July 27, 2021

Have a nice day! Before presenting the Digest for today, I want to highlight that in few hours the ISME-LatinAmerica 2021 meeting will start. Additionally, I also want to highlight a Call from the Institut Pasteur for the creation of new groups (applications available until next November 30). Now, enjoy this digest!

Human and General Microbiome

Review: Discovery and mining of enzymes from the human gut microbiome – Baolei Jia – Trends in Biotechnology

Review: Antimicrobial peptides and proteins: Interaction with the skin microbiota – Franziska Rademacher – Experimental Dermatology

Review: Malnutrition and the microbiome as modifiers of early neurodevelopment – Elena J L Coley – Trends in Neurosciences

Review: Predictors of multidrug resistant Pseudomonas aeruginosa involvement in bloodstream infections – Sabina Herrera – Current Opinion in Infectious Diseases

Review: Diet Interventions for Irritable Bowel Syndrome: Separating the Wheat from the Chafe. – Emily Haller – Gastroenterology Clinics of North America

Review: Emerging Role of the Gut Microbiome in Irritable Bowel Syndrome – Prashant Singh – Gastroenterology Clinics of North America

Review: The Types and Proportions of Commensal Microbiota Have a Predictive Value in Coronary Heart Disease. – Lin Chen – Journal of Clinical Medicine

Review: Association of Microbiome with Oral Squamous Cell Carcinoma: A Systematic Review of the Metagenomic Studies. – Lee Su Mun – International Journal of Environmental Research and Public Health

Book Chapter: The Role of H(2)S in the Gastrointestinal Tract and Microbiota – Ailin Xiao – Advances in Hydrogen Sulfide Biology 

Research Highlight: CNMa-CNMa receptor at microbiome-gut-brain axis: novel target to regulate feeding decision – Liyuan Peng – Signal Transduction and Targeted Therapy

Household environmental microbiota influences early-life eczema development – Le Duc Huy Ta – Environmental Microbiology

Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment – Morteza Roodgar – Genome Research

Combined mechanical and oral antibiotic bowel preparation is associated with prolonged recurrence-free survival following surgery for colorectal cancer – Lindsey M Zhang – Journal of Surgical Oncology

Field evaluation of the gut microbiome composition of pre-school and school-aged children in Tha Song Yang, Thailand, following oral MDA for STH infections. – Katharina Stracke – PLoS Neglected Tropical Diseases

Characteristics of the bacterial microbiota in the upper respiratory tract of children – Wei Cao – European archives of Oto-rhino-laryngology

Exploring Gut Microbiota in Patients with Colorectal Disease Based on 16S rRNA Gene Amplicon and Shallow Metagenomic Sequencing – Yuanfeng Liu – Frontiers in Molecular Biosciences

The Intestinal Microbiome Predicts Weight Loss on a Calorie-Restricted Diet and Is Associated With Improved Hepatic Steatosis – Tien S Dong – Frontiers in Nutrition

16S rRNA gene amplicon sequencing of gut microbiota in gestational diabetes mellitus and their correlation with disease risk factors – J Wei – Journal of Endocrinological Investigation

Analyses of publicly available Hungatella hathewayi genomes revealed genetic distances indicating they belong to more than one species – Laura E Hernández-Juárez – Virulence

Estrogen-related receptor alpha (ERRα) is a key regulator of intestinal homeostasis and protects against colitis – Allan Tran – Scientific Reports

Predicting dental caries increment using salivary biomarkers in a remote Indigenous Australian child population – Surani Fernando – BMC Oral Health

Beneficial Microbes, Treatments, and Compounds

Human milk oligosaccharide 2′-fucosyllactose supplementation improves gut barrier function and signaling in the vagal afferent pathway in mice – Sunhye Lee – Food & Function

Lactobacillus casei LC89 exerts antidiabetic effects through regulating hepatic glucagon response and gut microbiota in type 2 diabetic mice – Yongli Zhang – Food & Function

The roles of different Bacteroides fragilis strains in protecting against DSS-induced ulcerative colitis and related functional genes – Chen Wang – Food & Function

Probiotics Fermentation Technology, a Novel Kefir Product, Ameliorates Cognitive Impairment in Streptozotocin-Induced Sporadic Alzheimer’s Disease in Mice – Nesrine S El Sayed – Oxidative Medicine and Cellular Longevity

Vaccarin enhances intestinal barrier function in type 2 diabetic mice – Jiang-Nan Sun – European Journal of Pharmacology

Personalized Postprandial Glucose Response-Targeting Diet Versus Mediterranean Diet for Glycemic Control in Prediabetes – Orly Ben-Yacov – Diabetes Care

Animal Microbiome

Dietary supplementation of alpha-lipoic acid mitigates the negative effects of heat stress in broilers – Sanjeev Wasti – PloS One

On the move: sloths and their epibionts as model mobile ecosystems – Maya Kaup – Biological reviews of the Cambridge Philosophical Society

Plant Microbiome

The discovery of pivotal fungus and major determinant factor shaping soil microbial community composition associated with rot root of American ginseng. – Lixia Tian – Plant Signaling & Behavior

Environmental Microbiome

Description of Microbial Communities of Phosphate Mine Wastes in Morocco, a Semi-Arid Climate, Using High-Throughput Sequencing and Functional Prediction. – Najoua Mghazli – Frontiers in Microbiology

Characterization of eukaryotic microbiome and associated bacteria communities in a drinking water treatment plant – Patricia Soler – The Science of the Total Environment

Dynamics of bacterial and archaeal communities along the composting of tannery sludge – Ademir Sergio Ferreira Araujo – Environmental Science and Pollution Research International

Other Microbes

Prioritization of potential drug targets and antigenic vaccine candidates against Klebsiella aerogenes using the computational subtractive proteome-driven approach. – Vijina Chakkyarath – Journal of proteins and proteomics

Genomic evolution of antimicrobial resistance in Escherichia coli – Pimlapas Leekitcharoenphon – Scientific Reports

Microbiome Analysis Tools and Techniques

Strainberry: automated strain separation in low-complexity metagenomes using long reads. – Riccardo Vicedomini – Nature Communications

Visualization of Gut Microbiota-host Interactions via Fluorescence In Situ Hybridization, Lectin Staining, and Imaging – Katharine M Ng – Journal of Visualized Experiments (JoVE)

A newly developed PCR-based method revealed distinct Fusobacterium nucleatum subspecies infection patterns in colorectal cancer – Dexi Bi – Microbial Biotechnology

A protocol for characterization of extremely preterm infant gut microbiota in double-blind clinical trials – Magalí Martí – STAR Protocols

Transformation and differential abundance analysis of microbiome data incorporating phylogeny – Chao Zhou – Bioinformatics

July 24, 2021

Have a nice weekend! Today in this Digest, we have a set of papers covering different aspects of the human microbiome in health and disease. For example, connections between gut microbiota and different clinical parameters in patients with inflammatory bowel disease, and another study showing a relationship between TMAO and heart damage.  

Human and General Microbiome

Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease – Jonathan Wei Jie Lee – Cell Host & Microbe

Gut Microbiota-generated Metabolite, Trimethylamine-N-oxide, And Subclinical myocardial damage: a multicenter study from Thailand – Vichai Senthong – Scientific Reports

Association Between The Urogenital Microbiome And Surgical Treatment Response In Women Undergoing Mid-urethral Sling Surgery for Mixed Urinary Incontinence – Holly E Richter – American Journal Of Obstetrics And Gynecology

Review: Personalized Approach To Childhood Obesity: Lessons From Gut Microbiota And Omics studies. Narrative review and insights from the 29th European childhood obesity congress – Aneta Gawlik – Pediatric Obesity

Review: The complex interplay of gut microbiota with the five most common cancer types: from carcinogenesis to therapeutics to prognosis – Kayla Jaye – Critical Reviews In Oncology/hematology

Clostridium culturomicium sp. nov. and Clostridium jeddahitimonense sp. nov., Novel members of the Clostridium genus isolated from the stool of an obese Saudi Arabian. – Hoang Thong Kieu – Current Microbiology

Effect Of Intestinal Microbiota Imbalance Associated With Chronic Hepatitis B Virus infection on the expression of microRNA‑192 and GLP‑1 – Yinghui Liu – Molecular Medicine Reports

Variations In The Oral Microbiome Are Associated With Depression In Young Adults – Benjamin Wingfield – Scientific Reports

Comparative Analysis Of The Bronchoalveolar Microbiome In Portuguese Patients With different chronic lung disorders – Susana Seixas – Scientific Reports

Microbiome and COVID19

Review: Recent Advance Of ACE2 And Microbiota Dysfunction In COVID-19 Pathogenesis – Zhidan Yu – Heliyon

Animal Microbiome

Review: T Cell Subsets And Environmental Factors In Citrobacter rodentium Infection – Brigitta Stockinger – Current Opinion In Microbiology

Chitinibacter bivalviorum sp. nov., Isolated From The Gut Of The Freshwater Mussel Anodonta arcaeformis – Jee-Won Choi – International Journal Of Systematic And Evolutionary Microbiology

Beneficial Microbes and Compounds

Nanocapsule-mediated Sustained H2 Release In The Gut Ameliorates Metabolic dysfunction-associated fatty liver disease – Zhaokui Jin – Biomaterials

Aryl Hydrocarbon Receptor Activation By Lactobacillus reuteri Tryptophan Metabolism alleviates Escherichia coli-induced mastitis in mice – Caijun Zhao – PLoS Pathogens

Grape Seed Proanthocyanidins Reduced The Overweight Of C57BL/6J Mice through modulating adipose thermogenesis and gut microbiota. – Haiping Du – Food & Function

Plant Microbiome

Distribution Of The Potential Pathogenic Alternaria On Plant Leaves Determines foliar fungal communities around the disease spot – Jiemeng Tao – Environmental Research

Prolonged Drought Imparts Lasting Compositional Changes To The Rice Root Microbiome – Christian Santos-Medellín – Nature Plants

News & Views: Drought Dampens Microbiome Development – Yi Song – Nature Plants

Built Environment

Factors Associated With Elevated Levels Of Antibiotic Resistance Genes In Sewer sediments and wastewater – Eramo Alessia – Environmental Science

Microbiome Techniques and Analysis

A Novel, Scalable, And Modular Bioreactor Design For Dynamic Simulation Of The digestive tract – Salam Habib – Biotechnology And Bioengineering

Assessment Of Biolog Ecoplate(TM) Method For Functional Metabolic Diversity Of aerotolerant pig fecal microbiota – A Checcucci – Applied Microbiology And Biotechnology

Structural Identifiability Of The Generalized Lotka-Volterra Model For Microbiome studies – Christopher H Remien – Royal Society Open Science

Validation Of The MYChrOme™ Culture Plate For Detection And Differentiation Of Rapid-Growing Nontuberculous Mycobacteria in potable and non-potable water: AOAC  Performance Tested MethodSM 062101 – Katherine E Fisher – Journal Of AOAC International

July 23, 2021

Happy Friday!

It’s an exciting day here because I’m packing for fieldwork! In just a few short days I’ll be sampling from a saline aquifer in Illinois. For those of you who aren’t lucky enough to be going into the field, today’s digest is packed with a wide range of articles. Topics covered include the wild spider gut microbiome, the presence of antibiotic resistance genes in an Ohio river, the mosquito virome, the plant rhizosphere, and more.

Happy reading!

Human gut microbiome

Preprint: Phenotypic and genomic diversification in complex carbohydrate degrading human gut bacteria – Pudlo et al. – bioRxiv

Animal experiments

Effect of biochanin A on the rumen microbial community of Holstein steers consuming a high fiber diet and subjected to a subacute acidosis challenge – Harlow et al. – PLOS ONE

Ear wound healing in MRL/MpJ mice is associated with gut microbiome composition and is transferable to non-healer mice via microbiome transplantation – Velasco et al. – PLOS ONE

Animal microbiome

Preprint: Increased microbial diversity and decreased prevalence of common pathogens in the gut microbiomes of wild turkeys compared to domestic turkeys – Craft et al. – bioRxiv

Interspecific variation and functional traits of the gut microbiome in spiders from the wild: The largest effort so far – Tyagi et al. – PLOS ONE

Plant, root, and soil microbiome

Preprint: Tillage intensity and plant rhizosphere selection shape bacterial-archaeal assemblage diversity and nitrogen cycling genes – Cloutier et al. – bioRxiv

Water and extremophile microbiome

Preprint: An Ohio State Scenic River Shows Elevated Antibiotic Resistance Genes, Including Acinetobacter Tetracycline and Macrolide Resistance, Downstream of Wastewater Treatment Plant Effluent – Murphy – bioRxiv

Biogeochemistry of the Antrim Shale Natural Gas Reservoir – Stemple et al. – ACS Earth and Space Chemistry

Built environment

Preprint: Novel municipal sewage-associated bacterial genomes and their potential in source tracking – Linder et al. – bioRxiv

Preprint: Structure of bacterial communities in Japanese-style bathrooms: Comparative sequencing of bacteria in shower water and showerhead biofilms using a portable nanopore sequencer – Fujiyoshi et al. – bioRxiv

Phages and viruses

Preprint: Dynamic surveillance of mosquitoes and their viromes in Wuhan during 2020 – Ren et al. – bioRxiv


Simple mapping-based quantification of a mock microbial community using total RNA-seq data – Moriya – PLOS ONE

Preprint: Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota – Shibata et al. – bioRxiv

July 22, 2021

Human and General Microbiome

The Change Of Gut Microbiota In MDD Patients Under SSRIs Treatment – Yang Shen – Scientific Reports

Minimal-moderate Variation Of Human Oral Virome And Microbiome In IgA Deficiency – Maria José de la Cruz Peña – Scientific Reports

Weight Shapes The Intestinal Microbiome In Preterm Infants: Results Of A Prospective observational study – Fardou H Heida – BMC Microbiology

Functional Heterogeneity In The Fermentation Capabilities Of The Healthy Human Gut microbiota – Thomas Gurry – PloS One

Characterization Of The Blood And Neutrophil-specific Microbiomes And Exploration Of potential bacterial biomarkers for sepsis in surgical patients – Chenyang Wang – Immunity, Inflammation And Disease

Cognitive Function Improvement After Fecal Microbiota Transplantation In In Alzheimer’s dementia patient: a case report – Soo-Hyun Park – Current Medical Research And Opinion

Amplicon And Metagenomic Analysis Of Middle East Respiratory Syndrome (MERS) Coronavirus and the Microbiome in Patients with Severe MERS – Waleed Aljabr – mSphere

Dental Plaque Microbial Resistomes Of Periodontal Health And Disease And Their Changes after Scaling and Root Planing Therapy – Yutong Kang – mSphere

Archaea Are Rare And Uncommon Members Of The Mammalian Skin Microbiome – Alexander K Umbach – mSystems

Association Between Human Genetic Variants And The Vaginal Bacteriome Of Pregnant Women – Wei Fan – mSystems

Population-wide Diversity And Stability Of Serum Antibody Epitope Repertoires against human microbiota – Thomas Vogl – Nature Medicine

Dynamic Colonization Of Microbes And Their Functions After Fecal Microbiota Transplantation for Inflammatory Bowel Disease – Nathaniel D Chu – mBio

Review: Tryptophan Metabolites Modulate Inflammatory Bowel Disease And Colorectal Cancer By affecting immune system – Moein Ala – International Reviews Of Immunology

Review: From Gut Microbiota To Host Appetite: Gut Microbiota-derived Metabolites As Key regulators – Hui Han – Microbiome

The Roles Of Cytoplasmic Lipid Droplets In Modulating Intestinal Uptake Of Dietary Fat – Alyssa S Zembroski – Annual Reviews Of Nutrition

Review: Intestinal Microbiota In The SARS-CoV-2 Infection: What Is Known? – Patrícia Brito Rodrigues – Advances In Experimental Medicine And Biology

Review: The Microbiota-Gut-Brain Axis And Epilepsy – Qiang Yue – Cellular And Molecular Neurobiology

In Brief: Microbiota Links To Immunotherapy Toxicity – Sarah Seton-Rogers – Nature Reviews Cancer

Opinion: Forming Consensus To Advance Urobiome Research – Linda Brubaker – mSystems

Beneficial Microbes and Compounds

A High-protein Diet Containing Inulin/oligofructose Supports Body Weight Gain associated with lower energy expenditure and carbohydrate oxidation, and alters faecal microbiota in C57BL/6 mice – Franziska Koch – Journal Of Nutritional Science

Immunosuppressive Activity Is Attenuated By Astragalus polysaccharides Via remodeling the gut microenvironment in melanoma mice – Guiqing Ding – Cancer Science

Review: The Interaction Effect Between Tea Polyphenols And Intestinal Microbiota: Role In ameliorating neurological diseases – Mengyu Hong – Journal Of Food Biochemistry

Review: Nutritional Interventions And The Gut Microbiome In Children – Saurabh Mehta – Annual Reviews Of Nutrition

Animal Microbiome and Animal Models

Interspecific Variation And Functional Traits Of The Gut Microbiome In Spiders From the wild: The largest effort so far. – Kaomud Tyagi – PloS One

Vibrio vulnificus Induces The Death Of A Major Bacterial Species In The Mouse Gut via cyclo-Phe-Pro. – Jeong-A Kim – Microbiome

Maternal Cecal Microbiota Transfer Rescues Early-life Antibiotic-induced Enhancement of type 1 diabetes in mice. – Xue-Song Zhang – Cell Host & Microbe

Comprehensive Cultivation Of The Swine Gut Microbiome Reveals High Bacterial Diversity and Guides Bacterial Isolation in Pigs. – Xiaofan Wang – mSystems

Plant Microbiome

Drought Stress And Plant Ecotype Drive Microbiome Recruitment In Switchgrass – Tie-Yuan Liu – Journal Of Integrative Plant Biology

Microbe-dependent Heterosis In Maize – Maggie R Wagner – Proceedings Of The National Academy Of Sciences Of The United States Of America

Review: Prioritizing Host Phenotype To Understand Microbiome Heritability In Plants – Maggie R Wagner – The New Phytologist

Microbiome Analysis and Techniques

On The Robustness Of Inference Of Association With The Gut Microbiota In Stool, rectal swab and mucosal tissue samples – Shan Sun – Scientific Reports

Amplicon Sequence Variants Artificially Split Bacterial Genomes Into Separate Clusters. – Patrick D Schloss – MSphere

Linking Plasmid-based Beta-lactamases To Their Bacterial Hosts Using Single-cell fusion PCR – Peter J Diebold – eLife

An Integrated Machine Learning Framework For A Discriminative Analysis Of schizophrenia using multi-biological data. – Peng-Fei Ke – Scientific Reports

An Intestinal Gut Organ Culture System For Analyzing Host-Microbiota Interactions – Shalhevet Azriel – Journal Of Visualized Experiments (JoVE)

July 16, 2021

Today’s digest features studies on environmental contamination of carbapenem-resistant Klebsiella pneumoniae in China (spoiler: extensive contamination, but has negligible impact on patient colonisation), the dynamic change and correlation of microbiome from different body sites to the treatment response as well as immune-related adverse events of immunotherapy in lung cancer patients, and more.

Also, check out a regularly-updated collection of FREE, ONLINE microbiome events. Happy Friday!

Human microbiome

*Prospective correlation between the patient microbiome with response to and development of immune-mediated adverse effects to immunotherapy in lung cancer – Justin Chau – BMC Cancer

Gut microbiome

Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner – Emmanuel Montassier – Nature Microbiology

Identification and engraftment of new bacterial strains by shotgun metagenomic sequence analysis in patients with recurrent Clostridioides difficile infection before and after fecal microbiota transplantation and in healthy human subjects – Sandeep Verma – PlosOne

Differences in the individual curative effect of acupuncture for obese women with polycystic ovary syndrome based on metagenomic analysis: study protocol for a randomized controlled trial – Huaying Fan – Trials

Comparative Analysis of 16S rRNA Gene and Metagenome Sequencing in Pediatric Gut Microbiomes – Danielle Peterson – Frontiers in Microbiology


*Spread of Carbapenem-Resistant Klebsiella pneumoniae in an Intensive Care Unit: A Whole-Genome Sequence-Based Prospective Observational Study – Li Wei – Microbiology Spectrum

*Linezolid- and multidrug-resistant enterococci in raw commercial dog food, Europe, 2019–2020 – Ana R. Freitas – Emerging Infectious Diseases

Identification of pathogen(s) in infectious diseases using shotgun metagenomic sequencing and conventional culture: a comparative study – Huan Chen – PeerJ

Predicting antibiotic resistance gene abundance in activated sludge using shotgun metagenomics and machine learning – Yuepeng Sun – Water Research

Animal microbiome

Assessing the relationship between the rumen microbiota and feed efficiency in Nellore steers – Déborah Romaskevis Gomes Lopes – Journal of Animal Science and Biotechnology

Animal experiment

An osmotic laxative renders mice susceptible to prolonged Clostridioides difficile colonization and hinders clearance – Sarah Tomkovich – bioRxiv


Critical Assessment of Metagenome Interpretation – the second round of challenges – F. Meyer – bioRxiv

Disentangling environmental effects in microbial association networks – Maria Deutschmann – bioRxiv

Webinars &c

Microbiome Virtual International Conference #MVIF – September 14

July 14, 2021

General microbiome

Bacteriophage-Bacteria Interactions in the Gut: From Invertebrates to Mammals – Kirsch et al. – Annual Review of Virology

Helicobacter pylori infection has a detrimental impact on the efficacy of cancer immunotherapies – Oster et al. – Gut

Pregnancy and early life

Cervicovaginal microbiota and metabolome predict preterm birth risk in an ethnically diverse cohort – Flaviani et al. – JCI Insight

[REVIEW][Early-life gut microbiota and its connection to metabolic health in children: Perspective on ecological drivers and need for quantitative approach – Jian et al. – EBBioMedicine

Associations of air pollution and greenness with the nasal microbiota of healthy infants: A longitudinal study – Gisler et al. – Environmental Research

Human respiratory microbiome

Multi-omics profiling predicts allograft function after lung transplantation – Watzenböck et al. – European Respiratory Journal

Metagenomic Analysis Reveals A Possible Association Between Respiratory Infection and Periodontitis – Liu et al. – Genomics, Proteomics & Bioinformatics

Human skin microbiome

[REVIEW]Novel mechanisms of microbial crosstalk with skin innate immunity – Chinnappan & Harris-Tyron – Experimental Dermatology

Shifts in the skin bacterial and fungal communities of healthy children transitioning through puberty – Park et al. – Journal of Investigative Dermatology

Human gut microbiome

Gut-microbiota-targeted diets modulate human immune status – Wastyk et al. – Cell

[REVIEW]Silent hypoxia in COVID-19: a gut microbiota connection – Gopal et al. – Current Opinion in Physiology

[REVIEW]The Athlete and Gut Microbiome: Short-chain Fatty Acids as Potential Ergogenic Aids for Exercise and Training – Bongiovanni, Yin & Heaney

Identification and engraftment of new bacterial strains by shotgun metagenomic sequence analysis in patients with recurrent Clostridioides difficile infection before and after fecal microbiota transplantation and in healthy human subjects – Verma et al. – PLOS One

Kefir Ameliorates Specific Microbiota-Gut-Brain Axis Impairments in a Mouse Model Relevant to Autism Spectrum Disorder – van de Wouw et al. – Brain, Behavior, and Immunity

Animal microbiome

Comparative analysis of oral-gut microbiota between captive and wild long-tailed macaque in Thailand – Sawaswong et al. – Scientific Reports

Impact of the dietary inclusion of dried food residues on the apparent nutrient digestibility and the intestinal microbiota of dogs – Paßlack et al. – Archives of Animal Nutrition

Triphenyltin exposure causes changes in health-associated gut microbiome and metabolites in marine medaka – He et al. – Environmental Pollution

The microbial metabolite p-Cresol induces autistic-like behaviors in mice by remodeling the gut microbiota – Bermudez-Martin et al. – Microbiome

Microbes in space

Seven years of Progress in Determining Fungal Diversity and Characterization of Fungi Isolated from the Japanese Experiment Module KIBO, International Space Station – Satoh et al. – Microbiology and Immunology

Food microbiology

[REVIEW]Virome studies of food production systems: time for ‘farm to fork’ analyses – Mahony & van Sinderen – Current Opinion in Biotechnology


D-MANOVA: fast distance-based multivariate analysis of variance for large-scale microbiome association studies – Chen & Zhang – Bioinformatics

Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model – Hosoda, Fukunaga & Hamada – Bioinformatics

[PREPRINT]Stool Studies Don’t Pass the Sniff Test: A Systematic Review of Human Gut Microbiome Research Suggests Widespread Misuse of Machine Learning – Quinn – arXiv


Characterizing Microbiomes via Sequencing of Marker Loci: Techniques To Improve Throughput, Account for Cross-Contamination, and Reduce Cost – Harrison, Randolph & Buerkle – mSystems

Two-Target Quantitative PCR To Predict Library Composition for Shallow Shotgun Sequencing – Cho et al. – mSystems

Statistical approaches for differential expression analysis in metatranscriptomics – Zhang et al. – Bioinformatics

Benchmark of 16S rRNA gene amplicon sequencing using Japanese gut microbiome data from the V1–V2 and V3–V4 primer sets – Kameoka et al. – BMC Genomics

In vitro models of gut digestion across childhood: current developments, challenges and future trends – Fournier et al. – Biotechnology Advances

July 09, 2021

Have a nice Friday! Today in this Digest, we highlight a study showing that two patients who received fecal transplants could resolve COVID19. We also highlight another study revealing differences between the microbiota from Tibetan and Han immigrants living at an altitude of 3,900 m. Today, this Digest also papers on many other topics.

Human and General Microbiome

Rapid Resolution Of COVID-19 After Faecal Microbiota Transplantation – Jarosław Biliński – Gut

Correlations Between Intestinal Microbial Community And Hematological Profile In Native Tibetans and Han Immigrants. – Yan Ma – Frontiers In Microbiology

Host-emitted Amino Acid Cues Regulate Bacterial Chemokinesis To Enhance colonization. – Catherine D Robinson – Cell Host & Microbe

Fecal Microbiota Transplant As A Potential Treatment For Parkinson’s Disease – A case series. – Arik Segal – Clinical Neurology And Neurosurgery

Translocated Microbiome Composition Determines Immunological Outcome In Treated HIV infection. – Krystelle Nganou-Makamdop – Cell

In-vivo Impact Of Common Cosmetic Preservative Systems In Full Formulation On The skin microbiome. – Barry Murphy – PloS One

Antibiotics Modulate Neoadjuvant Therapy Efficiency In Patients With Breast Cancer: a pilot analysis. – Xi Zhang – Scientific Reports

Fecal Sample Collection Methods And Time Of Day Impact Microbiome Composition And short chain fatty acid concentrations. – Jacquelyn Jones – Scientific Reports

The Association Between Serum Microbial DNA Composition And Symptoms Of Depression and anxiety in mood disorders. – Sang Jin Rhee – Scientific Reports

Gut Microbiota Signature Of Pathogen-dependent Dysbiosis In Viral Gastroenteritis – Taketoshi Mizutani – Scientific Reports

Translocation Of Vaginal Microbiota Is Involved In Impairment And Protection Of uterine health. – Jinfeng Wang – Nature Communications

Veillonellaceae family members uniquely alter the cervical metabolic microenvironment in a human three-dimensional epithelial model – Mary E Salliss – NPJ Biofilms And Microbiomes

Metagenome-wide Association Study Of Gut Microbiome Revealed Potential Microbial marker set for diagnosis of pediatric myasthenia gravis. – Peng Liu – BMC Medicine

Review: Theranostic Cells: Emerging Clinical Applications Of Synthetic Biology – Monica P McNerney – Nature Reviews Genetics

Review: Current And Future Biomarkers In Alcoholic Hepatitis – Stephanie M Rutledge – Clinics In Liver Disease

Review: Role Of Bile Acids In Inflammatory Liver Diseases – Ioannis Evangelakos – Seminars In Immunopathology

Microbiome, Food and Diet

Review: Interference Of Dietary Polyphenols With Potentially Toxic Amino Acid Metabolites derived from the colonic microbiota – Naschla Gasaly – Amino Acids

Suppressed Inflammation In Obese Children Induced By A High-fiber Diet Is Associated with the attenuation of gut microbial virulence factor genes. – Hui Li – Virulence

Technological And Environmental Features Determine The Uniqueness Of The Lambic Beer Microbiota And Production Process – Dries Bongaerts – Applied And Environmental Microbiology

Role Of Dietary Fiber In Safeguarding Intestinal Health After Pelvic Radiotherapy – Cecilia Bull – Current Opinion In Supportive And Palliative Care

Animal Microbiome

Captivity Reduces Diversity And Shifts Composition Of The Brown Kiwi Microbiome – Priscilla A San Juan – Animal Microbiome

Plant Microbiome

Nitrogen Deficiency-induced Bacterial Community Shifts In Soybean Roots – Wataru Yazaki – Microbes And Environments

Review: Metabolic Interactions In Beneficial Microbe Recruitment By Plants – Davar Abedini – Current Opinion In Biotechnology

Beneficial Microbes and Compounds

Matrix Effects On The Delivery Efficacy Of Bifidobacterium animalis subsp. lactis BB-12 on Fecal Microbiota, Gut Transit Time, and Short-Chain Fatty Acids in Healthy Young Adults – Zhaoyong Ba – mSphere

Exopolysaccharides From Lactobacillus plantarum NCU116 Facilitate Intestinal Homeostasis by Modulating Intestinal Epithelial Regeneration and Microbiota. – Xingtao Zhou – Journal Of Agricultural And Food Chemistry

Effect Of Herbal Medicine Daikenchuto On Gastrointestinal Symptoms Following laparoscopic colectomy in patients with colon cancer: A prospective randomized study. – Keita Hanada – Biomedicine & Pharmacotherapy = Biomedecine & Pharmacotherapie

Effects of co-fermented collagen peptide-jackfruit juice on the immune response and gut microbiota in immunosuppressed mice. – Tingting Ma – Food Chemistry

Review: Bacteriophage-mediated Modulation Of Microbiota For Diseases Treatment – Yu Zhang – Advanced Drug Delivery Reviews


Whole-Genome Sequencing Of Mycobacterium tuberculosis Directly From Sputum Samples – Amanda Claire Brown – Methods In Molecular Biology 

RecT Recombinase Expression Enables Efficient Gene Editing In Enterococcus – Victor Chen – Applied And Environmental Microbiology

July 07, 2021

General microbiome

Cross-Scale Analyses of Animal and Human Gut Microbiome Assemblies from Metacommunity to Global Landscape – Ma – mSystems

Multi-site human microbiome

Microbiota long-term dynamics and prediction of acute graft-versus-host disease in pediatric allogeneic stem cell transplantation – Ingham et al. – Microbiome

Human gut microbiome

Early melanoma invasivity correlates with gut fungal and bacterial profiles – Vitali et al. – British Journal of Dermatology

The Interplay between fasting, gut microbiota, and lipid profile – Mohammadzadeh et al. – IJCP

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Effect of Differences in the Microbiome of Cyp17a1-Deficient Mice on Atherosclerotic Background – Künstner et al. – Cells

Telmisartan induces a specific gut microbiota signature which may mediate its antiobesity effect – Beckmann et al. – Pharmacological Research

Novel insights into the genetically obese (ob/ob) and diabetic (db/db) mice: two sides of the same coin – Suriano et al. – Microbiome

Animal microbiome (for animals in the wild)

Shades of grey: host phenotype dependent effect of urbanization on the bacterial microbiome of a wild mammal – Stothart & Newman – Animal Microbiome

Untargeted fecal metabolome analysis in obese dogs after weight loss achieved by feeding a high-fiber-high-protein diet – Bermudez Sanches et al. – Metabolomics

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Holocene life and microbiome profiling in ancient tropical Lake Chalco, Mexico – Moguel et al. – Scientific Reports


ORFograph: search for novel insecticidal protein genes in genomic and metagenomic assembly graphs – Dvorkina et al. – Microbiome


Measuring and mitigating PCR bias in microbiota datasets – Silverman et al. PLOS Computational Biology

July 6, 2021

Several great papers today including a very interesting Cell paper on how Bifidobacterium interacts with the immune system and an mBio article on how different types of dietary fibre shape the gut microbiota.

To our Australian readers I’d like to wish a happy NAIDOC week, which is a time to celebrate the history, culture and achievements of Aboriginal and Torres Strait Islander peoples.

General microbiome

Microbiota regulate social behaviour via stress response neurons in the brain – Wu et al. Nature. 

Defining the resilience of the human salivary microbiota by a 520-day longitudinal study in a confined environment: the Mars500 mission – Bacci et al. Microbiome

A MicroRNA Gene Panel Predicts the Vaginal Microbiota Composition. Cheng et al. mSystems

Human gut microbiome

Gut microbiota mediate the FGF21 adaptive stress response to chronic dietary protein-restriction in mice – Martin et al. Nature Communications. 

Gut microbes impact stroke severity via the trimethylamine N-oxide pathway – Zhu et al. Cell Host & Microbe

Dietary Fiber Hierarchical Specificity: the Missing Link for Predictable and Strong Shifts in Gut Bacterial Communities – Centu-Jungles et al. mBio

Pregnancy and Early-Life

Bifidobacteria-mediated immune system imprinting early in life – Henrick et al. Cell

Animal microbiome

Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions – Lejal et al. Microbiome

Water Microbiome

Microbiome diversity and host immune functions influence survivorship of sponge holobionts under future ocean conditions – Posadas et al. ISME

Soil microbiome

A Community Effort: Combining Functional Amplicon Sequencing and Metagenomics Reveals Potential Biosynthetic Gene Clusters Associated with Protective Phenotypes in Rhizosphere Microbiomes – Winter. mSystems.


METAnnotatorX2: a Comprehensive Tool for Deep and Shallow Metagenomic Data Set Analyses – Milani et al. mSystems

July 4, 2021

Have a nice Sunday! (and a happy July 4th to Americans!) In this digest, we have a set of papers covering different areas of microbiome research, including 3 studies covering aspects of the relationship between COVID19 and microbiome, pan-genomic, and metatranscriptomic studies from probiotic microbes, and the role of the aryl hydrocarbon receptor in the host-microbiome communication.   

Human and General Microbiome

Review: The Relationship Between The Gut Microbiome And Neurodegenerative Diseases – Xueling Zhu – Neuroscience Bulletin

Systematic Review: Exploring The Role Of Respiratory Microbiome In Lung Cancer: A Systematic Review – Fabiana Perrone – Critical Reviews In Oncology/Hematology

Commensal Microbiota Regulates Skin Barrier Function And Repair Via Signaling through the aryl hydrocarbon receptor – Aayushi Uberoi – Cell Host & Microbe

Tryptophan-metabolizing Gut Microbes Regulate Adult Neurogenesis Via The Aryl hydrocarbon receptor – George Zhang Wei – Proceedings Of The National Academy Of Sciences Of The United States Of America

Mucosa-associated Gut Microbiota Reflects Clinical Course Of Ulcerative Colitis – Yuichiro Nishihara – Scientific Reports

Helicobacter pylori Infection-induced Changes In The Intestinal Microbiota Of 14-year-old or 15-year-old Japanese adolescents: a cross-sectional study – Toshihiko Kakiuchi – BMJ Open

The Infant Gut Resistome Is Associated With E. coli And Early-life Exposures – Rebecca M Lebeaux – BMC Microbiology

The Gut Microbiome Of Heart Failure With Preserved Ejection Fraction – Anna L Beale – Journal Of The American Heart Association

Association Of Gut Microbiomes With Lung And Esophageal Cancer: A Pilot Study – Weitao Shen – World Journal Of Microbiology & Biotechnology

Vaginal Lactobacilli And Vaginal Dysbiosis-Associated Bacteria Differently Affect Cervical Epithelial and Immune Homeostasis and Anti-Viral Defenses – Sabrina Nicolò – International Journal Of Molecular Sciences

Finding A Balance In The Vaginal Microbiome: How Do We Treat And Prevent The Occurrence of Bacterial Vaginosis? – Rebecca Jane Joseph – Antibiotics (MDPI)

Mycobiome And Cancer: What Is The Evidence? – Natalia Vallianou – Cancers

Characterizing The Effects Of Calcium And Prebiotic Fiber On Human Gut Microbiota Composition and Function Using a Randomized Crossover Design-A Feasibility Study – Lara S Yoon – Nutrients

Gut Microbiota Profile And Its Association With Clinical Variables And Dietary Intake in Overweight/Obese and Lean Subjects: A Cross-Sectional Study – Judit Companys – Nutrients

Microbiome and COVID19

Review: Modulation Of Gut Microbiota For The Prevention And Treatment Of COVID-19 – Jiezhong Chen – Journal Of Clinical Medicine

COVID-19 Lockdowns May Reduce Resistance Genes Diversity In The Human Microbiome And the Need for Antibiotics – João S Rebelo – International Journal Of Molecular Sciences

Reversion Of Gut Microbiota During The Recovery Phase In Patients With Asymptomatic or Mild COVID-19: Longitudinal Study  – Han-Na Kim – Microorganisms

Beneficial Microbes and Compounds

Flavonoids From Whole-Grain Oat Alleviated High-Fat Diet-Induced Hyperlipidemia Via Regulating Bile Acid Metabolism and Gut Microbiota in Mice – Ruiqian Duan – Journal Of Agricultural And Food Chemistry

Novel Targeted Biological Agents For The Treatment Of Atopic Dermatitis – Nan Yang – BioDrugs 

Escherichia coli Nissle 1917 As Adjuvant Therapy In Patients With Chronic Bacterial prostatitis: a non-blinded, randomized, controlled trial – Celeste Manfredi – World Journal Of Urology

Influence Of Lactobacillus Paracasei HII01 Supplementation On Glycemia And Inflammatory Biomarkers in Type 2 Diabetes: A Randomized Clinical Trial – Parichart Toejing – Foods (MDPI) 

Dietary Habits And Gut Microbiota In Healthy Adults: Focusing On The Right Diet. A Systematic Review – Giulia Gibiino – International Journal Of Molecular Sciences

Animal Microbiome

Review: Potential Of Bacillus velezensis As A Probiotic In Animal Feed: A Review – Fatima Khalid – Journal Of Microbiology

Metagenomics Analysis Revealed The Distinctive Ruminal Microbiome And Resistive profiles in dairy buffaloes – Hui-Zeng Sun – Animal Microbiome

Composition And Diversity Of Gut Microbiota In Pomacea canaliculata In Sexes And between developmental stages – Lian Chen – BMC Microbiology

Plant and Soil Microbiome

Microbiome-mediated Effects Of Habitat Fragmentation On Native Plant Performance – Kasey N Kiesewetter – The New Phytologist

Improvement Of Soil Microbial Diversity Through Sustainable Agricultural Practices and Its Evaluation by -Omics Approaches: A Perspective for the Environment, Food  Quality and Human Safety – Marta Bertola – Microorganisms (MDPI)

Leaf Metabolic Influence Of Glyphosate And Nanotubes On The Arabidopsis Thaliana phyllosphere – Mingjing Ke – Journal Of Environmental Sciences

Bioinformatics and Genomics

Comprehensive Pan-Genome Analysis Of Lactiplantibacillus plantarum Complete Genomes– Francesco M Carpi – Journal Of Applied Microbiology

Metagenomic And Metatranscriptomic Profiling Of Lactobacillus casei Zhang In The Human Gut – Jicheng Wang – NPJ Biofilms And Microbiomes

PhyLoSTM: A Novel Deep Learning Model On Disease Prediction From Longitudinal microbiome data – Divya Sharma – Bioinformatics

Joint Modeling Of Zero-inflated Longitudinal Proportions And Time-to-event Data With application to a gut microbiome study. – Jiyuan Hu – Biometrics