January 18, 2020

Check out today’s digest which includes very diverse microbiome research. I would like to highlight specifically these three 1) Indole-3-carbinol in the prevention of colitis and associated microbial dysbiosis, 2) A rapid and convenient derivatization method for the quantitation of short‐chain fatty acids in human feces, and 3) Role of complex microbiome human in vitro fertilization procedure. There are several other interesting articles in every section! Enjoy reading!

General microbiome

Review: Whole Food–Based Approaches to Modulating Gut Microbiota and Associated Diseases – Han Y –  Annual Review of Food Science and Technology

Microbiome signatures in neonatal central line associated bloodstream infections – Mohan Pammi – PLOS ONE

Human gut microbiome

Gut Microbiota Compositional and Functional Fingerprint in Patients with Alcohol Use Disorder and Alcohol Associated Liver Disease – Giovanni Addolorato – Liver INTERNATIONAL

Parkinson disease, levodopa and the gut microbiota‐when microbiology meets pharmacology – Harald Brüssow – Environmental Microbiology

Short chain fatty acids and methylamines produced by gut microbiota as mediators and markers in the circulatory system – Maksymilian Onyszkiewicz – Experimental Biology and Medicine

Prospective study reveals a microbiome signature that predicts the occurrence of post-operative enterocolitis in Hirschsprung disease (HSCR) patients– Weibing Tang – Gut Microbes

Review: Systematic review of human gut resistome studies revealed variable definitions and approaches – Jeferry Ho – Gut Microbes

Indole-3-carbinol prevents colitis and associated microbial dysbiosis in an IL-22–dependent manner – Philip B. Busbee – JCI Insight

The biotransformation of Bupleuri Radix by human gut microbiota – Cui Tang – Xenobiotica

Human oral microbiome

Signatures of oral microbiome in HIV-infected individuals with oral Kaposi’s sarcoma and cell-associated KSHV DNA – Marion Gruffaz – PLOS PATHOGENS

Review: A Systematic Review of the Root Canal Microbiota Associated with Apical Periodontitis: Lessons from Next‐Generation Sequencing – Daniel Manoil – Proteomics Clinical Applications

The influence and impact of smoking on red blood cell morphology and buccal microflora: A case‐control study – Khalid Hadi Aldosari – Journal of Clinical Laboratory Analysis

Human reproductive microbiome

The complex microbiome from native semen to embryo culture environment in human in vitro fertilization procedure – Jelena Štšepetova – Reproductive Biology and Endocrinology

Understanding the terms we use: support for using ‘sexually shared microbiota’ (SSM)
David Taylor-Robinson – International Journal of STD and AIDs

Human respiratory microbiome

Pharyngeal microbiome alterations during Neisseria gonorrhoeae infection – Antonella Marangoni – PLOS ONE

Animal microbiome / Animal experiments

Camellia Sinensis and Litsea Coreana Ameliorate Intestinal Inflammation and Modulate Gut Microbiota in Dextran Sulfate Sodium‐Induced Colitis Mice – Yan Liu

Improving Alzheimer’s disease by altering Gut Microbiota in tree shrews with ginsenoside Rg1 – Limei Wang – FEMS MICROBIOLOGY LETTERS

The composition of the perinatal intestinal microbiota in horse – A. Husso – Scientific Reports

Plant microbiome

The influence of host‐plant connectivity on fungal assemblages in the root microbiota of Brachypodium pinnatum – C. Mony – Ecology


A rapid and convenient derivatization method for quantitation of short‐chain fatty acids in human feces by ultra‐performance liquid chromatography‐tandem mass spectrometry – Huan Fu – Rapid communications in Mass Spectrometry

Microbiome news

It takes more than two to tango: Microbial communities influence animal sex and reproduction

December 9, 2019

Today’s microbiome digest is very short and includes a few interesting articles. Enjoy reading.

General microbiome

Review: Cannabinoids and the Microbiota‐Gut‐Brain‐Axis: Emerging Effects of Cannabidiol and Potential Applications to Alcohol Use Disorders – Hollis C. Karoly – Alcoholism Clinical and Experimental Research

Review: The Microbiome Factor in Drug Discovery and Development– Andrea Nuzzo – Chemical Research in Toxicology

Human microbiome

The intestinal microbiome potentially affects thrombin generation in human subjects – Yassene Mohammed – Journal of thrombosis and haemostasis

Expert insights: The potential role of the gut microbiome‐bile acid‐brain axis in the development and progression of Alzheimer’s disease and hepatic encephalopathy – Wei Jia – Medicinal Research Reviews

The human oral cavity microbiota composition during acute tonsillitis: a cross-sectional survey – Yun Kit Yeoh – BMC Oral Health

Review: The microbiota-gut-brain axis: An emerging role for the epigenome – Tijs Louwies – Experimental Biology and Medicine

Animal microbiome / Animal experiments

Seven-day Green Tea Supplementation Revamps Gut Microbiome and Caecum/Skin Metabolome in Mice from Stress – Eun Sung Jung – Scientific Reports

The Mercury-Tolerant Microbiota of the Zooplankton Daphnia Aids in Host Survival and Maintains Fecundity under Mercury Stress – Jiunn C. Fong – Environmental Science & Technology

Plant microbiome

Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection – Norma M. Morella – PNAS

December 8, 2019

Today’s microbiome digest includes several interesting reviews and perspectives mainly focusing on the role of human microbiome in allergic diseases, pancreatic health, aging, Cognitive Impairment, and IBS. Enjoy Saturday with the latest microbiome feed.

General microbiome

Mini review: Th9 cells in allergic diseases: a role for the microbiota?– Isabella Badolati – Scandavian of Immunology

Perspective: Microbiota in pancreatic health and disease: the next frontier in microbiome research – Ryan M. Thomas – Nature Reviews Gastroenterology & Hepatology

Review: Advancing functional and translational microbiome research using meta-omics approaches – Xu Zhang – Microbiome

Human microbiome

Perspective: The Unexplored World of Human Virome, Mycobiome, and Archaeome in Aging – Oscar Salvador Barrera-Vázquez – The Journals of Gerontology

Review: The Gut Microbiome as a Therapeutic Target for Cognitive Impairment – Yi Sun – The Journals of Gerontology

Relationship between the gut microbiome and energy/nutrient intake in a confined bioregenerative life support system (BLSS) – Juanjuan Chen – Applied and Environmental Microbiology

Brief report: Changes in gut microbial metagenomic pathways associated with clinical outcomes after the elimination of malabsorbed sugars in an IBS cohort – A. Mack – Gut microbes

Microbiota modification in hematology: still at the bench or ready for the bedside? – Christopher J. Severyn – Hematology Am Soc Hematol Educ Program

Gut microbial β-glucuronidases reactivate estrogens as components of the estrobolome that reactivate estrogens– Samantha M. Ervin – Journal of Biological Chemistry

The role of gut microbiota for the activity of medicinal plants traditionally used in the European Union for gastrointestinal disorders – Timo A.Thumann – Journal of Ethnopharmacology

Review: Berry polyphenols metabolism and impact on human gut microbiota and health– Laura Lavefve – Food and Function

Association of suboptimal health status with intestinal microbiota in Chinese youths – Qi Sun – Journal of Cellular and Molecular Medicine

Animal microbiome / Animal experiments

Dominant and Subordinate Relationship Formed by Repeated Social Encounters Alters Gut Microbiota in Greater Long-Tailed Hamsters – Jidong Zhao – Microbial Ecology

Cattle intestinal microbiota shifts following Escherichia coli O157:H7 vaccination and colonizationtravel – Raies A. Mir – PLOS ONE

Characterization of the cecal microbiome composition of Wenchang chickens before and after fattening – Zhen Tan – PLOS ONE

Plant microbiome

Resource Announcement: Bacteriome and Mycobiome in Nicotiana tabacum Fields Affected by Black Shank Disease – Xiaoyulong Chen – Plant disease

Characterization and discrimination of microbial community and co‐occurrence patterns in fresh and strong flavor style flue‐cured tobacco leaves – Qianying Zhang – Microbiology Open

Microbiome news

MaaT Pharma Announces the Presentation of Positive Data with Its Lead Microbiome Biotherapeutic in Intestinal-Predominant Acute Graft-versus-Host-Disease at the ASH 2019 Annual Meeting

October 20, 2019

In today’s microbiome digest, several interesting studies have been covered including a) the relationships between multidrug-resistant bacteria (MDRB) colonization and dysbiosis after liver transplantation, b) microbiome and host transcriptome signature in patients with Atopic dermatitis or psoriasis, c) in the animal microbiome section- effect of host genetics on the gut microbiome composition of Avian, Bovine, and Drosophila models, d) a study which shows Composition of gut microbiota can modulate adaptive immune responses in chickens to vaccination against influenza viruses, e) CSMD, a bioinformatics pipeline specifically developed to generate accurate species-level microbiome profiles for clinical samples with low microbial loads and many more. Enjoy your Sunday with the latest microbiome feed.

General microbiome

Research highlight: Your microbiome is what you eat – Ashley York – Nature Reviews Microbiology

Gastro-intestinal and oral microbiome signatures associated with healthy aging – Harinder Singh – GeroScience

The future of microbiome‐based therapeutics in clinical applications – Anukriti Sharma – Clinical Pharmacology and Therapeutics

Human gut microbiome

Colonizing multidrug-resistant bacteria and the longitudinal evolution of the intestinal microbiome after liver transplantation – Medini K. Annavajhala – Nature Communication

Normal gut microbiome in NMDA receptor encephalitis – Julia Herken – Neurology, Neuroimmunology and Neuroinflammation

Urolithin Metabotypes Can Determine the Modulation of Gut Microbiota in Healthy Individuals by Tracking Walnuts Consumption over Three Days – Izaskun García-Mantrana – Nutrients 

Fecal microbiota transplantation results in bacterial strain displacement in patients with inflammatory bowel diseases – Manli Zou – FEBS openbio

Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men – Ryan R. Cook – Scientific Reports

Human skin microbiome

Microbe-host interplay in atopic dermatitis and psoriasis – Nanna Fyhrquist – Nature Communications

Human reproductive tract microbiome

Review: Maternal microbiome and the hypertensive disorder of pregnancy, preeclampsia – Kalie F Beckers – American Journal of Physiology Heart and Circulatory Physiology

Animal microbiome / Animal experiments

Changes in Microbiota and Development of Nonspecific Inflammation of Genitals in Female C57Bl/6 Mice after Aerosol Infection with Mycobacterium tuberculosis – S. I. Kayukova – Bulletin of Experimental Biology and Medicine

Land-use change has host-specific influences on avian gut microbiomes – Priscilla A. San Juan – The ISME Journal

Host genetic effects upon the early gut microbiota in a bovine model with graduated spectrum of genetic variation – Peixin Fan – The ISME Journal

Host determinants of among-species variation in microbiome composition in drosophilid flies – Karen L. Adair – The ISME Journal

Faecal microbiome sequences in relation to the egg-laying performance of hens using amplicon-based metagenomic association analysis – A. A. Elokil – Animal

Of microbes and mange: consistent changes in the skin microbiome of three canid species infected with Sarcoptes scabiei mites – Alexandra L. DeCandia – Parasites & Vectors

Commensal gut microbiota can modulate adaptive immune responses in chickens vaccinated with whole inactivated avian influenza virus subtype H9N2 – AlexanderYitbarek – Vaccine


CSMD: A computational subtraction-based microbiome discovery pipeline for species-level characterization of clinical metagenomic samples – Yu Liu – Bioinformatics

Microbiome news


EcoBiome Innovation Center Launches MyEcoBiome™ Personal Soil Health Test

September 28, 2019

Dear microbiome digest readers, on this weekend we have covered interesting review articles focusing on factors that influence the temporal development of the infant microbiome, and  the role of gut microbiota in colorectal cancer, and research articles shows the role of microbiome in managing constipation, in Atopic Dermatitis, microbiome-host interaction in Respiratory Syncytial Virus Infection, Successful fecal microbiota transplantation for the treatment of recurrent Clostridium difficile infection, sputum microbiome in asthma and COPD and various research articles from Animal microbiome/Animal experiments section including fine-scale spatial structuring of the microbial composition and diversity along the length of murine colon. Enjoy reading.

General microbiome

Impact of a Plant Sterol- and Galactooligosaccharide-Enriched Beverage on Colonic Metabolism and Gut Microbiota Composition Using an In Vitro Dynamic Model – Virginia Blanco-Morales – Journal of Agricultural and Food Chemistry

Review: Temporal development of the infant gut microbiome – Rebecca E. Moore – Open Biology

Stool sampling and DNA isolation kits affect DNA quality and bacterial composition following 16S rRNA gene sequencing using MiSeq Illumina platform – Petra Videnska – Scientific Reports

The Honeybee Gut Microbiota Is Altered after Chronic Exposure to Different Families of Insecticides and Infection by Nosema ceranaeRégis Rouzé – Microbes and Environments

Human gut microbiome

Abundance of Probiotics and Butyrate‐Production Microbiome Manages Constipation Via Short‐Chain Fatty Acids Production and Hormones Secretion – Min Zhuang – Molecular Nutrition & Food Research

Review: Gut microbiota in colorectal cancer: mechanisms of action and clinical applications – Sunny H. Wong – Nature Reviews Gastroenterology & Hepatology

Changes in the gut microbiota during and after commercial helium-oxygen saturation diving in China – Yuan Y – Occupational and Environmental Medicine

Ninety-eight years old female successfully successfully treated with fecal microbiota transplantation after recurrent Clostridium difficile infection – Bermejo Boixareu C – Medicina Clínica

Human respiratory microbiome

Sputum microbiomic clustering in asthma and COPD reveals a Haemophilus‐predominant subgroup – Sarah Diver – Allergy

Microbiome-Transcriptome Interactions Related to Severity of Respiratory Syncytial Virus Infection – Abhijeet R. Sonawane – Scientific Reports

Human skin microbiome

Cheek Microbial Communities Vary in Young Children with Atopic Dermatitis in China – Song L. – Dermatology

Animal microbiome / Animal experiments

Dietary supplementation with the extract from Eucommia ulmoides leaves changed epithelial restitution and gut microbial community and composition of weanling piglets – Peng M – PLoS One

Geographical location influences the composition of the gut microbiota in wild house mice (Mus musculus domesticus) at a fine spatial scale – Sarah Goertz – PLoS One

Protective activities of polysaccharides from Cipangopaludina chinensis against high-fat-diet-induced atherosclerosis via regulating gut microbiota in ApoE-deficient mice – Qingping Xiong – Food & Function

2-O-beta-D-Glucopyranosyl-L-ascorbic acid, an Ascorbic Acid Derivative Isolated from the Fruits of Lycium Barbarum L., Modulates Gut Microbiota and Palliates Colitis in Dextran Sodium Sulfate-induced Colitis in Mice – Kaiyin Huang – Journal of Agricultural and Food Chemistry

Anti‐TNF‐α therapy alters the gut microbiota in proteoglycan‐induced ankylosing spondylitis in mice – Bin Liu – MicrobiologyOpen

A fiber-deprived diet disturbs the fine-scale spatial architecture of the murine colon microbiome – Alessandra Riva – Nature Communication

Antibiotic exposure disturbs the gut microbiota and its metabolic phenotype differently in rats with advanced-stage type 1 diabetes and age-matched controls – Hong Zheng – Journal of Proteome Research

Gut Microbiota and Metabolome Response of Decaisnea insignis Seed Oil on Metabolism Disorder Induced by Excess Alcohol Consumption – Xiaoxia LiuJournal of Agricultural and Food Chemistry

Microbiome news

Vaginal Microbiome and Women’s Health: More Research Needed

NAU researchers aim to find microbial link between two common respiratory diseases

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


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

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


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


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