April 05, 2019

Good morning everyone! In today’s microbiome digest, we have multiple research and review articles focusing on the role of microbiome in Prostate Cancer, Breast Cancer, Gastric Cancer, Allergy, Gut-Brain axis, Schizophrenia, Paediatric Crohn’s Disease, Nonalcoholic Fatty Liver Disease, Alveolar Osteitis, Renal Failure, Cholecystokinin Expression, Lipid Metabolism Disorder, Regulation of Blood Pressure and an independent section on Fecal Microbiota Transplantation. Additionally, two very interesting metagenomic studies have discovered specific microbial signature as well as link with choline degradation in the colorectal cancer patients. Enjoy reading.

General microbiome

Reivew: The Human Microbiota and Prostate Cancer: Friend or Foe? – Francesco Massari – Cancers

Microbiome—Microbial Metabolome—Cancer Cell Interactions in Breast Cancer—Familiar, but Unexplored – Edit Miko – Cells

Review: Fighting AMR in the Healthcare Environment: Microbiome-Based Sanitation Approaches and Monitoring Tools – Maria D’Accolti – Molecular Sciences

Gut microbiome

Gut microbial dysbiosis is associated with allergen-specific IgE responses in young children with airway allergies – Chih-Yung Chiu – World Allergy Organization Journal

Review: The gut virome: the ‘missing link’ between gut bacteria and host immunity? – Indrani Mukhopadhya – Therapeutic Advances in Gastroenterology

Regulatory T Cells and Plasmacytoid Dendritic Cells Within the Tumor Microenvironment in Gastric Cancer Are Correlated With Gastric Microbiota Dysbiosis: A Preliminary Study – Zongxin Ling – Frontiers in Immunology

Review: Impact of Different Types of Diet on Gut Microbiota Profiles and Cancer Prevention and Treatment – Rainer J. Klement – Medicina

Review: Glutamatergic Signaling Along The Microbiota-Gut-Brain Axis – Andreina Baj – Molecular Sciences

Investigation of the Gut Microbiome in Patients with Schizophrenia and Clozapine-Induced Weight Gain: Protocol and Clinical Characteristics of First Patient Cohorts –Gorbovskaya I. –  Neuropsychobiology

Review: Sex Differences in Gut Microbiota – Yong Sung Kim – The World Journal of MEN’s HEALTH

The Microbiome in Paediatric Crohn’s Disease—A Longitudinal, Prospective, 
Single-Centre Study – Shivani Kansal – Journal of Crohn’s and Colitis

A gut microbiome signature for cirrhosis due to nonalcoholic fatty liver disease – Cyrielle Caussy – Nature Communications

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation – Andrew Maltez Thomas – Nature Medicine

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer – Jakob Wirbel – Nature Medicine

Ceftriaxone and cefotaxime have similar effects on the intestinal microbiota in human volunteers treated by standard doses regimens – Charles Burdet – Antimicrobial Agents and Chemotherapy

Human respiratory microbiome

Mycobiome Sequencing and Analysis Applied to Fungal Community Profiling of the Lower Respiratory Tract During Fungal Pathogenesis – Lisa R. McTaggart – Frontiers in Microbiology

Reproductive tract microbiome

Identification and evaluation of the microbiome in the female and male reproductive tracts – Rivka Koedooder – Human reproduction update

Skin microbiome

Mast cell recruitment is modulated by hairless skin microbiome – Chia-Chi Wu – The Journal of Allergy and Clinical Immunology

Oral microbiome

A metagenomic study of patients with alveolar osteitis after tooth extraction. A preliminary case-control study – Laura Aguilar-Duran – Clinical Oral Investigations

Animal microbiome / Animal experiments

Interactions Between Commensal Bacteria and Enteric Neurons, via FPR1 Induction of ROS, Increase Gastrointestinal Motility in Mice – Bindu Chandrasekharan – Gastroenterology

Danshen can interact with intestinal bacteria from normal and chronic renal failure rats – Hongdie Cai – Biomedicine and Pharmacotherapy

Review: A place for taxonomic profiling in the study of the coral prokaryotic microbiome – Alejandra Hernandez-Agreda – FEMS Microbiology Letters

Fructose malabsorption induces cholecystokinin expression in the ileum and cecum by changing microbiota composition and metabolism – Xufei Zhang – THE FASEB JOURNAL

Spinach consumption ameliorates the gut microbiota and dislipaemia in rats with diet-induced non-alcoholic fatty liver disease (NAFLD) – Elvira-Torales LI – Food and Functions

Microbial Colonization in Adulthood Shapes the Intestinal Macrophage Compartment – Franziska Schmidt – Journal of Chron’s and Colitis

Feeding modes shape the acquisition and structure of the initial gut microbiota in newborn lambs – Yanliang Bi – Environmental Microbiology

Effects of dietary lipid sources on the intestinal microbiome and health of golden pompano (Trachinotus ovatus) – Cuihong You – Fish & Shellfish Immunology

Gut microbiota characterization and lipid metabolism disorder found in PCB77-treated female mice – Chi Y – Toxicology

Changes of gut microbiota between different weight reduction programs – Belle Yanyu Lin – Surgery for Obesity and Related Diseases

Microbiome-metabolomic analysis of the impact of Zizyphus jujuba cv. Muzao polysaccharides consumption on colorectal cancer mice fecal microbiota and metabolites – Xiaolong Ji – International Journal of Biological Macromolecules

Fecal Microbiota Transplantation

Critical Role of the Interaction Gut Microbiota – Sympathetic Nervous System in the Regulation of Blood Pressure – Marta Toral – Frontiers in Physiology

Faecal microbiota transplantation for the decolonisation of antibiotic-resistant bacteria in the gut: a systematic review and meta-analysis – Vera Tavoukjian – The Journal of Hospital Infection


Effect of a multistrain probiotic (Lactoflorene®Plus) on inflammatory parameters and microbiota composition in subjects with stress-related symptoms – Sara Soldi – Neurobiology of Stress

Probiotics, prebiotics, and low FODMAP diet for irritable bowel syndrome – What is the current evidence? – Soo Liang Ooi – Complementary Therapies in Medicine

Water and extremophile microbiome

Microbial Community of Saline, Alkaline Lakes in the Nebraska Sandhills Based on 16S rRNA Gene Amplicon Sequence Data – Nicole A. Fiore – Microbiology Resource Announcements


A Customized At-Home Stool Collection Protocol for Use in Microbiome Studies Conducted in Cancer Patient Populations – Stephanie R. Hogue – Microbial Ecology

Effect of storage and DNA extraction method on 16S rRNA-profiled fecal microbiota in Japanese adults – Yuki Kawada – Journal of Clinical Biochemistry and Nutrition


𝑊∗𝑑Wd∗-test: robust distance-based multivariate analysis of variance – Bashir Hamidi – Microbiome

Identification and reconstruction of novel antibiotic resistance genes from metagenomes – Fanny Berglund – Microbiome

April 04, 2019

In today’s microbiome digest, multiple research and review articles focusing on the role of host-associated microbiomes in various diseases including Type 2 Diabetes, Obesity, Urolithiasis, Bronchial Asthma, Cancer Immunotherapy, Hepatic Glycan Storage, Uveitis, Schizophrenia and the Development of the immune system. Enjoy reading.

General microbiome

Harnessing microbiota interactions to produce bioactive metabolites: communication signals and receptor proteins – Juan F Martin – Current Opinion in Pharmacology

Review: Prevention of allergy with diverse and healthy microbiota:an update – Diana Chernikova – Current Opinion in Pediatrics

State of the Art: Pharmacomicrobiomics: The holy grail to variability in drug response? – Anukriti Sharma – Clinical Pharmacology and Therapeutics

Gut microbiome

The alteration of gut microbiota in newly diagnosed type 2 diabetic patients – Pei-Chi Chen – Nutrition

Defining Dysbiosis in Patients with Urolithiasis – Anna Zampini – Scientific Reports

Review: Gut Microbiota, Host Organism, and Diet Trialogue in Diabetes and Obesity – Veronica Lazar – Frontiers in Nutrition

Metabolic activity of intestinal microflora in patients with bronchial asthma – Vladimir Irashkin – Clinics and Practice

Pharmacologic and Nonpharmacologic Therapies for the Gut Microbiota in Type 2 Diabetes – Robert Caesar – Canadian Journal of Diabetes

Review: Modulation of cancer immunotherapy efficacy by gut microbiota – Huo S – Discovery Medicine

Hepatic glycogen storage diseases are associated to microbial dysbiosis – Karina Colonetti – PLOS ONE

Implicating Dysbiosis of the Gut Fungal Microbiome in Uveitis, an Inflammatory Disease of the Eye – Rajagopalaboopathi Jayasudha – Immunology and Microbiology

Cohort profile: The LoewenKIDS Study – life-course perspective on infections, the microbiome and the development of the immune system in early childhood – Cornelia Gottschick – International Journal of Epidemiology

Case Report: Decreased Clostridium Abundance after Electroconvulsive Therapy in the Gut Microbiota of a Patient with Schizophrenia – Misako Kanayama – Case Reports in Psychiatry

Reproductive tract microbiome

Effects of oral probiotic supplements on vaginal microbiota during pregnancy: a randomised, double‐blind, placebo‐controlled trial with microbiome analysis – S Husain – BJOG 

Skin microbiome

Review: The Cutaneous Microbiome: Implications for Dermatology Practice – Megan A. Sander

Animal microbiome / Animal experiments

Intestinal microbiota of broilers submitted to feeding restriction and its relationship to hepatic metabolism and fat mass: Fast-growing strain – Raquel Lunedo – Journal of Animal Physiology and Animal Nutrition

Phytate degradation, intestinal microbiota, microbial metabolites and immune values are changed in growing pigs fed diets with varying calcium–phosphorus concentration and fermentable substrates – Charlotte Maria Elisabeth Heyer – Journal of Animal Physiology and Animal Nutrition

Review: The importance of scale in comparative microbiome research: New insights from the gut and glands of captive and wild lemurs – Lydia K. Greene – American Journal of Primatology

A dietary isothiocyanate-enriched moringa (Moringa oleifera) seed extract improves glucose tolerance in a high-fat-diet mouse model and modulates the gut microbiome – Asha Jaja-Chimedza – Journal of Functional Foods

Musca domestica Cecropin (Mdc) Alleviates Salmonella typhimurium-Induced Colonic Mucosal Barrier Impairment: Associating With Inflammatory and Oxidative Stress Response, Tight Junction as Well as Intestinal Flora – Lun Zhang – Frontiers in Microbiology

The Effects of Unfermented and Fermented Cow and Sheep Milk on the Gut Microbiota – Elizabeth A. Rettedal – Frontiers in Microbiology

Water and extremophile microbiome

Microbiota of the Hickey Run Tributary of the Anacostia River – Robin Cagle – Microbiology Resource Announcements


Review: Statistical Analysis of Metagenomics Data – M. Luz Calle – Genomics and Informatics

March 25, 2019

Good morning everyone! In today’s microbiome digest, we have multiple research and review articles about the role of microbiome in various diseases including neurodevelopmental, biliary Cholangitis, obesity-associated CRC, bariatric surgery, atopic dermatitis, schizophrenia, respiratory tract infection and autoimmunity, and an independent section on Fecal Microbiota Transplantation. Enjoy reading.

General microbiome

Talking about a microbiome revolution – John F. Cryn – Nature Microbiology

Review: Crosstalk between neutrophils and the microbiota – Dachuan Zhang – Blood

 Gut microbiome

Alteration of gut microbiota by a westernized lifestyle and its correlation with insulin resistance in non‐diabetic Japanese men – Mami Yamashita – Journal of Diabetes Investigation

Association of the Infant Gut Microbiome With Early Childhood Neurodevelopmental Outcomes – Joanne E. Sordillo – JAMA Netw Open

Comprehensive Analysis of Serum and Fecal Bile Acid Profiles and Interaction with Gut Microbiota in Primary Biliary Cholangitis – Weihua Chen – Clinical Reviews in Allergy & Immunology

Gut microbiome meta-analysis reveals dysbiosis is independent of body mass index in predicting risk of obesity-associated CRC – K Leigh Greathouse – BMJ Open Gastroenterology

Gut microbiota specific signatures are related to the successful rate of bariatric surgery – Gutiérrez-Repiso C – American Journal of Transplantation Research

Differences in Systemic IgA Reactivity and Circulating Th Subsets in Healthy Volunteers With Specific Microbiota Enterotypes – Christina Grosserichter-Wagener – Frontiers in Immunology

Gut microbiota profile in children affected by atopic dermatitis and evaluation of intestinal persistence of a probiotic mixture – Sofia Reddel – Scientific Reports

Prebiotic effect of predigested mango peel on gut microbiota assessed in a dynamic in vitromodel of the human colon (TIM-2) – Sonia G. Sáyago-Ayerdi – Food Research International

Review: The gut microbiota promotes the pathogenesis of schizophrenia via multiple pathways – Xiuxia Yuan – Biochemical and Biophysical Research Communications

Evidence for an association of gut microbial Clostridia with brain functional connectivity and gastrointestinal sensorimotor function in patients with irritable bowel syndrome, based on tripartite network analysis – Jennifer S. Labus – Microbiome

A multi-omic cohort as a reference point for promoting a healthy human gut microbiome – Zhuye Jie – bioRxiv

Human respiratory microbiome

The microbiological characteristics of lower respiratory tract infection in patients with neuromuscular disorders: An investigation based on a multiplex polymerase chain reaction to detect viruses and a clone library analysis of the bacterial 16S rRNA gene sequence in sputum samples – Masato Ogawa – Journal of Microbiology, Immunology and Infection

Vaginal micorbiome

Cervicovaginal microbiota and local immune response modulate the risk of spontaneous preterm delivery – Michal A. Elovitz – Nature Communications

Animal microbiome / Animal experiments

Autoimmunity-Associated Gut Commensals Modulate Gut Permeability and Immunity in Humanized Mice – Baskar Balakrishnan – Military Medicine

Microbe and host interaction in gastrointestinal homeostasis – Rachael Horne – Psychopharmacology

Broiler gut microbiota and expressions of gut barrier genes affected by cereal type and phytogenic inclusion – VasileiosParaskeuas – Animal Nutrition

Manipulation of gut microbiota blunts the ventilatory response to hypercapnia in adult rats – Karen M. O’Connor – EbioMedicine

Beneficial Effects of Potentilla discolor Bunge Water Extract on Inflammatory Cytokines Release and Gut Microbiota in High-Fat Diet and Streptozotocin-Induced Type 2 Diabetic Mice – Lihua Han – Nutrients

Effects of gut-derived endotoxin on anxiety-like and repetitive behaviors in male and female mice – Christopher T. Fields – Biology of Sex Differences

Fecal Microbiota Transplantation

Recent Research on Fecal Microbiota Transplantation in Inflammatory Bowel Disease Patients – Monika Fischer – Gastroenterology and Hepatology

Assessing the viability of transplanted gut microbiota by sequential tagging with D-amino acid-based metabolic probes – Wei Wang – Nature Communications

Do we really understand how faecal microbiota transplantation works? Authors’ reply – Lito E. Papanicolas – EbioMeidicine

Water and extremophile microbiome

Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing – You Che – Microbiome

Evolution of microbial community and drug resistance during enrichment of tetracycline-degrading bacteria – Qiang Wang – Ecotoxicology and Environmental Safety


A generic multivariate framework for the integration of microbiome longitudinal studies with other data types – Antoine Bodein – bioRxiv

March 18, 2019

Good morning everyone! In today’s microbiome digest, we have a limited number of articles including reviews, studies and meeting report about the role of microbiome in various health and disease including Atopic Dermatitis, microbiome as a therapeutic target. And many more. Enjoy reading.

General microbiome

Exploring the impacts of raw materials and environments on the microbiota in Chinese Daqu starter – Hai Du – International Journal of Food Microbiology

Review: Microbiome diurnal rhythmicity and its impact on host physiology and disease risk – Samuel Philip Nobs – EMBO reports

Gut microbiome

Unconjugated and secondary bile acid profiles in response to higher-fat, lower-carbohydrate diet and associated with related gut microbiota: A 6-month randomized controlled-feeding trial – Yi Wan – Clinical Nutrition

Meeting report: Exploring human host–microbiome interactions in health and disease—how to not get lost in translation – Sarah Lebeer – Genome Biology

Interactions between a pathogenic Blastocystissubtype and gut microbiota: in vitro and in vivo studies – John Anthony Yason – Microbiome

Review: Intestinal microbiome as a novel therapeutic target for local and systemic inflammation – KazuhikoUchiyama – Pharmacology & Therapeutics

The Role of Probiotics and Prebiotics in the Prevention and Treatment of ObesityTomás Cerdo – Nutrients

Skin microbiome

Host-microbial Dialogues in Atopic Dermatitis – Tetsuro Kobayashi – International immunology

Animal microbiome / Animal experiments

Effect of different challenge models to induce necrotic enteritis on the growth performance and intestinal microbiota of broiler chickens – C Bortoluzzi – Poultry Science

The Effect of Inulin on Lifespan, Related Gene Expression and Gut Microbiota in InRp5545/TM3 Mutant Drosophila melanogaster: A Preliminary Study – Yuling Dong – Nutrients


Streaming histogram sketching for rapid microbiome analytics – Will PM Rowe – Microbiome

Modelling microbiome recovery after antibiotics using a stability landscape framework – Shaw LP – ISME Journal

February 18, 2019

Good morning everyone, the focus of today’s digest is the gut microbiome specifically their association with liver disease, obesity, diabetes, allergic asthma, autism, and multiple sclerosis, and a method for alignment-free metagenomic binning. Enjoy reading.

General microbiome

Review: The role of the microbiome in immunologic development and its implication for pancreatic cancer immunotherapy – Vrishketan Sethi – Gastroenterology

Gut microbiome

Review: Gut microbiota in liver disease: Too much is harmful, nothing at all is not helpful eitherPhillipp Hartmann – American Journal of Physiology Gastrointestinal and Liver Physiology

Metabolic improvement in obese patients after duodenal–jejunal exclusion is associated with intestinal microbiota composition changes – C. de Jonge – International Journal of Obesity

Does birth mode modify associations of maternal pre-pregnancy BMI and gestational weight gain with the infant gut microbiome? – Sirtaj B. Singh – International Journal of Obesity

Reduced Akkermansia muciniphila and Faecalibacterium prausnitzii levels in the gut microbiota of children with allergic asthma – M. Demirci – Allergologia et Immunopathologia

Autism Spectrum Disorder (ASD) with and without Mental Regression Is Associated with Changes in the Fecal Microbiota – Julio Plaza-Díaz – Nutrients

Dietary supplementation with strawberry induces marked changes in the composition and functional potential of the gut microbiome in diabetic mice – Chrissa Petersen – The Journal of Nutritional Biochemistry

Viewpoint: Gut microbes and depression: Still waiting for Godot – Timothy G. Dinan – Brain, Behavior, and Immunity

Gut microbiota-dependent CCR9+CD4+ T cells are altered in secondary progressive multiple sclerosis – Atsushi Kadowaki – Brain

Potential biomarkers to predict outcome of faecal microbiota transfer for recurrent Clostridioides difficileinfection – Fedja Farowski – Digestive and Liver Disease

Animal microbiome

Rare gut microbiota associated with breeding success, hormone metabolites and ovarian cycle phase in the critically endangered eastern black rhino – Rachel E. Antis – Microbiome

Animal experiments

High dietary fat intake induces a microbiota signature that promotes food allergy – Maryam Hussain – Journal of Allergy and Clinical Immunology

The Alternate Consumption of Quercetin and Alliin in the Traditional Asian Diet Reshaped Microbiota and Altered Gene Expression of Colonic Epithelial Cells in Rats – Juntong Yu – Health, Nutrition, and Food

Obesogenic diet in aging mice disrupts gut microbe composition and alters neutrophil:lymphocyte ratio, leading to inflamed milieu in acute heart failure – Vasundhara Kain – FASEB JOURNAL

Effects of protease and phytase supplements on small intestinal microbiota and amino acid digestibility in broiler chickens – D Borda-Molina – Poultry Science

Serotonin Transporter Deficiency is Associated with Dysbiosis and Changes in Metabolic Function of the Mouse Intestinal Microbiome – Megha Singhal – Scientific Reports


A signal processing method for alignment-free metagenomic binning: multi-resolution genomic binary patterns –  Samaneh Kouchaki – Scientific Reports

Microbes in News

A defined set of 11 bacterial strains from the human gut can protect against infection and target cancer in mice

February 11, 2019

Good morning everyone, in today’s digest we have several interesting research articles including the role of microbiome in ovarian carcinoma, pediatric atopic dermatitis, lung cancer, review articles focusing on the gut microbiome and Energy Homeostasis, interplay between microbiome and immune system, gut microbiome in cardiovascular disease, microbiome in oral cancer, a method for simulating metagenomes and microbial communities, and a very interesting work focusing the role of host and microbiome on drug response. Enjoy reading.

General microbiome

Haemolymph microbiome of the cultured spiny lobster Panulirus ornatus at different temperatures – Mei C. Ooi – Scientific Reports

The biodiversity Composition of Microbiome in Ovarian Carcinoma Patients – Bo Zhou – Scientific Reports

Environmental sources of bacteria and genetic variation in behavior influence host-associated microbiota – Alexandra A. Mushegian – Applied and Environmental Microbiology

Review: Gut Microbiota and Energy Homeostasis in Fish – Robyn Lisa Butt – Frontiers in Endocrinology

Visualizing microbiome–immune system interplay Janet C Siebert – Immunotherapy

Gut microbiome

Comparative analysis of the gut microbiota in centenarians and young adults shows a common signature across genotypically non-related populations – Ngangyola Tuikhar – Mechanisms of Ageing and Development

Influence of proton pump inhibitors on microbiota in chronic liver disease patients – Kenta Yamamoto – Hepatology International

Review: Gut microbiota: A new protagonist in the risk of cardiovascular disease? – Antonio García-Ríos – Clínica e Investigación en Arteriosclerosis

Gut microbiota community characteristics and disease-related microorganism pattern in a population of healthy Chinese people – Wen Zhang – Scientific Reports

Primer: Evolutionary change in the human gut microbiome: From a static to a dynamic view – Isabel Gordo – PLOS Biology

Selecting a Single Stereocenter: The Molecular Nuances that Differentiate β-Hexuronidases in the Human Gut Microbiome – Pellock, Samuel J – Biochemistry

Mining the Core Gut Microbiome from a Sample Indian Population – Abhijit S. Kulkarni – Indian Journal of Microbiology

Skin and respiratory microbiome

The nasal and skin microbiome are associated with disease severity in pediatric atopic dermatitis – J.E.E. Totte – British Journal of Dermatology banner

The microbiome in lung cancer tissue and recurrence-free survival – Brandilyn A Peters – Cancer Epidemiology, Biomarkers & Prevention

Microbiome dysbiosis is associated with disease duration and increased inflammatory gene expression in systemic sclerosis skin – Michael E. Johnson – Arthritis Research and Therapy

Oral microbiome

Review: The microbiome and oral cancer: More questions than answers – Claire M. Healy – Oral Oncology

Plant microbiome

Metabarcoding reveals that rhizospheric microbiota of Quercus pyrenaica is composed by a relatively small number of bacterial taxa highly abundant – Ana V. Lasa – Scientific Reports

Review: Green Technology: Bacteria-Based Approach Could Lead to Unsuspected Microbe–Plant–Animal Interactions – Daniela Bulgari – Microorganisms

Microbial diversity and bioremediation of rhizospheric soils from Trindade Island – Brazil – Celia Marcela Camacho-Montealegre – Journal of Environmental Management

Animal experiments

Testosterone disruptor effect and gut microbiome perturbation in mice: Early life exposure to doxycycline – Xiang Hou – Chemosphere

MLKL deficiency inhibits DSS-induced colitis independent of intestinal microbiota – Jie Zhang – Molecular Immunology

JinQi Jiangtang Tablet Regulates Gut Microbiota and Improve Insulin Sensitivity in Type 2 Diabetes Mice – Ying Cao – Journal of Diabetes Research

Microbiome and drug metabolism

Separating host and microbiome contributions to drug pharmacokinetics and toxicity Michael Zimmermann – Science


CAMISIM: simulating metagenomes and microbial communities – Adrian Fritz – Microbiome

Microbes in News

Depressed? Your Gut Microbiome Might Be to Blame



December 24, 2018

Good morning everyone, Today’s digest mainly focusing on the methods such as SigClust a novel clustering algorithm, mm-tSNE a method for visualizing high-dimensional data and aMiAD – a novel microbial diversity association test. Additionally, several review articles and research using human as well as animal experiments showing the relationship of the gut microbiome in Alzheimer’s, Parkinson, atopic dermatitis, antidepressant and anti-inflammatory, heart failure, NAFLD, irritable bowel syndrome and colorectal cancer and their role in the protection against the acute arsenic toxicity. Enjoy Reading.

General microbiome

Review: The microbiome of the nose – Matthew Rawls – Annals of Allergy, Asthma, and Immunology

The Gut Microbiome in Food Allergy – William Zhao – Annals of Allergy, Asthma, and Immunology

Prenatal stress enhances postnatal plasticity: The role of microbiota – Sarah Hartman – Developmental Psychobiology

Review: The gut microbiome and heart failure – Adilah F. Ahmad – Current Opinion in Cardiology

Synthetic consortia of nanobody‐coupled and formatted bacteria for prophylaxis and therapy interventions targeting microbiome dysbiosis‐associated diseases and co‐morbidities – Kenneth Timmis – Microbial Biotechnology

Gut microbiome

The gut microbiota-derived metabolite trimethylamine N-oxide is elevated in Alzheimer’s disease – Nicholas M. Vogt – Alzheimer’s Research & Therapy

Stability and resilience of the intestinal microbiota in children in daycare – a 12 month cohort study – Martin Steen Mortensen – BMC Microbiology

Effects of diet on the childhood gut microbiome and its implications for atopic dermatitis – Mahboobeh Mahdavinia – The Journal of Allergy and Clinical Immunology

Editorial: Emerging evidence linking the gut microbiome to neurologic disorders – Jessica A. Griffiths – Genome Medicine

Metabolomics and 16S rRNA sequencing of human colorectal cancers and adjacent mucosa – Mun Fai Loke – Plos One

Review: Impact of maternal HIV exposure, feeding status, and microbiome on infant cellular immunity – Sonwabile Dzanibe – Journal of Leukocyte Biology

Review: Inherited nongenetic influences on the gut microbiome and immune system – Kathryn A. Knoop – Birth Defects Research

New insights into porcine milk N-glycome and the potential relation with offspring gut microbiome – Chunlong Mu – Journal of Proteome Research

Unraveling gut microbiota in Parkinson’s disease and atypical parkinsonism – Michela Barichella – Movement Disorders

Fecal SCFAs and SCFA-producing bacteria in gut microbiome of human NAFLD as a putative link to systemic T-cell activation and advanced disease – Monika Rau – United European Gastroenterology Journal

Skin microbiome

A tryptophan metabolite of the skin microbiota attenuates inflammation in atopic dermatitis via the aryl hydrocarbon receptor – Jinlei Yu – The Journal of Allergy and Clinical Immunology

Nasal microbiome

Competition among nasal bacteria suggests a role for siderophore-mediated interactions in shaping the human nasal microbiota – Reed M. Stubbendieck – Applied and Environmental Microbiology

Plant Microbiome

Metabolic niches in the rhizosphere microbiome: New tools and approaches to analyse metabolic mechanisms of plant-microbe nutrient exchange – Richard P Jacoby – Journal of Experimental Botany

Animal experiments

Chronic stress-induced gut dysfunction exacerbates Parkinson’s disease phenotype and pathology in a rotenone-induced mouse model of Parkinson’s disease – Hemraj B.Dodiya – Neurobiology of Disease

Ketamine interactions with gut-microbiota in rats: relevance to its antidepressant and anti-inflammatory properties – Bruk Getachew – BMC Microbiology

Dietary l-Tryptophan Supplementation Enhances the Intestinal Mucosal Barrier Function in Weaned Piglets: Implication of Tryptophan-Metabolizing Microbiota – Haiwei Liang – International Journal of Molecular Science

In Vivo Effects of Einkorn Wheat (Triticum monococcum) Bread on the Intestinal Microbiota, Metabolome, and on the Glycemic and Insulinemic Response in the Pig Model – Francesca Barone – Nutrients

Diet-Independent Correlations between Bacteria and Dysfunction of Gut, Adipose Tissue, and Liver: A Comprehensive Microbiota Analysis in Feces and Mucosa of the Ileum and Colon in Obese Mice with NAFLD – Eveline Gart – International Journal of Molecular Science

Abnormality in Maternal Dietary Calcium Intake During Pregnancy and Lactation Promotes Body WEIGHT gain by Affecting the Gut Microbiota in Mouse Offspring – Ping Li – Molecular Nutrition Food Research

Bilberry anthocyanin extract promotes intestinal barrier function and inhibits digestive enzyme activity by regulating the gut microbiota in aging rats – Jing Li – Food and Function

The gut microbiome is required for full protection against acute arsenic toxicity in mouse models – Michael Coryell – Nature Communications

Gut microbiota was modulated by moxibustion stimulation in rats with irritable bowel syndrome – Xiaomei Wang – Chinese Medicine


Rapid analysis of metagenomic data using signature-based clustering – Timothy Chappell – BMC Bioinformatics

Nonlinear expression and visualization of nonmetric relationships in genetic diseases and microbiome data – Xianchao Zhu – BMC Bioinformatics

Coupled dynamics of intestinal microbiome and immune system—A mathematical study – Akane Hara – Journal of Theoretical Biology

An adaptive microbiome α-diversity-based association analysis method – Hyunwook Koh – Scientific Reports

December 18, 2018

Good morning everyone. Today’s digest will cover recent studies focusing on the diet derived changes in the gut microbiome, the role of gut microbiome on brain health, inflammatory responses, autism, cystic fibrosis, hepatic steatosis using animal experiments, and reviews highlight the tumor genomics along with the microbiome and secretome as a new strategy in colorectal cancer. Enjoy reading.

General microbiome

Review: Is microbiome a target for the management of allergy associated diseases in children? – Ribaldone DG – European Review for Medical and Pharmacological Sciences

Review: Integrating tumor genomics into studies of the microbiome in colorectal cancer Michael B Burns – Gut Microbes

Gut microbiome

Assessing the in vivo data on low/no-calorie sweeteners and the gut microbiota – Alexandra R.Lobach – Food and Chemical Toxicology

Review: Analysing the Secretome of Gut Microbiota as the Next Strategy For Early Detection of Colorectal Cancer – Putri‐Intan‐Hafizah Megat Mohd Azlan – Proteomics

Review: Bottoms up: the role of gut microbiota in brain health – Nina Radisavljevic – Environmental Microbiology

Treponema species enrich the gut microbiota of traditional rural populations but are absent from urban individuals – E. Angelakis – New Microbes and New Infections

Comparative Microbiome Signatures and Short-Chain Fatty Acids in Mouse, Rat, Non-human Primate, and Human Feces – Ravinder Nagpal – Frontiers in Microbiology

Synergistic convergence of microbiota-specific systemic IgG and secretory IgA – Jehane Fadlallah – The Journal of Allergy and Clinical Immunology

Water and extremophile microbiome

Microbial community composition and diversity in the Indian Ocean deep sea REY-rich muds – Shuyan Wang – PLOS One

Animal experiments

Following spinal cord injury, PDE4B drives an acute, local inflammatory response and a chronic, systemic response exacerbated by gut dysbiosis and endotoxemia – Scott A.Myer – Neurobiology of Disease

The Acute Influence of Acid Suppression with Esomeprazole on Gastrointestinal Microbiota and Brain Gene Expression Profiles in a Murine Model of Restraint Stress – RobertMacLaren – Neuroscience

Microbial communities in swine lungs and their association with lung lesions – Tao Huang – Microbial Biotechnology

Report: Gut microbial compositions mirror caste‐specific diets in a major lineage of social insects – Saria Otani – Environmental Microbiology Reports

Diet‐Induced Dysbiosis and Genetic Background Synergize With Cystic Fibrosis Transmembrane Conductance Regulator Deficiency to Promote Cholangiopathy in Mice – Dominique Debray – Hepatology Communications

The valproic acid rat model of autism presents with gut bacterial dysbiosis similar to that in human autism – Fang Liu – Molecular Autism

Amelioration of hepatic steatosis is associated with modulation of gut microbiota and suppression of hepatic miR-34a in Gynostemma pentaphylla (Thunb.) Makino treated mice – Ning Jia – Nutritiion and Metabolism

Isolated Rearing at Lactation Increases Gut Microbial Diversity and Post-weaning Performance in PigsIsolated Rearing at Lactation Increases Gut Microbial Diversity and Post-weaning Performance in Pigs – Tsungcheng Tsai – Frontiers in Microbiology

Echinococcus granulosus Infection Results in an Increase in Eisenbergiella and Parabacteroides Genera in the Gut of Mice – Jianling Bao – Frontiers in Microbiology


Evaluation of metabolite-microbe correlation detection methods – YijunYou – Analytical Biochemistry

Microbes in News

Gut bacteria link to immunotherapy sparks interest – Brian Owens – Nature Biotechnology


December 1, 2018

Today’s microbiome digest will have more on gut microbiome, animal experiments along with one method DiTaxa for host phenotype and biomarker detection. Enjoy reading.

 General microbiome

Pre-transplant recovery of microbiome diversity without recovery of the original microbiome – Armin Rashidi – Bone Marrow Transplantation

Review: Importance of gut microbiota in obesity – Isabel Cornejo-Pareja – European Journal of Clinical Nutrition

Gut Microbiome and Plasma Microbiome-Related Metabolites in Patients With Decompensated and Compensated Heart Failure – Tomohiro Hayashi – Circulation Journal

Review: The lung and gut microbiome: what has to be taken into consideration for cystic fibrosis? – Geneviève Héry-Arnaud – Journal of Cystic Fibrosis

Gut microbiome

Impacts of dietary silver nanoparticles and probiotic administration on the microbiota of an in-vitro gut model – Cristina Cattò – Environmental Pollution

The Gut Microbiome: A Difficult Target for Translational Studies of Clostridium Difficile Colonization – Richard Kellermayer – Journal of Pediatric Gastroenterology and Nutrition

Altered gut microbiota after traumatic splenectomy is associated with endotoxemia – Hua Zhu – Emerging Microbes & Infections

Gut Microbiota Modulates Interactions Between Polychlorinated Biphenyls and Bile Acid Homeostasis – Sunny Lihua Cheng – Toxicological Sciences

The intestinal microbiome and its relevance for functionality in older persons – Andrea Ticinesi – Current Opinion in Clinical Nutrition and Metabolic Care

Gut Microbiota Disruption in Septic Shock Patients: A Pilot Study – You-Dong Wan – Medical Science Monitor

Microbial Biomarkers of Intestinal Barrier Maturation in Preterm Infants – Bing Ma – Frontiers in Microbiology

Review: Microbial impact on cholesterol and bile acid metabolism: current status and future prospects – Aicha Kriaa – Journal of Lipid Research

Respiratory microbiome

Characterising the respiratory microbiome – Rebecca L. Watson – European Respiratory Journal

Vaginal microbiome

Characterization of vaginal microbiota in Thai women – Auttawit Sirichoat – PeerJ

Normal vaginal microbiome in women with primary Sjögren’s syndrome-associated vaginal dryness – van der Meulen TA – Annals of the Rheumatic Diseases

Animal experiments

On the role of corticosterone in behavioral disorders, microbiota composition alteration and neuroimmune response in adult male mice subjected to maternal separation stress – HosseinAmini-Khoei – International Immunopharmacology

Insights into a Possible Mechanism Underlying the Connection of Carbendazim-Induced Lipid Metabolism Disorder and Gut Microbiota Dysbiosis in Mice – Cuiyuan Jin – Toxicological Sciences

General Anesthesia Alters the Diversity and Composition of the Intestinal Microbiota in Mice – Mara A. Serbanescu – Anesthesia & Analgesia

Lactobacillus helveticus KLDS1.8701 alleviates D-galactose-induced aging by regulating Nrf-2 and gut microbiota in mice – Bailiang Li – Food and Function

The Host Microbiota Contributes to Early Protection Against Lung Colonization by Mycobacterium tuberculosisAlexia Dumas – Frontiers in Immunology

Cesarean Section Induces Microbiota-Regulated Immune Disturbances in C57BL/6 Mice – Line Fisker Zachariassen – The Journal of Immunology


DiTaxa: Nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection – Ehsaneddin Asgari – Bioinformatics

November 24, 2018

In today’s microbiome digest there are various papers on human, animal and plant microbiome specifically the microbiome of coral, Honey Bee, Welsh Mountain ponies, root and rhizosphere. Enjoy reading.

Events and jobs

Senior Bioinformatics Scientist, Microbiome

General microbiome

Essay: Microbiome dynamics in obesity – Christoph A. Thaiss – Science

Human microbiome diversity: implications in health, disease, and applications – Kathryn J. Pflughoeft – Annual Reviews

Gut microbiome

Review: Gut microbiota and aging – Francesca Mangiola – European Review for Medical and Pharmacological Sciences

Review: Microbial community reshaped in gastric cancer – L.-L. Wang – European Review for Medical and Pharmacological Sciences

Differential clustering of faecal and mucosa‐associated microbiota in healthy individuals – Adam Carstens – Journal of Digestive Diseases

The prevalence and transcriptional activity of the mucosal microbiota of ulcerative colitis patients – Aina E. Fossum Moen – Scientific Reports

Skin microbiome

The Influence of Habitat and Phylogeny on the Skin Microbiome of Amphibians in Guatemala and Mexico – Silas Ellison – Microbial Ecology

Respiratory microbiome

Inhaled nanomaterials and the respiratory microbiome: clinical, immunological and toxicological perspectives – Tuang Yeow Poh – Particle and Fibre Toxicology

Animal experiments

An intermittent hypercaloric diet alters gut microbiota, prefrontal cortical gene expression and social behaviours in rats – Reichelt AC – Nutritional Neuroscience

Animal microbiome

Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny – F. Joseph Pollock – Nature Communications

Gut and Whole-Body Microbiota of the Honey Bee Separate Thriving and Non-thriving Hives – Céline Ribière – Microbial Ecology

Gut microbiome composition is associated with spatial structuring and social interactions in semi-feral Welsh Mountain ponies – Rachael E. Antwis – Microbiome

Plant, root, and soil microbiome

The structure and function of the global citrus rhizosphere microbiome – Jin Xu – Nature Communications

Root microbiome response to treated wastewater irrigation – AvihaiZolti – Science of The Total Environment

Water and extremophile microbiome

New archaeal viruses discovered by metagenomic analysis of viral communities in enrichment cultures – Ying Liu – Environmental Microbiology

Probiotics / prebiotics

Review: Probiotics, prebiotics and synbiotics for weight loss and metabolic syndrome in the microbiome era – R. Ferrarese – European Review for Medical and Pharmacological Sciences