May 17, 2019

Today’s digest featuring a detailed contribution of the human microbiome to carcinogenesis, some interesting research, and reviews focusing on the microbial role in combat neurodegeneration, neuroimmune alterations, metabolism of lipids and N-ε-Carboxymethyllysine and an antibiotic resistome from healthy pig metagenome. Enjoy reading.

General microbiome

International Cancer Microbiome Consortium consensus statement on the role of the human microbiome in carcinogenesis – Alasdair J Scott – Gut

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

Review: The Use of Defined Microbial Communities To Model Host-Microbe Interactions in the Human Gut – Janneke Elzinga – Microbiology and Molecular Biology Reviews

Gut microbiome

The bacterial communities of the small intestine and stool in children with short bowel syndrome – Steven L. Zeichner – PLOS ONE

Review: Modification of the gut microbiome to combat neurodegeneration – Andrew Octavian Sasmita Reviews in the Neurosciences

Markers of dysbiosis in patients with ulcerative colitis and Crohn’s disease – Danilova NA – Terapevticheskiĭ Arkhiv

Mid-life microbiota crises: middle age is associated with pervasive neuroimmune alterations that are reversed by targeting the gut microbiome – Marcus Boehme – Molecular Psychiatry

Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease Almut Heinken – Microbiome

Anaerobic Degradation of N-ε-Carboxymethyllysine, A Major Glycation End Product, By Human Intestinal Bacteria – Thi Phuong Nam Bui – Journal of Agricultural and Food Chemistry

Letter: Lipopolysaccharide from Gut Microbiota Modulates α-Synuclein Aggregation and Alters Its Biological Function – Dipita Bhattacharyya – ACS Chemical Neuroscience

Respiratory 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

Could the Sputum Microbiota Be a Biomarker That Predicts Mortality after Acute Exacerbations of Chronic Obstructive Pulmonary Disease?Jun-Chieh J. Tsay – American Journal of Respiratory and Critical Care Medicine

Skin microbiome

Amphibian Host and Skin Microbiota Response to a Common Agricultural Antimicrobial and Internal Parasite – Obed Hernández-Gómez – Microbial Ecology

Plant microbiome

Engineering banana endosphere microbiome to improve Fusarium wilt resistance in banana – Yupei Liu – Microbiome

Review: Ecology and Evolution of Plant Microbiomes – Viviane Cordovez – Annual Review of Microbiology

Animal microbiome / Animal experiments

Does MHC heterozygosity influence microbiota form and function? – M. A. Wadud Khan – PLOS ONE

Faecal microbiota shift during weaning transition in piglets and evaluation of AO blood types as shaping factor for the bacterial community profile – Vincenzo Motta – PLOS ONE

CD1d Modulates Colonic Inflammation in NOD2−/− Mice by Altering the Intestinal Microbial Composition Comprising Acetatifactor murisChansu Lee – Journal of Chron’s and Colitis

Switching on the light: using metagenomic shotgun sequencing to characterize the intestinal microbiome of Atlantic cod – Even Sannes Riiser – Environmental Microbiology

Predicting residual feed intake status using rumen microbial profiles in ewe lambs – Melinda J Ellison – Journal of Animal Science

Antibiotic resistomes of healthy pig faecal metagenomes Aoife Joyce – Microbial Genomics

Extract of ice plant (Mesembryanthemum crystallinum) ameliorates hyperglycemia and modulates the gut microbiota composition in type 2 diabetic Goto-Kakizaki rats – Chengcheng Zhang – Food and Function

Absence of gut microbiota during early life affects anxiolytic Behaviors and monoamine neurotransmitters system in the hippocampal of mice – Jun-Xi Pan – Journal of the Neurological Science

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

Fecal Viral Diversity of Captive and Wild Tasmanian Devils Characterized Using Virion-Enriched Metagenomics and Metatranscriptomics – Rowena Chong – Journal of Virology

Depression Promotes the Onset of Irritable Bowel Syndrome through Unique Dysbiosis in Rats – Takeshi Takajo – Gut and Liver

Hepatic progenitor cell activation is induced by the depletion of the gut microbiome in mice – Fei Wang – MicrobiologyOpen


Saccharomyces boulardii CNCM I-745 changes lipidemic profile and gut microbiota in a hamster hypercholesterolemic model – F. Briand – Beneficial Microbes


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