inactive Adults – Williams et al. – The Journal of Nutrition

Helicobacter pylori infection affects the human gastric microbiome, as revealed by metagenomic sequencing – Wang et al. – FEBS Openbio

Microbiota dynamics in a randomized trial of gut decontamination during allogeneic hematopoietic cell transplantation – Severyn et al. – JCI insight

Review: Direct and indirect mechanisms by which the gut microbiota influence host serotonin systems – Legan et al. – Neurogastroenterology & Motility

Tree-Based Analysis of Dietary Diversity Captures Associations Between Fiber Intake and Gut Microbiota Composition in a Healthy US Adult Cohort – Kable et al. – The Journal of Nutrition

Spatial distribution of live gut microbiota and bile acid metabolism in various parts of human large intestine – Chinda et al. – Scientific Reports

Review: Understanding the mechanism underlying the anti-diabetic effect of dietary component: a focus on gut microbiota – Zhao et al. – Critical Reviews in Food Science and Nutrition

Intestinal AMPK modulation of microbiota mediates crosstalk with brown fat to control thermogenesis – Zhang et al. Nature Communications

Impact of wheat aleurone on biomarkers of cardiovascular disease, gut microbiota and metabolites in adults with high body mass index: a double-blind, placebo-controlled, randomized clinical trial – Fava et al. – European Journal of Nutrition

Oral microbiome

Alterations in the oral microbiome of individuals with a healthy oral environment following COVID-19 vaccination – Uehara et al. – BMC Oral Health

Respiratory microbiome

Age-related changes in the nasopharyngeal microbiome are associated with SARS-CoV-2 infection and symptoms among children, adolescents, and young adults – Hurst et al. – Clinical Infectious Diseases

Animal microbiome / Animal experiments

Animal gut microbiome mediates the effects of antibiotic pollution on an artificial freshwater system – Zhu et al. – Journal of Hazardous Materials

Metagenomic analysis explores the interaction of aged microplastics and roxithromycin on gut microbiota and antibiotic resistance genes of Carassius auratusZhang et al. – Journal of Hazardous Materials

Identification and functional expression of a new xylose isomerase from the goat rumen microbiome in Saccharomyces cerevisiaeColombo et al. – Letters in Applied Microbiology

Extensive metagenomic analysis of the porcine gut resistome to identify indicators reflecting antimicrobial resistance – Zhou et al. – Microbiome

Mucosal fungi promote gut barrier function and social behavior via Type 17 immunity – Leonardi et al. – Cell

Gut microbiota drives age-related oxidative stress and mitochondrial damage in microglia via the metabolite N6-carboxymethyllysine – Mossad et al. – Nature Neuroscience

Kaempferol acts on bile acid signaling and gut microbiota to attenuate the tumor burden in ApcMin/+ mice – Li et al.- European Journal of Pharmacology

Changes of gut microbiota in diabetic nephropathy and its effect on the progression of kidney injury – Cai et al. – Endocrine

The Novel Interplay between Commensal Gut Bacteria and Metabolites in Diet-Induced Hyperlipidemic Rats Treated with Simvastatin – Zhang et al. – Journal of Proteome Research

Changes to gut amino acid transporters and microbiome associated with increased E/I ratio in Chd8+/− mouse model of ASD-like behavior – Yu et al. – Nature Communications

Novel Selenium Peptides Obtained from Selenium-Enriched Cordyceps militarisAlleviate Neuroinflammation and Gut Microbiota Dysbacteriosis in LPS-Injured Mice – Wu et al. – Journal of Agricultural and Food Chemistry

Microbiome-metabolomics analysis of the effects of decreasing dietary crude protein content on goat rumen mictobiota and metabolites – Zhu et al. – Animal Bioscience


Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics – Goussarov et al. – Environmental Microbiome

July 11, 2021

Good morning everyone!

In today’s microbiome digest, we can learn more about the influence of host genetics on the gut microbiome from the research by Laura et. al., and a perspective by Liliana et. al. Also, this digest contains interesting methods/tools/pipelines such as a Robust covariance estimation method by Yong He et. Al., a new pipeline for structural characterization and classification of RNA-Seq microbiome data by Racedo et. Al, and a k-mer based tool ‘kASA’ for taxonomic analysis of metagenomic data.

Enjoy reading. Happy Sunday.

General microbiome

Review: Non-zero-sum microbiome immune system interactions – Timur Tuganbaev – European Journal of Immunology

Review: Intersection of FcγRIIB, the microbiome, and checkpoint inhibitors in antitumor immunity – Kirsten M. Baecher – Cancer Immunology, Immunotherapy

Evaluating extraction methods to study canine urine microbiota – Ryan Mrofchak – PLOS ONE

Gut microbiome

Review: The potential of outdoor environments to supply beneficial butyrate-producing bacteria to humans – Joel E. Brame – Science of The Total Environment

Gut microbiome heritability is nearly universal but environmentally contingent – Laura Grieneisen – Science

Perspective: Host genetics influence the gut microbiome– Liliana Cortes-Ortiz – Science

Isoflavone diet ameliorates experimental autoimmune encephalomyelitis through modulation of gut bacteria depleted in patients with multiple sclerosis – Samantha N. Jensen – Science Advances

Skin microbiome

Monitoring Infection and Antibiotic Treatment in the Skin Microbiota of Farmed European Seabass (Dicentrarchus Labrax) Fingerlings – Daniela Rosado – Microbial Ecology

Respiratory microbiome

Metagenomic Next-Generation Sequencing for the Diagnosis of Pneumocystis jirovecii Pneumonia in Non-HIV-Infected Patients: A Retrospective Study – Juan Jiang – Infectious Diseases and Therapy

Optimal primer selection for sinus microbiome profiling: A comparative analysis of the V1-V3 and V3-4 16S target regions – James Connell – International forum of Allergy and Rhinology

Detection of Chlamydia psittaci in both blood and bronchoalveolar lavage fluid using metagenomic next-generation sequencing – Yuan, Yingpu – Medicine

Animal microbiome / Animal experiments

Review: New insights into the microbiota of wild mice – Ho-Keun Kwon – Mammalian Genome

Bacterial communities of indoor surface of stingless bee nests – Leandro Pio de Sousa – PLOS ONE

Elucidating the optimum added dosage of Diatomite during co-composting of pig manure and sawdust: Carbon dynamics and microbial communityXiunaRen – Science of The Total Environment

Punicic acid ameliorates obesity and liver steatosis by regulating gut microbiota composition in mice – Gaofeng Yuan – Food and Function

Arc1 and the microbiota together modulate growth and metabolic traits in Drosophila – Scott A. Keith – Development

Plant, root and soil microbiome

Diversity and Interactomics of Bacterial Communities Associated with Dominant Trees During Tropical Forest Recovery – Angel A. Becerra-Lucio – Current Microbiology

Land-use types shape soil microbial compositions under rapid urbanization in the Xiong’an New Area, China – Can Wang – Science of The Total Environment

Insights into the Endophytic Bacterial Microbiome of Crocus sativus: Functional Characterization Leads to Potential Agents that Enhance the Plant Growth, Productivity, and Key Metabolite Content – Tanveer Ahmad – Microbial Ecology

Using a high-throughput sequencing technology to evaluate the various forage source epiphytic microbiota and their effect on fermentation quality and microbial diversity of Napier grass – Niaz Ali – Archives of Microbiology

Global homogenization of the structure and function in the soil microbiome of urban greenspaces – Manuel Delgado-Baquerizo – Science Advances

Water microbiome

Anaerobic fermentation of hydrothermal liquefaction wastewater of dewatered sewage sludge for volatile fatty acids production with focuses on the degradation of organic components and microbial community compositions – Zheng Chen – Science of The Total Environment


Robust covariance estimation for high-dimensional compositional data with application to microbial communities analysis – Yong He – Statistics in Medicine

A new pipeline for structural characterization and classification of RNA-Seq microbiome dataSebastian Racedo – BioData Mining.

Taxonomic analysis of metagenomic data with kASA – Silvio Weging – Nucleic Acids Res

Rapid and simultaneous determination of histidine metabolism intermediates in human and mouse microbiota and biomatrices – Inmaculada Acuña – Biofactors

April 29, 2021

Good morning from Los Angeles! Today’s microbiome digest includes various interesting research and review articles. Enjoy reading.

General microbiome

The Functional Significance of Bacterial Predators – Bruce A. Hungate – mBio

Anaerobic Microbial Metabolism of Dichloroacetate – Gao Chen – mBio

Review: Recipient factors in faecal microbiota transplantation: one stool does not fit all – Camille Danne – Nature Reviews Gastroenterology and Hepatology

Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition – Clarisse Marotz – mSystems

Gut microbiome

Review: Diet-Microbiota-Brain Axis in Alzheimer’s Disease – Halle J Kincaid – Annals of Nutrition and Metabolism

Review: The significance of the gut microbiome in children with functional constipation – Monika Kwiatkowska – Advances in Clinical and Experimental Medicine

Oral microbiome

Review: Focus on the cariogenic process: microbial and biochemical interactions with teeth and oral environment – G Dipalma – Journal Of Biological Regulators And Homeostatic Agents

Respiratory microbiome

Review: A scoping review of longitudinal airway microbiota studies – Tary Yin – Expert Review of Respiratory Medicine

Vaginal microbiome

Longitudinal Profiling of the Macaque Vaginal Microbiome Reveals Similarities to Diverse Human Vaginal Communities – Nicholas S. Rhoades – mSystems

Association of Vaginal Microbiota with Signs and Symptoms of the Genitourinary Syndrome of Menopause across Reproductive Stages – Michelle Shardell – The Journal of Gerontology


Targeted Delivery of Probiotics: Perspectives on Research and Commercialization – K.S. Yoha – Probiotics and Antimicrobial Proteins

Animal microbiome / Animal experiments

A Single Microbiome Gene Alters Murine Susceptibility to Acute Arsenic Exposure – Qian Wang – Toxicological Sciences

Lipocalin 2 modulates dendritic cell activity and shapes immunity to influenza in a microbiome dependent manner – Martin L Watzenboeck – PloS Pathogen

Macrobdella decora: Old World Leech Gut Microbial Community Structure Conserved in a New World Leech – Emily Ann McClure – Applied and Environmental Microbiology

Influence of Anacardium occidentale leaf supplementation in broiler chicken diet on performance, caecal microbiota, blood chemistry, immune status, carcass, and meat quality – K. Adeyemi – British Poultry Science

Effects of three different mannans on obesity and gut microbiota in high-fat diet-fed C57BL/6J mice – Yajian Song – Food & Function

The fecal microbiota of piglets during weaning transition and its association with piglet growth across various farm environments – Diana Luise – PLOS ONE

Species-specific but not phylosymbiotic gut microbiomes of New Guinean passerine birds are shaped by diet and flight-associated gut modifications – Kasun H. Bodawatta – Proceedings of the Royal Society B

Perturbation of gut microbiota plays an important role in micro/nanoplastics-induced gut barrier dysfunction – Jiyan Qiao – Nanoscale

Ameliorative Effect of Dietary Tryptophan on Neurodegeneration and Inflammation in d-Galactose-Induced Aging Mice with the Potential Mechanism Relying on AMPK/SIRT1/PGC-1α Pathway and Gut Microbiota – Jia Yin – Journal of Agricultural Food Chemistry

Plant, root and soil microbiome

Soybean Root Nodule and Rhizosphere Microbiome: Distribution of Rhizobial and Nonrhizobial Endophytes – Parris Mayhood – Applied and Environmental Microbiology

Hyperlocal Variation in Soil Iron and the Rhizosphere Bacterial Community Determines Dollar Spot Development in Amenity Turfgrass – Ming-Yi Chou – Applied and Environmental Microbiology

Manure-Based Amendments Influence Surface-Associated Bacteria and Markers of Antibiotic Resistance on Radishes Grown in Soils with Different Textures – Giselle K. P. Guron – Applied and Environmental Microbiology

Water microbiome

Human‐ and Infrastructure‐associated Bacteria in Greywater – M. Nagarkar – Journal of Applied Microbiology

February 8, 2021

Good morning from Minneapolis!

Today’s microbiome digest includes several interesting research and review articles. Enjoy reading!

General microbiome

Review: The intestinal neuro-immune axis: crosstalk between neurons, immune cells, and microbes – Amanda Jacobson – Mucosal Immunology

Review: The Role of the Gut Microbiome, Immunity, and Neuroinflammation in the Pathophysiology of Eating Disorders – Michael J. Butler – Nutrients

Review: The microbiome and host mucosal interactions in urinary tract diseases – Bernadette Jones-Freeman – Mucosal Immunology

Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota – Francesco Durazzi – Scientific Reports

Perspective: Modulating gut microbiota to treat cancer – Christopher H. Woelk – Science

Sequence Meets Function—Microbiota And Cardiovascular Disease – Myungsuk Kim – Cardiovascular Research

Human gut microbiome

Fecal microbiota transplant overcomes resistance to anti–PD-1 therapy in melanoma patients – Diwakar Davar – Science

Fecal microbiota transplant promotes response in immunotherapy-refractory melanoma patients – Erez N Baruch – Science

Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt – Simone Rampelli – Communications Biology

Meta-omics characteristics of intestinal microbiota associated to HBeAg seroconversion induced by oral antiviral therapy – Yu-Li Zeng – Scientific Reports

Anti-cancer and anti-inflammatory effects elicited by short chain fatty acids produced by Escherichia coli isolated from healthy human gut microbiota – Atchareeya Nakkarach – Microbial Cell Factories

Exploiting the Microbiota for the Diagnosis of Anal Precancerous Lesions in Men Who Have Sex With Men – Raquel Ron – Journal of Infectious Disease

Distribution characteristics of intestinal microbiota during pregnancy and postpartum in healthy women – Shengtang Qin – The Journal of Maternal-Fetal & Neonatal Medicine

Co-Occurrence of Symptoms and Gut Microbiota Composition Before Neoadjuvant Chemotherapy and Radiation Therapy for Rectal Cancer: A Proof of Concept – Velda J Gonzalez-Mercado – Biological Research For Nursing

Oral and respiratory microbiome

Development of a robust protocol for the characterization of the pulmonary microbiota – Nathan Dumont-Leblond – Communications Biology

Lung microbiota associations with clinical features of COPD in the SPIROMICS cohort – Kristopher Opron – npj Biofilms and Microbiomes

Animal microbiome / Animal experiments

Changes in the gut microbial community of the eastern newt (Notophthalmus viridescens) across its three distinct life stages – Samantha S Fontaine – FEMS Microbiology Ecology

Altered Gut Microbiota is Involved in the Anti‐Hypertensive Effects of Vitamin C in Spontaneously Hypertensive Rat – Ying Li – Molecular Nutrition and Food Research

Long Term High Protein Diet Feeding Alters the Microbiome and Increases Intestinal Permeability, Systemic Inflammation and Kidney Injury in Mice – Matthew Snelson- Molecular Nutrition and Food Research

Low-dose exposure of glyphosate-based herbicides disrupt the urine metabolome and its interaction with gut microbiota – Jianzhong Hu – Scientific Reports

Metagenomics of antimicrobial and heavy metal resistance in the cecal microbiome of fattening pigs raised without antibiotics – Paiboon Tunsagool – Applied and Environmental Microbiology

IL-17 controls central nervous system autoimmunity through the intestinal microbiome – Tommy Regen – Science Immunology

The skin microbiome of Xenopus laevis and the effects of husbandry conditions – Maya Z. Piccinni – Animal Microbiome

Effects of dietary oregano essential oil supplementation on growth performance, intestinal antioxidative capacity, immunity and intestinal microbiota in yellow-feathered chickens – Dong Ruan – Journal of Animal Science

Composition and acquisition of the microbiome in solitary, ground-nesting alkali bees – Karen M. Kapheim – Scientific Reports

The impact of the gut microbiome on memory and sleep in Drosophila – Valeria Silva – Journal of Experimental Biology

Probiotics / prebiotics

Prebiotic dietary fibre intervention improves fecal markers related to inflammation in obese patients: results from the Food4Gut randomized placebo-controlled trial – Audrey M. Neyrinck – European Journal of Nutrition

Plant, root, and soil microbiome

Reduced tillage, cover crops and organic amendments affect soil microbiota and improve soil health in Uruguayan vegetable farming systems – Victoria Cerecetto – FEMS Microbiology Ecology

Tillage shapes the soil and rhizosphere microbiome of barley – but not its susceptibility towards Blumeria graminis f. sp. Hordei – Nina Bziuk – FEMS Microbiology Ecology

The rhizosphere microbiome plays a role in the resistance to soil-borne pathogens and nutrient uptake of strawberry cultivars under field conditions – Cristina Lazcano – Scientific Reports

16S rRNA gene-based microbiome analysis identifies candidate bacterial strains that increase the storage time of potato tubers – Franziska Buchholz – Scientific Reports

Methods and techniques

Boolean implication analysis unveils candidate universal relationships in microbiome data – Daniella Vo – BMC Bioinformatics

Review: Advances in modelling the human microbiome–gut–brain axis in vitro – Chrysanthi-Maria Moysidou

MB-GAN: Microbiome Simulation via Generative Adversarial Network – Ruichen Rong – GigaScience

October 10, 2020

Good morning everyone! 

Highlights of today’s microbiome digest include: 

  • A genome-wide association study showed an association between host genetic variants and the gut microbiome in the Chinese population.
  • Association of sugar intake with the gut microbiome composition in the Malmö Offspring Study.
  • Gut microbial changes in Holstein cows from birth to adulthood.
  •  Fecal microbiome and antimicrobial resistance profiles in healthy Australian foals.
  • A new method for the detection of functional potential from metagenomic sequences.

Enjoy reading!

General microbiome

Review: Interactions among microbes, the immune system, and the circadian clock – John F. Brooks – Seminars in Immunopathology

Comment: Know Your Model: Microbiota & phenotypes – Michelle N. Perry – Lab Animal

The wasted chewing gum bacteriome – Leila Satari – Scientific Reports

A realism-based approach to an ontological representation of symbiotic interactions – Matthew Diller – BMC Medical Informatics and Decision Making

Review: Multi-omics tools for studying microbial biofilms: current perspectives and future directions – Chaminda J. Seneviratne – Critical Reviews in Microbiology

Review: Challenges & opportunities for phage-based in situ microbiome engineering in the gut – Peter J Voorhees

Human gut microbiome

Review: Modulation of the Microbiome in Parkinson’s Disease: Diet, Drug, Stool Transplant, and Beyond – Ethan G. Brown – Neurotherapeutics

Review: Gut microbiome and anorexia nervosa: The relationship between microbiome and gut-brain interaction in the context of anorexia nervosa – J. Seitz – Nervenarzt

The interplay between host genetics and the gut microbiome reveals common and distinct microbiome features for complex human diseases – Fengzhe Xu – Microbiome

Gut microbiota composition in relation to intake of added sugar, sugar-sweetened beverages and artificially sweetened beverages in the Malmö Offspring Study – Stina Ramne – European Journal of Nutrition

Gut microbiome mediated epigenetic regulation of brain disorder and application of machine learning for multi-omics data analysis – Harpreet Kaur – Genome

Review: The Gut Microbiome and Bone Strength – Macy Castaneda – Current Osteoporosis Reports

Review: Effects of Antibiotic Treatment on Gut Microbiota and How to Overcome Its Negative Impacts on Human Health – Camila Fontoura Acosta Ribeiro

Mechanisms linking the human gut microbiome to prophylactic and treatment strategies for COVID-19 – Gemma E Walton- British Journal of Nutrition

Oral and respiratory microbiome

Toll like Receptor signalling by Prevotella histicola activates alternative NF-κB signalling in Cystic Fibrosis bronchial epithelial cells compared to P. aeruginosa – Anne Bertelsen – PloS One

Vaginal microbiome

Effect of a Nonoptimal Cervicovaginal Microbiota and Psychosocial Stress on Recurrent Spontaneous Preterm Birth – Kristin D Gerson – American Journal of Perinatology

Animal microbiome / Animal experiments

Enteromorpha prolifera Diet Drives Intestinal Microbiome Composition in Siganus oramin – Yan Xu – Current Microbiology

High-Fat Proteins Drive Dynamic Changes in Gut Microbiota, Hepatic Metabolome, and Endotoxemia-TLR-4-NFκB-Mediated Inflammation in Mice – Muhammad Ijaz Ahmad – J. Agric. Food Chem

Dynamic change of the gastrointestinal bacterial ecology in cows from birth to adulthood – Chun Y. Guo – Microbiology Open

Effects of seasonality and previous logging on faecal helminth-microbiota associations in wild lemurs – I. I. de Winter – Scientific Reports

Effects of inulin and isomalto-oligosaccharide on diphenoxylate-induced constipation, gastrointestinal motility-related hormones, short-chain fatty acids, and the intestinal flora in rats – Junhong Lan – Food & Function

Probiotic-fermented blueberry juice prevents obesity and hyperglycemia in high fat diet-fed mice in association with modulating the gut microbiota – Hao Zhong – Food & Function

Faecal microbiota and antimicrobial resistance gene profiles of healthy foals – Yuhong Liu – Equine Veterinary Journal

Sows affect their piglets’ faecal microbiota until fattening but not their Salmonella enterica shedding status – Guillaume Lariviere-Gauthier – Letters in Applied Microbiology

Probiotics / prebiotics

Review: Current status of probiotics for prevention and management of gastrointestinal cancers – Abdul Arif Khan – Expert Opinion on Biological Therapy

Plant, root, and soil microbiome

Characterization of the Leaf Microbiome from Whole-Genome Sequencing Data of the 3000 Rice Genomes Project – Veronica Roman-Reyna – Rice

Air, water and extremophile microbiome

Review: Urbanisation reduces the abundance and diversity of airborne microbes – but what does that mean for our health? A systematic review – Emily J. Flies – Science of The Total Environment

Impact of a synthetic fungicide (fosetyl-Al and propamocarb-hydrochloride) and a biopesticide (Clonostachys rosea) on soil bacterial, fungal, and protist communities – BertrandFournier – Science of The Total Environment


RBUD: A New Functional Potential Analysis Approach for Whole Microbial Genome Shotgun Sequencing – Zhikai Xing – Microorganisms

August 30, 2020

Good morning everyone! In today’s microbiome digest we have several reviews and research articles focused on the human microbiome, some animal studies, few interesting methods such as Kraken2 for 16S rRNA analysis, and Convolutional Neural Network for prediction of host phenotypes from microbial samples. Enjoy reading!!

General microbiome

Review: CRISPR screens in the era of microbiomes – François Rousset – Current Opinion in Microbiology

Chapter: Genetic Transformation of Fusobacterium nucleatum – Akihiro Yoshida – Methods in Molecular Biology

Perspective: Gut microbiota: a potential therapeutic target for Parkinson’s disease – José Fidel Baizabal-Carvallo – Neural Regeneration Research

Processing has differential effects on microbiota accessible carbohydrates in whole grains during in vitro fermentation – Caroline Smith – Applied Environmental Microbiology

Human gut microbiome

Gut microbiota and oral contraceptive use in overweight and obese patients with polycystic ovary syndrome – Nesrin Damla Eyupoglu – The Journal of Clinical Endocrinology and Metabolism

Diversity analysis of gut microbiota between healthy controls and those with atopic dermatitis in a Chinese population – Siqi Ye – The Journal of Dermatology

Faecal microbiota transplantation for the treatment of diarrhoea induced by tyrosine-kinase inhibitors in patients with metastatic renal cell carcinoma – Gianluca Ianiro – Nature Communications

Integrated microbiota and metabolite profiles link Crohn’s disease to sulfur metabolism – Amira Metwaly – Nature Communications

Review: The potential role of the gut microbiota in shaping host energetics and metabolic rate – Elle C Lindsay – Journal of Animal Ecology

Oral and respiratory microbiome

Microbiological analysis of endodontically treated teeth with apical periodontitis before and after endodontic retreatment– Marlos Barbosa-Ribeiro – Clinical Oral Investigation

2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals – Judith Neukamm – BMC Biology

Comparing the nasal bacterial microbiome diversity of allergic rhinitis, chronic rhinosinusitis and control subjects – Weigang Gan – European Archives of Oto-Rhino-Laryngology

Maternal Oral Health Influences Infant Salivary MicrobiomeK. Ramadugu – Journal of Dental Research

Animal microbiome / Animal experiments

Dietary supplementation of sodium sulfate improves rumen fermentation, fiber digestibility and plasma metabolome through modulating rumen bacterial communities in steers – Yuchao Zhao – Applied Environmental Microbiology

Salmonella enterica serovar Typhimurium Temporally Modulates the Enteric Microbiota and Host Responses to Overcome Colonization Resistance in Swine – Danisa M Bescucci – Applied Environmental Microbiology

Germ-Free Conditions Modulate Host Purine Metabolism, Exacerbating Adenine-Induced Kidney Damage – Eikan Mishima – Toxins

Conventional Co-Housing Modulates Murine Gut Microbiota and Hematopoietic Gene Expression – Jichun Chen – International Journal of Molecular Sciences

Plant, root, and soil microbiome

Suppression of rice planthopper populations without affecting the rice microbiota by the entomopathogenic fungus Metarhizium anisopliae – Yifan Peng – Applied Environmental Microbiology

Water and extremophile microbiome

Dissolved microcystin release coincident with lysis of a Microcystis-dominated bloom in western Lake Erie attributed to a novel cyanophage – McKindles et al – Applied Environmental Microbiology


Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2 – Jennifer Lu – Microbiome

Chapter: Predicting Host Phenotype Based on Gut Microbiome Using a Convolutional Neural Network Approach – Derek Reiman – Artificial Neural Networks


Review: Application of Next Generation Sequencing in Laboratory Medicine – Yiming Zhong – Annals of laboratory medicine



July 11, 2020

Good morning everyone. Today’s digest includes various interesting articles such as: 1) mNGS-based approach for broad-range detection of pathogens associated with CNS infections, 2) dynamics of diarrheal pathogenesis and antimicrobial resistance transmission using gut microbiome and resistome profiling, 3) comparison urinary and bladder mucosa-associated microbiome composition in bladder cancer patients, 4) regulation of vaginal microbiome composition and stability by ovarian hormones, diet and exercise, 5) Chokeberry polyphenols can reduce the body weight of HFD-fed rats by accelerating energy homeostasis and thermogenesis in interscapular brown adipose tissue, 6) Comparison of taxonomic composition and diversity of bacterial and fungal communities in synanthropic and non-synanthropic mound-building mouse, and 7) an information retrieval system for large metagenomic datasets to recover missing content from genome bins. Enjoy reading. Happy weekend.

General microbiome

Commentary: mSphere of Influence: Translating Gut Microbiome Studies To Benefit Human Health – Anna M. Seekatz – mSphere

A metagenomics-based diagnostic approach for central nervous system infections in hospital acute care setting – Mohammad Rubayet Hasan – Scientific Reports

Human microbiome

Metagenomic analysis of gut microbiome and resistome of diarrheal fecal samples from Kolkata, India, reveals the core and variable microbiota including signatures of microbial dark matter – Rituparna De – Gut Pathogens

Bladder cancer-related microbiota: examining differences in urine and tissue samples– Bassel Mansour – Scientific Reports

Daily Vaginal Microbiota Fluctuations Associated with Natural Hormonal Cycle, Contraceptives, Diet, and Exercise – Stephanie D. Song – mSphere

Dynamics of the lung microbiome in intensive care patients with chronic obstructive pulmonary disease and community-acquired pneumonia – Wei-Chang Huang – Scientific Reports

Animal microbiome / Animal experiments

The polyphenol-rich extract from chokeberry (Aronia melanocarpa L.) modulates gut microbiota and improves lipid metabolism in diet-induced obese rats – Yue Zhu – Nutrition and Metabolism

Changes in the gut microbiota mediate the differential regulatory effects of two glucose oxidases produced by Aspergillus niger and Penicillium amagasakiense on the meat quality and growth performance of broilers – Shengru Wu – Journal of Animal Science and Biotechnology

The effects of atrazine on the microbiome of the eastern oyster: Crassostrea virginicaAdrian Britt – Scientific Reports

How being synanthropic affects the gut bacteriome and mycobiome: comparison of two mouse species with contrasting ecologies – Barbora Bendová – BMC Microbiology

Fruit and vegetable microbiome

Exploring bacteria diversity in commercialized table olive biofilms by metataxonomic and compositional data analysis – Antonio Benítez-Cabello – Scientific Reports

Plant, root and soil microbiome

Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules – Dan Naylor – mBio

Water microbiome

Metagenomic water quality monitoring with a portable laboratory – Kishor Acharya – Water Research


Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity – C. Titus Brown – Genome Biology

May 18, 2020

Good morning everyone. Today’s microbiome digest is very short specifically the human gut microbiome section. I have included only one study in this section which shows no association of gut microbiome and fecal calprotectin levels with enteropathy in preterm infants. Additionally, I have covered several interesting reviews and research articles to explore the role of the gut microbiome in Type 1 diabetes and Hashimoto’s thyroiditis, ameliorates ulcerative colitis, aging process, regulation of energy metabolism and oxidative stress. I hope you will enjoy today’s feed.

General microbiome

Fungal communities and their association with nitrogen-fixing bacteria affect early decomposition of Norway spruce deadwood – María Gómez-Brandón – Scientific Reports

Review: Gut microbiota and metabolites in the pathogenesis of endocrine disease – Fenneman AC – Biochemical Society Transactions

Review: Role of the Phytochemical Compounds like Modulators on Gut Microbiota and Oxidative Stress – Yordan Martínez – Current Pharmaceutical Design

Human gut microbiome

Faecal calprotectin and gut microbiota do not predict enteropathy in very preterm infants – Florence Campeotto – Acta Paediatrica

Animal microbiome / Animal experiments

Lizhong decoction ameliorates ulcerative colitis in mice via modulating gut microbiota and its metabolites – Junfeng Zou – Applied microbial and cell physiology

Age-related compositional changes and correlations of gut microbiome, serum metabolome, and immune factor in rats – Xia Zhang – GeroScience

The Beneficial Effects of Lippia Citriodora Extract on Diet‐Induced Obesity in Mice are Associated with the Modulation in the Gut Microbiota Composition – Patricia Diez‐Echave – Molecular Nutrition and Food Research

The gut microbiota attenuates muscle wasting by regulating energy metabolism in chemotherapy-induced malnutrition rats – Haitao Chen – Cancer Chemotherapy and Pharmacology

Slc26a3 deletion alters pH‐microclimate, mucin biosynthesis, microbiome composition and increases Tnfα expression in murine colon – A. Kini – Acta Physiologica

Tibet plateau probiotic mitigates chromate toxicity in mice by alleviating oxidative stress in gut microbiota – Pengya Feng – Communications Biology

Antimicrobial peptide GH12 prevents dental caries by regulating dental plaque microbiota – Wentao Jiang – Microbial Ecology


Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets – Isabel F. Escapa – Microbiome

Review: Metaproteomics: A strategy to study the taxonomy and functionality of the gut microbiota – Yuqiu Wang – Journal of Proteomics

Microbes in news

DOE scientists identify microbial link in gut-memory connection

March 7, 2020

In today’s microbiome digest I have included several interesting articles including a) role of gut microbial metabolite in cardiovascular disease, role of microbiome in cancer treatment outcomes, comparison of small bowel microbiome with the stool samples, microbiome and metabolome of dairy cows with different feed intake levels, role of dietary cellulose in preventing the gut inflammation via modulation in microbiome, and so on. I hope you will enjoy today’s feed.

General microbiome

The microbiome modulating activity of bile acids – Tian, Yuan – Gut Microbes

PostScript Letter: Microbiome alterations in IBS – Ian B Jeffery – Gut

Human gut microbiome

A Cardiovascular Disease-Linked Gut Microbial Metabolite Acts via Adrenergic Receptors – Nemet I – Cell

The Fecal Microbiome in Infants with Biliary Atresia Associates with Bile Flow after Kasai Portoenterostomy – Tessier MEM – Journal of Pediatric Gastroenterology and Nutrition

Mapping the Segmental Microbiomes in the Human Small Bowel in Comparison with Stool: A REIMAGINE Study – Gabriela G. S. Leite – Digestive Diseases and Sciences

Modulation of the intestinal microbiota and the metabolites produced by the administration of ice cream and a dietary supplement containing the same probiotics – Vivian Cristina da Cruz Rodrigues – British Journal of Nutrition

Predictable modulation of cancer treatment outcomes by the gut microbiota – Yoshitaro Heshiki – Microbiome

Animal microbiome / Animal experiments

Microbial composition of enigmatic bird parasites: Wolbachia and Spiroplasma are the most important bacterial associates of quill mites (Acariformes: Syringophilidae) – Eliza Glowska – MicrobiologyOpen

Combined signature of rumen microbiome and metabolome in dairy cows with different feed intake levels – Y Q Li – Journal of Animal Science

Comparative Analysis of Gut Microbiota in Two Populations of Argopecten purpuratus (Lamarck, 1819) Based on 16S rRNA Gene Amplicon Data – Wilbert Serrano – Microbiology Resource Announcements

Dietary cellulose prevents gut inflammation by modulating lipid metabolism and gut microbiota – Yeji Kim – Gut Microbes

Gut microbiome shifts with urbanization and potentially facilitates a zoonotic pathogen in a wading bird – Maureen H. Murray- PLOS ONE

Water and extremophile microbiome

Tuning up microbiome analysis to monitor WWTPs’ biological reactors functioning– de Celis M – Scientific Reports

Metagenome Sequences from Tidal Marsh and Marine Sediment from the Great Bay Estuary of New Hampshire – Brian M. Moore – Microbiology Resource Announcements

Microbes in news

Gut Microbiome Could Determine Cancer Immunotherapy Success


January 25, 2020

In today’s microbiome digest various interesting aspects of microbiome research has been covered such as 1) a summary report by Marc G. Chevrette on one of my favorite research of the decade – “A metagenomic strategy for harnessing the chemical repertoire of the human microbiome”, 2) Oral administration of hydrogels promoted intestinal barrier function, suppressed the pro-inflammatory mRNA expression, 3) Association of low fiber intake in chronic heart failure, and several other interesting articles! Enjoy reading! Happy Weekend!

General microbiome

From Metagenomes to Molecules: Innovations in Functional Metagenomics Unlock Hidden Chemistry in the Human Microbiome – Marc G. Chevrette – Biochemistry

A systematic review of economic evaluation in fecal microbiota transplantation – Thomas Stalder – Infection Control & Hospital Epidemiology

Review: Microbial Contribution to the Human Metabolome: Implications for Health and Disease – William Van Treuren – Annual Review of Pathology

Human gut microbiome

Low fibre intake is associated with gut microbiota alterations in chronic heart failure – Cristiane C.K. Mayerhofer – ESC Heart Fail

Review: Establishing or Exaggerating Causality for the Gut Microbiome: Lessons from Human Microbiota-Associated Rodents – Jens Walter – Cell

Compositional flux within the intestinal microbiota and risk for bloodstream infection with gram-negative bacteria – Igor Stoma – Clinical Infectious Diseases

Comparative Analysis of Gut Microbiota Following Changes in Training Volume Among Swimmers– Jarrad Timothy Hampton-Marcell – International Journal of Sports Medicine

Diversity, compositional and functional differences between gut microbiota of children and adults – Djawad Radjabzadeh – Scientific Reports

Environmental and intrinsic factors shaping gut microbiota composition and diversity and its relation to metabolic health in children and early adolescents: A population-based study – Sofia Moran-Ramos – Gut Microbes

Human skin microbiome

Impact of the early-life skin microbiota on the development of canine atopic dermatitis in a high-risk breed birth cohort– S. Rodriguez-Campos – Scientific Reports

Human respiratory microbiome

The lung microbiota: role in maintaining pulmonary immune homeostasis and its implications in cancer development and therapy – Michele Sommariva – Cellular and Molecular Life Sciences

Lung Microbiota Predict Clinical Outcomes in Critically Ill Patients – Robert P. Dickson – American Journal of Respiratory and Critical Care Medicine

Animal microbiome / Animal experiments

Functional dynamics of bacterial species in the mouse gut microbiome revealed by metagenomic and metatranscriptomic analyses – Youn Wook Chung – PLOS ONE

Effect of Lactobacillus acidophilus D2/CSL (CECT 4529) supplementation in drinking water on chicken crop and caeca microbiome– De Cesare A – PLOSE ONE

Differential effects of synthetic psychoactive cathinones and amphetamine stimulants on the gut microbiome in mice – Angoa-Pérez M – PLOSE ONE

Modulation of inflammatory response and gut microbiota in ankylosing spondylitis mouse model by bioactive peptide IQW – Gang Liu – Journal of Applied Microbiology

Effect of cereal soaking and carbohydrase supplementation on growth, nutrient digestibility and intestinal microbiota in liquid-fed grow-finishing pigs – Alberto Torres-Pitarch – Scientific Reports

Anesthesia and surgery induce age-dependent changes in behaviors and microbiota – Ning Liufu – Aging

Amyloid–Polyphenol Hybrid Nanofilaments Mitigate Colitis and Regulate Gut Microbial Dysbiosis – Bing Hu – ACS Nano

Clostridium butyricum Modulates the Microbiome to Protect Intestinal Barrier Function in Mice with Antibiotic-Induced Dysbiosis – Mao Hagihara – iScience

Microbes in news

Can our microbiome accurately identify diseases … and predict death?