May 18, 2020

Good morning everyone. Today’s microbiome digest is very short specifically the human gut microbiome section. I have included only one study in this section which shows no association of gut microbiome and fecal calprotectin levels with enteropathy in preterm infants. Additionally, I have covered several interesting reviews and research articles to explore the role of the gut microbiome in Type 1 diabetes and Hashimoto’s thyroiditis, ameliorates ulcerative colitis, aging process, regulation of energy metabolism and oxidative stress. I hope you will enjoy today’s feed.

General microbiome

Fungal communities and their association with nitrogen-fixing bacteria affect early decomposition of Norway spruce deadwood – María Gómez-Brandón – Scientific Reports

Review: Gut microbiota and metabolites in the pathogenesis of endocrine disease – Fenneman AC – Biochemical Society Transactions

Review: Role of the Phytochemical Compounds like Modulators on Gut Microbiota and Oxidative Stress – Yordan Martínez – Current Pharmaceutical Design

Human gut microbiome

Faecal calprotectin and gut microbiota do not predict enteropathy in very preterm infants – Florence Campeotto – Acta Paediatrica

Animal microbiome / Animal experiments

Lizhong decoction ameliorates ulcerative colitis in mice via modulating gut microbiota and its metabolites – Junfeng Zou – Applied microbial and cell physiology

Age-related compositional changes and correlations of gut microbiome, serum metabolome, and immune factor in rats – Xia Zhang – GeroScience

The Beneficial Effects of Lippia Citriodora Extract on Diet‐Induced Obesity in Mice are Associated with the Modulation in the Gut Microbiota Composition – Patricia Diez‐Echave – Molecular Nutrition and Food Research

The gut microbiota attenuates muscle wasting by regulating energy metabolism in chemotherapy-induced malnutrition rats – Haitao Chen – Cancer Chemotherapy and Pharmacology

Slc26a3 deletion alters pH‐microclimate, mucin biosynthesis, microbiome composition and increases Tnfα expression in murine colon – A. Kini – Acta Physiologica

Tibet plateau probiotic mitigates chromate toxicity in mice by alleviating oxidative stress in gut microbiota – Pengya Feng – Communications Biology

Antimicrobial peptide GH12 prevents dental caries by regulating dental plaque microbiota – Wentao Jiang – Microbial Ecology


Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets – Isabel F. Escapa – Microbiome

Review: Metaproteomics: A strategy to study the taxonomy and functionality of the gut microbiota – Yuqiu Wang – Journal of Proteomics

Microbes in news

DOE scientists identify microbial link in gut-memory connection

March 7, 2020

In today’s microbiome digest I have included several interesting articles including a) role of gut microbial metabolite in cardiovascular disease, role of microbiome in cancer treatment outcomes, comparison of small bowel microbiome with the stool samples, microbiome and metabolome of dairy cows with different feed intake levels, role of dietary cellulose in preventing the gut inflammation via modulation in microbiome, and so on. I hope you will enjoy today’s feed.

General microbiome

The microbiome modulating activity of bile acids – Tian, Yuan – Gut Microbes

PostScript Letter: Microbiome alterations in IBS – Ian B Jeffery – Gut

Human gut microbiome

A Cardiovascular Disease-Linked Gut Microbial Metabolite Acts via Adrenergic Receptors – Nemet I – Cell

The Fecal Microbiome in Infants with Biliary Atresia Associates with Bile Flow after Kasai Portoenterostomy – Tessier MEM – Journal of Pediatric Gastroenterology and Nutrition

Mapping the Segmental Microbiomes in the Human Small Bowel in Comparison with Stool: A REIMAGINE Study – Gabriela G. S. Leite – Digestive Diseases and Sciences

Modulation of the intestinal microbiota and the metabolites produced by the administration of ice cream and a dietary supplement containing the same probiotics – Vivian Cristina da Cruz Rodrigues – British Journal of Nutrition

Predictable modulation of cancer treatment outcomes by the gut microbiota – Yoshitaro Heshiki – Microbiome

Animal microbiome / Animal experiments

Microbial composition of enigmatic bird parasites: Wolbachia and Spiroplasma are the most important bacterial associates of quill mites (Acariformes: Syringophilidae) – Eliza Glowska – MicrobiologyOpen

Combined signature of rumen microbiome and metabolome in dairy cows with different feed intake levels – Y Q Li – Journal of Animal Science

Comparative Analysis of Gut Microbiota in Two Populations of Argopecten purpuratus (Lamarck, 1819) Based on 16S rRNA Gene Amplicon Data – Wilbert Serrano – Microbiology Resource Announcements

Dietary cellulose prevents gut inflammation by modulating lipid metabolism and gut microbiota – Yeji Kim – Gut Microbes

Gut microbiome shifts with urbanization and potentially facilitates a zoonotic pathogen in a wading bird – Maureen H. Murray- PLOS ONE

Water and extremophile microbiome

Tuning up microbiome analysis to monitor WWTPs’ biological reactors functioning– de Celis M – Scientific Reports

Metagenome Sequences from Tidal Marsh and Marine Sediment from the Great Bay Estuary of New Hampshire – Brian M. Moore – Microbiology Resource Announcements

Microbes in news

Gut Microbiome Could Determine Cancer Immunotherapy Success


January 25, 2020

In today’s microbiome digest various interesting aspects of microbiome research has been covered such as 1) a summary report by Marc G. Chevrette on one of my favorite research of the decade – “A metagenomic strategy for harnessing the chemical repertoire of the human microbiome”, 2) Oral administration of hydrogels promoted intestinal barrier function, suppressed the pro-inflammatory mRNA expression, 3) Association of low fiber intake in chronic heart failure, and several other interesting articles! Enjoy reading! Happy Weekend!

General microbiome

From Metagenomes to Molecules: Innovations in Functional Metagenomics Unlock Hidden Chemistry in the Human Microbiome – Marc G. Chevrette – Biochemistry

A systematic review of economic evaluation in fecal microbiota transplantation – Thomas Stalder – Infection Control & Hospital Epidemiology

Review: Microbial Contribution to the Human Metabolome: Implications for Health and Disease – William Van Treuren – Annual Review of Pathology

Human gut microbiome

Low fibre intake is associated with gut microbiota alterations in chronic heart failure – Cristiane C.K. Mayerhofer – ESC Heart Fail

Review: Establishing or Exaggerating Causality for the Gut Microbiome: Lessons from Human Microbiota-Associated Rodents – Jens Walter – Cell

Compositional flux within the intestinal microbiota and risk for bloodstream infection with gram-negative bacteria – Igor Stoma – Clinical Infectious Diseases

Comparative Analysis of Gut Microbiota Following Changes in Training Volume Among Swimmers– Jarrad Timothy Hampton-Marcell – International Journal of Sports Medicine

Diversity, compositional and functional differences between gut microbiota of children and adults – Djawad Radjabzadeh – Scientific Reports

Environmental and intrinsic factors shaping gut microbiota composition and diversity and its relation to metabolic health in children and early adolescents: A population-based study – Sofia Moran-Ramos – Gut Microbes

Human skin microbiome

Impact of the early-life skin microbiota on the development of canine atopic dermatitis in a high-risk breed birth cohort– S. Rodriguez-Campos – Scientific Reports

Human respiratory microbiome

The lung microbiota: role in maintaining pulmonary immune homeostasis and its implications in cancer development and therapy – Michele Sommariva – Cellular and Molecular Life Sciences

Lung Microbiota Predict Clinical Outcomes in Critically Ill Patients – Robert P. Dickson – American Journal of Respiratory and Critical Care Medicine

Animal microbiome / Animal experiments

Functional dynamics of bacterial species in the mouse gut microbiome revealed by metagenomic and metatranscriptomic analyses – Youn Wook Chung – PLOS ONE

Effect of Lactobacillus acidophilus D2/CSL (CECT 4529) supplementation in drinking water on chicken crop and caeca microbiome– De Cesare A – PLOSE ONE

Differential effects of synthetic psychoactive cathinones and amphetamine stimulants on the gut microbiome in mice – Angoa-Pérez M – PLOSE ONE

Modulation of inflammatory response and gut microbiota in ankylosing spondylitis mouse model by bioactive peptide IQW – Gang Liu – Journal of Applied Microbiology

Effect of cereal soaking and carbohydrase supplementation on growth, nutrient digestibility and intestinal microbiota in liquid-fed grow-finishing pigs – Alberto Torres-Pitarch – Scientific Reports

Anesthesia and surgery induce age-dependent changes in behaviors and microbiota – Ning Liufu – Aging

Amyloid–Polyphenol Hybrid Nanofilaments Mitigate Colitis and Regulate Gut Microbial Dysbiosis – Bing Hu – ACS Nano

Clostridium butyricum Modulates the Microbiome to Protect Intestinal Barrier Function in Mice with Antibiotic-Induced Dysbiosis – Mao Hagihara – iScience

Microbes in news

Can our microbiome accurately identify diseases … and predict death?

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