December 23, 2019

In today’s digest read about the subway microbiome (from surface and air samples collected at 16 subway stations in Oslo, Norway), role of Staphylococcus epidermidis in healthy maturation of the nasal microbiome, effect of storage and time on urinary microbiome, and more. Happy Holidays!

General microbiome

The emergence of microbiome centres – Jennifer B. H. Martiny – Nature Microbiology

Subway microbiome

*The subway microbiome: seasonal dynamics and direct comparison of air and surface bacterial communities– Jostein Gohli – Microbiome

Gut microbiome

Engineered E. coli Nissle 1917 for the delivery of matrix-tethered therapeutic domains to the gut– Pichet Praveschotinunt – Nature Communications

Urinary microbiome

*The urinary microbiota composition remains stable over time and under various storage conditions – Caspar Bundgaard-Nielsen – bioRxiv

Vaginal microbiome

Review: Genetic Heterogeneity and Taxonomic Diversity among Gardnerella Species – Joana Castro – Trends in Microbiology

Nasal microbiome

*Staphylococcus epidermidis Contributes to Healthy Maturation of the Nasal Microbiome by Stimulating Antimicrobial Peptide Production – Qian Liu – Cell Host & Microbes

Animal microbiome

Characterization of the Pig Gut Microbiome and Antibiotic Resistome in Industrialized Feedlots in China – Chunlai Wang – mSystems

Animal experiments

Altered microbiota composition reflects enhanced communication in 15q11-13 CNV mice– Dian Eurike Septyaningtrias – Neuroscience Research

Plant/root/soil microbiome

Time after Time: Temporal Variation in the Effects of Grass and Forb Species on Soil Bacterial and Fungal Communities – S. Emilia Hannula – mBio

Habitat filtering shapes the differential structure of microbial communities in the Xilingol grassland– Jie Yang – Scientific Reports

Water microbiome

Metagenomic Insights into the Effects of Seasonal Temperature Variation on the Activities of Activated Sludge– Chenbing Ai – Microorganisms

Viruses

Plant virome reconstruction and antiviral RNAi characterization by deep sequencing of small RNAs from dried leaves – Victor Golyaev – Scientific Reports

Bioinformatics

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise – Valentina Peona – bioRxiv

Transcriptome assembly from long-read RNA-seq alignments with StringTie2– Sam Kovaka – Genome Biology

Deconvoluting the diversity of within-host pathogen strains in a multi-locus sequence typing framework – Guo Liang Gan – BMC Bioinformatics

The Generalized Matrix Decomposition Biplot and Its Application to Microbiome Data – Yue Wang – mSystems

December 20, 2019

This may be our last edition of the Microbiome Digest before the holidays kick in. A rich and dynamic Digest brings you all things microbiome (apologies for the tight formatting). An encouraging report on how we can reduce antimicrobial resistance organically, an amazing recovery of a human genome and an oral microbiome from chewed birch pitch thousands of years ago, and a network analysis reveals four levels of hierarchical trophic interactions in the human gut microbiome. Enjoy Reading and Happy Holidays!
Events
BMC Medicine’s upcoming collection, New Frontiers in Diagnosis, Treatment and Management of Neuromuscular Disorders, is soliciting submissions.
Current Issue of The ISME Journal
The 9th Gut Microbiota for Health World Summit – March 7 and 8 2020 in Madrid, Spain
General microbiology
High-order interactions distort the functional landscape of microbial consortia – Sanchez-Gorostiaga & Bajić et al. – PLoS Biology
Antimicrobial resistance
Human skin microbiome
Human oral microbiome
** A 5700 year-old human genome and oral microbiome from chewed birch pitch – Theis Z. T. Jensen et al. – Nature Communications
Press: Ancient “Chewing Gum” Reveals a 5,700-Year-Old Microbiome – Jim Daley – Scientific American
Human respiratory microbiome
Press: Child asthma flare-ups coincide with microbiome changes – JULIA EVANGELOU STRAIT-WUSTL – Futurity
Human gut microbiome
Human vaginal microbiome
Human gut-microbiota-brain axis
Review: Tryptophan Metabolism: A Link Between the Gut Microbiota and Brain – Kan Gao et al. – Advances in Nutrition
Cancer microbiome
Metabolomics
The total microbiome functions in bacteria and fungi – Robert Starke et al. – Journal of Proteomics
Animal experiments
Animal microbiome
Plant, root and soil microbiome
Root microbiomes as indicators of seagrass health – Belinda C Martin et al. – FEMS Microbiology Ecology
Water and extremophile microbiome
Phages and viruses
Technology
Manipulating rod-shaped bacteria with optical tweezers – Zheng Zhang et al. – Scientific Reports
Bioinformatics
** Evidence for a multi-level trophic organization of the human gut microbiome – Tong Wang et al. – PLoS Computational Biology
Microbes in the news
The microbiome is fundamental to both health and disease – Fabian Brockotter – Poultry World
Low FODMAP Diet Helps IDB Patients – Kenny Walter – MDMAG
Oral Health: Caring for the Other Microbiome – Julia Peterman – Whole Foods Magazine
Non-microbiology pick

 

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

December 6, 2019

Today’s post is about metabolic networks of the human gut microbiota with host, how aging affects microbial world in humans, microbiome in honey bee and lifestyle dependent gut microbiota gradients in diverse Indian population. Have a nice weekend!

General microbiome

Review: Metabolic networks of the human gut microbiota – Susannah Selber-Hnatiw – Microbiology

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 Unexplored World of Human Virome, Mycobiome, and Archaeome in Aging – Oscar Salvador Barrera-Vázquez – Journal of Gerontology

Review: Nanotechnology intervention of the microbiome for cancer therapy – Wantong Song – Nature Nanotechnology

Commentary: Gut microbiome influences exercise response – Claire Greenhill – Nature Reviews Endocrinology

Human microbiome

Bacterial DNA induces the formation of heat-resistant disease-associated proteins in human plasma – Victor Tetz – Scientific Reports

Lifestyle induced microbial gradients: An Indian perspective – Rashmi Singh – Frontiers in Microbiology

Microbiota, type 2 diabetes and non-alcoholic fatty liver disease: protocol of an observational study – Benedetta M. Motta – Journal of Translational Medicine

Antibiotic exposure and the risk of colorectal adenoma and carcinoma: systematic review and meta‐analysis of observational studies – Leigh N. Sanyaolu – Colorectal Disease

Higher frequency of vertebrate‐infecting viruses in the gut of infants born to mothers with type 1 diabetes – Ki Wook Kim – Pediatric Diabetes

Animal experiments

Integrative analysis of the gut microbiota and metabolome in rats treated with rice straw biochar by 16S rRNA gene sequencing and LC/MS-based metabolomics – Jie Han – Scientific Reports

Division of labor in honey bee gut microbiota for plant polysaccharide digestion – Hao Zheng – PNAS

The effect of carbohydrate sources: Sucrose, invert sugar and components of mānuka honey, on core bacteria in the digestive tract of adult honey bees (Apis mellifera) – Michelle A. Taylor – PlosOne

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

Cattle intestinal microbiota shifts following Escherichia coli O157:H7 vaccination and colonization travel – Raies A. Mir – PlosOne

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

SOD1 deficiency alters gastrointestinal microbiota and metabolites in mice – Haruka Sagi – Experimental Gerontology

Plant, soil, root microbiome

Host-mediated microbiome engineering (HMME) of drought tolerance in the wheat rhizosphere – Michael D. Jochum – PlosOne

Arctic tundra soil bacterial communities active at subzero temperatures detected by stable isotope probing – Preshita S. Gadkari – FEMS Microbiology Ecology

Techniques

Comparison of extraction methods for recovering ancient microbial DNA from paleofeces – Richard W. Hagan – American Journal of Physical Anthropology

Microbes in the news

How Microbiomes Affect Fear – Quanta Magazine

Rainforest Dwellers and Urbanites Have Consistently Different Microbiomes – Scientific American

Human Microbiome Modulators Market is Furbishing worldwide with Bayer, BioGaia, Chr. Hansen Holding, DowDuPont – News Description