Aug 11, 2019

In Sunday’s microbiome digest read about a genomic approach which identified large number of novel proteins from human microbiome, how gut microbiome modulates the pancreatic adenocarcinoma microbiome landscape, detailed investigation of host-microbiome interactions via screening of human microbiome-derived metabolites against G-protein-coupled receptors, homeostasis of brain-gut-microbiota axis in functional dyspepsia rats, modelling of microbial communities using artificial neural networks and in the techniques section Gupta et. al. compared the diagnostic efficacy of Amplicon sequencing and traditional culture methods. Happy weekend. Enjoy reading.

General microbiome

Review Essay: At the Intersection of Microbiota and Circadian Clock: Are Sexual Dimorphism and Growth Hormones the Missing Link to Pathology? – Benjamin D. Weger – BioEssays

Gut microbiome

Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes – Hila Sberro – Cell

Tumor Microbiome Diversity and Composition Influence Pancreatic Cancer Outcomes – Erick Riquelme – Cell

Mapping Interactions of Microbial Metabolites with Human G-Protein-Coupled Receptors – Dominic A. Colosimo – Cell Host & Micorbe

The Association between Gut Microbiota Composition and Body Mass Index in Chinese Male College Students, as Analyzed by Next-generation Sequencing – Yanrong Lv – British Journal of Nutrition

Influence of Helicobacter pylori Infection and Atrophic Gastritis on the Gut Microbiota in a Japanese Population – Iino C – Digestion

Gut microbiome response to a modern Paleolithic diet in a Western lifestyle context – Monica Barone – PLOS ONE

Early Ecasseliflavus gut colonization and outcomes of allogeneic hematopoietic cell transplantation – Armin Rashidi – PLOS ONE

Vaginal microbiome

Review: The vaginal microbiome in uterine transplantation – BP Jones – BJOG

Animal microbiome / Animal experiments

16S rRNA Gene Amplicon Sequence Data from Chicken Cecal Feces from Vietnam and Thailand – Nachiko Takeshita – Microbiology Resource Announcements

Modification of the equine gastrointestinal microbiota by Jerusalem artichoke meal supplementation – M. Glatter – PLOS ONE

Effect of 1-Deoxynojirimycin Isolated from Mulberry Leaves on Glucose Metabolism and Gut Microbiota in a Streptozotocin-Induced Diabetic Mouse Model – Teng-Gen Hu – Journal of Natural Products

Different microbiomes are found in healthy breeder ducks and those with foot pad dermatitis – S M Qin – Poultry Science

Effects of early-life lactoferrin intervention on growth performance, small intestinal function and gut microbiota in suckling piglets – Ping Hu – Food and Function

Child compound Endothelium corneumattenuates gastrointestinal dysmotility through regulating the homeostasis of brain-gut-microbiota axis in functional dyspepsia rats – YixinHe – Journal of Ethnopharmacology

Water and extremophile microbiome

Modelling the influence of environmental parameters over marine planktonic microbial communities using artificial neural networks – F.H.Coutinho – Science of The Total Environment

Biomonitoring detoxification efficiency of an algal-bacterial microcosm system for treatment of coking wastewater: Harmonization between Chlorella vulgaris microalgae and wastewater microbiome – MariamHassan – Science of The Total Environment

Environmental Microbiome

Hospital Microbiome Variations As Analyzed by High-Throughput Sequencing – Marwa T. ElRakaiby – OMICS

Techniques

Amplicon sequencing provides more accurate microbiome information in healthy children compared to culturing – Shashank Gupta – Communications Biology

Microbiome news

The microbiome explained: how a vast army of gut bacteria regulates body’s functioning

How snuggling close affects bats’ microbiome

Advertisements

July 15, 2019

Today we have covered several interesting studies including the effect of drugs such as levofloxacin and penconazole, vitamin E, and raw potato starch on the microbiome composition. Microbial diversity of bharals (Pseudois nayaur) is also explored under wild and captive conditions. Additionally, researchers from Gordon’s group have investigated the interactions between therapeutic diet, microbiota development, and growth recovery. Hope readers will enjoy today’s digest.

General microbiome

Review: The impact of microbiome in urological diseases: a systematic review – Joseph K. M. Li – International Urology and Nephrology

Impact of Pristine Graphene on Intestinal Microbiota Assessed Using a Bioreactor-Rotary Cell Culture System – Mohamed H. Lahiani – ACS Applied Materials & Interfaces

Review: Host–microbial dialogues in atopic dermatitis – Tetsuro Kobayashi – International Immunology

Human gut microbiome

A sparse covarying unit that describes healthy and impaired human gut microbiota development – Arjun S. Raman – Science

Effects of microbiota-directed foods in gnotobiotic animals and undernourished children – Jeanette L. Gehrig – Science

Insights: Gut Microbiota and Short Chain Fatty Acids: Influence on the Autonomic Nervous System – Jessica Bruning – Neuroscience Bulletin

Human gut microbiome changes during a 10 week Randomised Control Trial for micronutrient supplementation in children with attention deficit hyperactivity disorder – Aaron J. Stevens – Scientific Reports

Characterization of gut microbiota, bile acid metabolism, and cytokines in intrahepatic cholangiocarcinoma – Xiaodong Jia – Hepatology

Effect of Synbiotic Supplementation in a Very‐Low‐Calorie Ketogenic Diet on Weight Loss Achievement and Gut Microbiota: A Randomized Controlled Pilot Study – Carolina Gutiérrez‐Repiso – Molecular Nutrition and Food Research

Animal microbiome / Animal experiments

Effects of Potential Probiotic Strains on the Fecal Microbiota and Metabolites of d-Galactose-Induced Aging Rats Fed with High-Fat Diet – Lee-Ching Lew – Probiotics and Antimicrobial Proteins

Characterization of bacterial community changes and antibiotic resistance genes in lamb manure of different incidence – Ling-cong Kong – Scientific Reports

Comparison of gut microbiota diversity between wild and captive bharals (Pseudois nayaur) – Xiangwen Chi – BMC Veterinary Research

The effects of desynchronosis on the gut microbiota composition and physiological parameters of rats – Ksenia M. Klimina – BMC Microbiology

Low gut microbiota diversity and dietary magnesium intake are associated with the development of PPI-induced hypomagnesemia – Lisanne M. M. Gommers – The FASEB Journal

The role of commensal microbes in the lifespan of Drosophila melanogasterHye-Yeon Lee – Aging

The effect of levofloxacin on the lung microbiota of laboratory rats – Sade M. B. Finn – Experimental Lung Research

Impacts of penconazole and its enantiomers exposure on gut microbiota and metabolic profiles in mice – Zhiyuan Meng – Journal of Agricultural and Food Chemistry

Evaluation of the impact of in ovo administered bacteria on microbiome of chicks through 10 days of age – K M Wilson – Poultry Science

Vitamin E (α-tocopherol) consumption influences gut microbiota composition – Yukyung Choi – International Journal of Food Sciences and Nutrition

CRTAM Shapes the Gut Microbiota and Enhances the Severity of Infection – Araceli Perez-Lopez – The Journal of Immunology

Metaproteomic investigation to assess gut microbiota shaping in newborn mice: A combined taxonomic, functional and quantitative approach – Stefano Levi Mortera – Journal of Proteomics

Bacillus subtilis Strain DSM 29784 Modulates the Cecal Microbiome, Concentration of Short-Chain Fatty Acids, and Apparent Retention of Dietary Components in Shaver White Chickens during Grower, Developer, and Laying Phases – Mohamed Neijat – Applied and Environmental Microbiology

Effect of raw potato starch on the gut microbiome and metabolome in mice – So-Jung Bang – International Journal of Biological Macromolecules

Edgeworthia gardneri (Wall.) Meisn. water extract improves diabetes and modulates gut microbiota – Zhiwen Zhang – Journal of Ethnopharmacology

Plant, root, and soil microbiome

Review: Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales – Regina L. Wilpiszeski – Applied and Environmental Microbiology

Water and extremophile microbiome

Metagenomic insights into microbial diversity in a groundwater basin impacted by a variety of anthropogenic activities – Prinpida Sonthiphand – Environmental Science and Pollution Research

Metagenomic insights to understand transient influence of Yamuna River on taxonomic and functional aspects of bacterial and archaeal communities of River Ganges – Rachel Samson – Science of The Total Environment

Techniques

Tracing seafood at high spatial resolution using NGS-generated data and machine learning: Comparing microbiome versus SNPs – Massimo Milan – Food Chemistry

Microbiome news

The Gut Microbiome Can Be a Boon or a Bane for Cardiovascular Health – SHAWNA WILLIAMS

The human microbiome is a treasure trove waiting to be unlocked

July 6, 2019

Today’s microbiome digest featuring a variety of research and review articles highlighting the role of gut microbiota-derived signals to the beta cells are necessary for proper insulin trafficking, a microfluidic chip designed by Roberta et. al. to mimic interactions between microorganisms and host tissue, the innovative role of exosomes in the pathogenesis of CRC, and a very interesting study in mice shows the host mitochondrial genotype influence the gut microbiota species diversity. Happy weekend. Enjoy reading.

General microbiome

Review: Translating Recent Microbiome Insights in Otitis Media into Probiotic Strategies – Marianne F. L. van den Broek – Clinical Microbiology Reviews

Research Highlight : Microbiota guides insulin trafficking in beta cells – Ozren Stojanović – Cell Research

Human gut microbiome

Human-gut-microbiome on a chip – Roberta Poceviciute – Nature Biomedical Engineering

Gut microbial profile is altered in biliary atresia – Junfeng Wang – Biliary and Pancreatic

The specific use of alginate from Laminaria japonica by Bacteroidesspecies determined its modulation of the Bacteroides community – Chunging Ai – Food & Function

Lactose and Bovine Milk Oligosaccharides Synergistically Stimulate B. longum subsp. longum Growth in a Simplified Model of the Infant Gut Microbiome – Louise M.A. Jakobsen – Journal of proteome research

Review: Probiotics and constipation: mechanisms of action, evidence for effectiveness and utilisation by patients and healthcare professionals – Eirini Dimidi – Proceedings of the Nutrition Society

In Vitro Digestion and Fermentation of Three Polysaccharide Fractions from Laminaria japonica and Their Impact on Lipid Metabolism-Associated Human Gut Microbiota – Jie Gao – Journal of Agricultural and Food Chemistry

Review: Role of intestinal microbiota and metabolites in inflammatory bowel disease – Li-Na Dong – Chinese Medical Journal

Review: The malignant role of exosomes in the communication among colorectal cancer cell, macrophage and microbiome – Jinjie Wu – Carcinogenesis

Human respiratory microbiome

Microbial Composition of the Human Nasopharynx Varies According to Influenza Virus Type and Vaccination Status – Tao Ding – mBio

Animal microbiome / Animal experiments

Full‐length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysis – Terje Klemetsen – MicrobiologyOpen

Protein and carbohydrate intakes alter gut microbial community structure in crickets: A Geometric Framework approach – Soon Hwee Ng – FEMS Microbiology Ecology

Caulerpa lentillifera polysaccharides enhance the immunostimulatory activity in immunosuppressed mice in correlation with modulating gut microbiota – Yujiao Sun – Food & Function

Diet Consisting of Balanced Yogurt, Fruit and Vegetables Modifies the Gut Microbiota and Protects Mice Against Nonalcoholic Fatty Liver Disease – Chao‐Yue Kong – Molecular Nutrition Food Research

Unraveling the effects of the gut microbiota composition and function on horse endurance physiology – Sandra Plancade – Scientific Reports

Inulin and metformin ameliorate polycystic ovary syndrome via anti-inflammation and modulating gut microbiota in mice – Jing Xue – Endocrine Journal

Antiretroviral therapy administration in healthy rhesus macaques is associated with transient shifts in intestinal bacterial diversity and modest immunological perturbations – Alexandra M. Ortiz – Journal of Virology

Microbiota-Driven Tonic Interferon Signals in Lung Stromal Cells Protect from Influenza Virus Infection– Konrad C.Bradley – Cell Reports

Microbial and metabolomic remodeling by a formula of Sichuan dark tea improves hyperlipidemia in apoE-deficient mice – Lingzhi Li – PLOS ONE

Effect of chronic and acute heat challenges on fecal microbiota composition, production and thermoregulation traits in growing pigs – M Le Sciellour – Journal of Animal Science

Metaproteomics characterization of the alphaproteobacteria microbiome in different developmental and feeding stages of the poultry red mite Dermanyssus gallinae (De Geer, 1778) – José Francisco Lima-Barbero – Journal of Animal Science

L. plantarumL. fermentum, and B. breveBeads Modified the Intestinal Microbiota and Alleviated the Inflammatory Response in High-Fat Diet–Fed Mice – Qingshen Sun – Probiotics and Antimicrobial Proteins

Host mitochondria influence gut microbiome diversity: A role for ROS – Tal Yardeni – Science Signaling

Potential effects of rapeseed peptide Maillard reaction products on aging-related disorder attenuation and gut microbiota modulation in D-galactose induced aging mice – Shudong He – Food & Function

The piglet mycobiome during the weaning transition: a pilot study – Katie L Summers – Journal of Animal Science

A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions R. John Wallace – Science Advances

Microbiome in news

Dairy cow microbiome could yield the key to eco-friendly agriculture 

June 21, 2019

Today’s microbiome digest featuring the milestones in the human microbiota research along with a very interesting stochastic model to explain microbiome composition in host organisms and a review focusing on the effect of antipsychotic medications on the microbiome and weight gain. Additionally, there are some interesting studies from animal microbiome/animal experiments section such as the role of rumen microbiota in altering average daily gain and feed efficiency and microbiome of deposit feeder Capitella teleta. Enjoy reading. 

General microbiome

Milestones in human microbiota research – Nature

Neutrality in the Metaorganism – Michael Sieber – PLOS Biology

Gut microbiome

Novel Inter‐omic Analysis Reveals Relationships Between Diverse Gut Microbiota and Host Immune Dysregulation in HLA‐B27‐Induced Experimental Spondyloarthritis – Tejpal Gill – Arthritis And Rheumatology

Review: The effects of antipsychotic medications on microbiome and weight gain in children and adolescents – Tali Bretler – BMC Medicine

Oral microbiome

Fretibacterium sp. human oral taxon 360 is a novel biomarker for periodontitis screening in the Japanese population – Thatawee Khemwong – PLOS ONE

Animal microbiome / Animal experiments

Effects of dietary supplementation with lysozyme on the structure and function of the cecal microbiota in broiler chickens – Yun Xia – PLOS ONE

Potential role of rumen microbiota in altering average daily gain and feed efficiency in meat goats fed simple and mixed pastures using bacterial tag-encoded FLX amplicon pyrosequencing – Byeng Ryel Min – Journal of Animal Science

Modulation of the gut microbiota by a galactooligosaccharide protects against heavy metal lead accumulation in mice – Qixiao Zhai – Food & Function

Modulating effects of polysaccharides from the fruits of Lycium barbarum on the immune response and gut microbiota in cyclophosphamide-treated mice – Yu Ding – Food & Function

Sinapine reduces non-alcoholic fatty liver disease in mice by modulating the composition of the gut microbiota – Youdong Li – Food & Function

Glycated fish protein supplementation modulated gut microbiota composition and reduced inflammation but increased accumulation of advanced glycation end products in high-fat diet fed rats – Zhenjie Mao – Food & Function

The deposit feeder Capitella teleta has a unique and relatively complex microbiome likely supporting its ability to degrade pollutants – RebeccaHochstein – Science of The Total Environment

Microbiome news

Study Finds Link Between Gut Microbiome and Spread of Breast Cancer

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

Prebiotics/Probiotics

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

Prebiotics/Probiotics

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

Methods

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

Bioinformatics

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

Bioinformatics

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