January 18, 2019

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

Methods

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

January 10, 2020

In today’s weekend post- maternal antibodies targeting microbiota protect mice from neonatal infection, exercise improves gestational diabetes in rodent models, bacterial signature in NAFLD and TMAO as negative predictor of human embryo quality. Happy reading and a nice weekend!

General microbiome

Adolescence and aging: impact of adolescence inflammatory stress and microbiota alterations on brain development, aging and neurodegeneration – Nour Yahfoufi – The Journal of Geronotology

Preclinical and clinical relevance of probiotics and synbiotics in colorectal carcinogenesis: a systematic review – Bruna C.S. Cruz – Nutrition Reviews

Gut microbiota: a new piece in understanding hepatocarcinogenesis – An Zhou – Cancer Letters

Gut Microbiota, Diet, and Chronic Diseases: The Role Played by Oxidative Stress – Elisardo C. Vasquez – Oxidative Medicine and Cellular Longevity

New insights on the colonization of the human gut by health-promoting bacteria – Sinead T. Morrin – Applied Microbiology and Biotechnology

Human microbiome

Salivary microbiota and inflammation‐related proteins in patients with psoriasis – Daniel Belstrøm – Oral Diseases

Oral butyrate does not affect innate immunity and islet autoimmunity in individuals with longstanding type 1 diabetes: a randomised controlled trial – Pieter F. de Groot – Diabetologia

Fusobacterium nucleatum in the colorectum, and its association with cancer risk and survival: a systematic review and meta-analysis – Christian Gethings-Behncke – Cancer Epidemiology Biomarkers and Prevention

Potential impact of removing metronidazole from treatment armamentarium of mild acute Clostridioides difficile infection – Shani Zilberman-Itskovich – Future Medicine

Intrahepatic bacterial metataxonomic signature in non-alcoholic fatty liver disease Silvia Sookoian – Gut

Microbial imbalance in inflammatory bowel disease patients at different taxonomic levels – Mohammad Tauqeer Alam – Gut Pathogens

Early life microbiota

Antibiotic Resistance Genes in the Gut Microbiota of Children with Autistic Spectrum Disorder as Possible Predictors of the Disease – Alexey S. Kovtun – Microbial Drug Resistance

Trimethylamine-N-oxide is present in human follicular fluid and is a negative predictor of embryo quality – R.A.Nagy – Human Reproduction

Animal experiments

Microbiota-targeted maternal antibodies protect neonates from enteric infection – Wen Zheng – Nature

Characterization of metabolic and inflammatory profiles of transition dairy cows fed an energy-restricted diet – Giulia Esposito – Journal of Animal Science

Microbiota dependent production of butyrate is required for the bone anabolic activity of PTH – Jau-Yi Li – Journal of Clinical Investigation

Betaine addition as a potent ruminal fermentation modulator under hyperthermal and hyperosmotic conditions in vitro – Mubarik Mahmood – Journal of the Science of Food and Agriculture

Investigating temporal microbial dynamics in the rumen of beef calves raised on two farms during early life – Eóin O’Hara – FEMS Microbial Ecology

Dietary Xanthan Gum Alters Antibiotic Efficacy against the Murine Gut Microbiota and Attenuates Clostridioides difficile Colonization – Matthew K. Schnizlein – mSphere

Post‐natal co‐development of the microbiota and gut barrier function follows different paths in the small and large intestine in piglets – Alexis Pierre Arnaud – Faseb Journal

Phellinus linteus polysaccharide extract improves insulin resistance by regulating gut microbiota composition – Yangyang Liu – Faseb Journal

Exercise improves metabolic function and alters the microbiome in rats with gestational diabetes – Dayana Mahizir – Faseb Journal

Microbial reconstitution reverses early female puberty induced by maternal high-fat diet during lactation – Mengjie Wang – Endocrinology

Fecal microbiota as a noninvasive biomarker to predict the tissue iron accumulation in intestine epithelial cells and liver – Bingdong Liu – Faseb Journal

Techniques

Systematic Analysis of Impact of Sampling Regions and Storage Methods on Fecal Gut Microbiome and Metabolome Profiles – Yali Liang – mSphere

December 29, 2019

Have a nice sunday!  Today we have papers about the microbiome in martial arts athletes, more research about Fusobacterium and colorectal cancer, the effect of light in atopic dermatitis and the effect of alcohol binge in a mouse model, among other papers.  

Human and General Microbiome

Review: The Gut-Liver-Kidney axis: novel regulator of fatty liver associated chronic kidney disease – Desh Raj – Pharmacological Research

Characteristics of the gut microbiota in professional martial arts athletes: A comparison between different competition levels – Ru Liang – PLoS One

The balance between breast cancer and the immune system: challenges for prognosis and clinical benefit from immunotherapies – Constantin N. Baxevanis – Seminars in Cancer Biology

Review: Host- and Microbiota-Derived Extracellular Vesicles, Immune Function, and Disease Development – Laurence Macia – International Journal of Molecular Sciences

Recent advances in understanding the natural history of the otitis media microbiome and its response to environmental pressures – Robyn L. Marsh – International Journal of Pediatric Otorhinolaryngology

Association of autophagy status with amount of Fusobacterium nucleatum in colorectal cancer – Koichiro Haruki – The Journal of Pathology

Effects of 308 nm excimer light treatment on the skin microbiome of atopic dermatitis patients – Yuko Kurosaki – Photodermatology, Photoimmunology and Photomedicine

Rapid Multiplex Real-Time PCR Method for the Detection and Quantification of Selected Cariogenic and Periodontal Bacteria – Jan Lochman – Diagnostics

Review: Biomarkers of a Healthy Nordic Diet-From Dietary Exposure Biomarkers to Microbiota Signatures in the Metabolome – Rikard Landberg – Nutrients

 

Animal Microbiome

Gut microbiota of provisioned and wild rhesus macaques (Macaca mulatta) living in a limestone forest in southwest Guangxi, China – Ting Chen – MicrobiologyOpen

The Diversity of the Endobiotic Bacterial Communities in the Four Jellyfish Species – Qing Liu – Polish Journal of Microbiology

Switching to a Healthy Diet Prevents the Detrimental Effects of Western Diet in a Colitis-Associated Colorectal Cancer Model – Charlotte Gröschel – Nutrients

The Effect of Thermal Stress on the Bacterial Microbiome of Exaiptasia diaphana – Leon M. Hartman – Microorganisms

Pretreatment with Yeast-Derived Complex Dietary Polysaccharides Suppresses Gut Inflammation, Alters the Microbiota Composition, and Increases Immune Regulatory Short-Chain Fatty Acid Production in C57BL/6 Mice – Radhika Gudi – The Journal of Nutrition

Long-lasting microbial dysbiosis and altered enteric neurotransmitters in adult rats following adolescent binge ethanol exposure – Ryan P. Vetreno – Addiction Biology

 

Beneficial Microbes and Compounds

Minireview: Use of Synbiotics for Ulcerative Colitis Treatment – Marianna Roselli –  Current Clinical Pharmacology

The Structure Features and Improving Effects of Polysaccharide from Astragalus membranaceus on Antibiotic-Associated Diarrhea – Shanshan Ll – Antibiotics

Deep-Fried Atractylodis Rhizoma Protects against Spleen Deficiency-Induced Diarrhea through Regulating Intestinal Inflammatory Response and Gut Microbiota – Kun Shi – International Journal of Molecular Sciences

Hafnia alvei HA4597 Strain Reduces Food Intake and Body Weight Gain and Improves Body Composition, Glucose, and Lipid Metabolism in a Mouse Model of Hyperphagic Obesity – Nicolas Lucas – Microorganisms

 

Wastewater Microbiome

Microbiome changes and oxidative capability of an anaerobic PCB dechlorinating enrichment culture after oxygen exposure – Bruna Matturro – New Biotechnology

 

Plant Microbiome

Tomato RNA-seq Data Mining Reveals the Taxonomic and Functional Diversity of Root-Associated Microbiota – Bruna Matturro – Microorganisms

Metagenome sequencing of fingermillet-associated microbial consortia provides insights into structural and functional diversity of endophytes – M. K. Prasannakumari – 3 Biotech 

Resilience to multiple stressors in an aquatic plant and its microbiome – Anna M. O’Brien – American Journal of Botany

 

Techniques

Scalable and cost-effective ribonuclease-based rRNA depletion for transcriptomics – Yiming Huang – Nucleic Acids Research

December 18, 2019

Good morning/afternoon all microbiome lovers!

Coming back from 4th Thunen Sumposium on Soil Metagenomics (11-13.12, Germany), the first section of today’s digest will highlight some work emphasized during the conference. Pay special attention to Amy Willis work (UoW) dealing with amplification bias in 16S analyses, among else. You are more than welcome to check the conference and the bioinformatic workshops schedule, as you’ll find interesting, inspiring and useful studies and tools that are relevant even if you’re not working on soil-associated habitats.

Have a great day!

Soil Metagenomics insights

Rigorous Statistical Methods for Rigorous Microbiome Science, Amy Willis, mSystems. I highly recommended to be familiar with the Willis lab works and tools, for all of us working with amplicon-sequencing and metagenomics. Amy was kind enough to upload her conference materials to github, using this link.

Additionally, They just started a bio-statistics blog, so check this as well.

Consistent and correctable bias in metagenomic sequencing experiments, Michael R. McLaren, bioRxiv

Understanding and interpreting community sequencing measurements of the vaginal microbiome, HL Berman, BJOG

These two papers are from Benjamin Callahan group (NCSW). Even though he wasn’t at the conference, his work (et al.) were mentioned several times by other speakers, so I decided to emphasize these two papers.

The MG-RAST API explorer: an on-ramp for RESTful query composition, Tobias Paczian, BMC Bioinformatics. Folker Meyer, one of the developers of MG-RAST and its head, was actually at the conference with a great talk about both MG-RAST and the importance of pipelines and common workflow language in computational biology. Check this link and the MG-RAST API explorer, making it so much simpler to search, filter and efficiently use MG-RAST.

TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes, Felipe B Correa, bioRxiv. An amazing tool for searching and filtering soil-associated metagenomes in different databases, plus simple codes for downloading. Take a look at more papers from the de-Rocha group.

Human microbiomoe

**Molecular messages in human microbiota, Matthew T. Henke and Jon Clardy, Science

Resident microbes of lactation rooms and daycares, Diana H. Taft, PeerJ

Female genital tract microbiota affecting the risk of preterm birth: What do we know so far? A Review, O. Tsonis, European J OBG & Reproductive Biology

Differences in Fecal Microbiomes and Metabolomes of People With vs Without Irritable Bowel Syndrome and Bile Acid Malabsorption, Ian B. Jeffery, Gastroenterology

Soil and Plant microbiome

Comparison of Microbial Community of Rhizosphere and Endosphere in Kiwifruit, Min-Jung Kim, Plant Patho J.

Soil microbial communities in diverse agroecosystems exposed to the herbicide glyphosate, Ryan M. Kepler, AEM

Soil exposed to silver nanoparticles reveals significant changes in community structure and altered microbial transcriptional profiles, Matthew J. Meier, Env. Pollution

Animal microbiome

Effects of disease, antibiotic treatment and recovery trajectory on the microbiome of farmed seabass (Dicentrarchus labrax), Danila Rosado, Scientific Reports

December 16, 2019

Good Morning! This Monday’s digest includes research papers investigating microbiomes of nearly sterile sites, respiratory tract, oral cavity, gastric fluid and many with animal experiments and animal microbiomes. A review about gut microbiota and depression is also included. Happy readings!

General microbiome
Essay: Framing the discussion of microorganisms as a facet of social equity in human health – Ishaq et al. – PLOS ONE

Human respiratory microbiome
Airway microbiome composition correlates with lung function and arterial stiffness in an age-dependent manner – Lee et al. – PLOS ONE

Dysbiosis of lower respiratory tract microbiome are associated with inflammation and microbial function variety – Li et al. – BMC Respiratory Research

Human oral microbiome
Oral Microbiota Composition and Antimicrobial Antibody Response in Patients with Recurrent Aphthous Stomatitis – Stehlikova et al. – MDPI Microorganisms

Human nearly-sterile sites
Molecular characterisation of the synovial fluid microbiome in rheumatoid arthritis patients and healthy control subjects – Mohsen Hammad et al. – PLOS ONE

Human gut microbiome
Helicobacter pylori antibody and pepsinogen testing for predicting gastric microbiome abundance – Choi et al. – PLOS ONE

Review: Gut‐microbiota‐brain axis in depression: The role of neuroinflammation – Carlessi et al. – European Journal of Neuroscience

Animal experiments
Effects of treatment with enrofloxacin or tulathromycin on fecal microbiota composition and genetic function of dairy calves – Foditsch et al. – PLOS ONE

Long-term high-grain diet altered the ruminal pH, fermentation, and composition and functions of the rumen bacterial community, leading to enhanced lactic acid production in Japanese Black beef cattle during fattening – Ogata et al. – PLOS ONE

CRISPR/Cas9-mediated gene deletion of the ompA gene in symbiotic Cedecea neteri impairs biofilm formation and reduces gut colonization of Aedes aegypti mosquitoes – Hegde et al. – PLOS ONE

Examining transmission of gut bacteria to preserved carcass via anal secretions in Nicrophorus defodiens – Miller et al. – PLOS ONE

Animal microbiome
California condor microbiomes: Bacterial variety and functional properties in captive-bred individuals – Jacobs et al. – PLOS ONE

Composition and structure of the culturable gut bacterial communities in Anopheles albimanus from Colombia – Galeano-Castaneda et al. – PLOS ONE

Estimating the degree to which distance and temperature differences drive changes in fish community composition over time in the upper Mississippi River – Larson et al. – PLOS ONE

Food microbiology
Resistome metagenomics from plate to farm: The resistome and microbial composition during food waste feeding and composting on a Vermont poultry farm – Eckstrom et al. – PLOS ONE

Bioturbation effect of fortified Daqu on microbial community and flavor metabolite in Chinese strong-flavor liquor brewing microecosystem – He et al. – Food Research International

Bioinformatics
Biomarker discovery in inflammatory bowel diseases using network-based feature selection – Abbas et al. – PLOS ONE

Techniques
Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing – Srivathsan et al. – BMC Biology

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