October 16, 2019

Happy Wednesday! Today’s digest includes the human gut virome, microbiome recovery after antibiotics, and the fungi growing on museum skeletons. Enjoy!

Pregnancy and early life

The vaginal microbial communities of healthy expectant Brazilian mothers and its correlation with the newborn’s gut colonization – Dobbler – World Journal of Microbiology and Biotechnology

Human skin microbiome

In vitro Antimicrobial Activity of Acne Drugs Against Skin-Associated Bacteria – Blaskovich – Scientific Reports

Human gut microbiome

Review: The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific – Shkoporov – Cell Host & Microbe

Review: Inflammatory Bowel Disease: A Potential Result from the Collusion between Gut Microbiota and Mucosal Immune System – Yue – Microorganisms

Individualized recovery of gut microbial strains post antibiotics – Koo – npj Biofilms and Microbiomes

Animal experiments

Depletion of dietary aryl hydrocarbon receptor ligands alters microbiota composition and function – Brawner – Scientific Reports

Rat H1 parvovirus infection leads to alterations in gut microbiota – Xiang – Pathogens and Disease

Positive effect of an electrolyzed reduced water on gut permeability, fecal microbiota and liver in an animal model of Parkinson’s disease – Bordoni – PLoS One

The Sulfate-Reducing Microbial Communities and Meta-Analysis of Their Occurrence during Diseases of Small–Large Intestine Axis – Kushkevych – Journal of Clinical Medicine

Plant, root, and soil microbiome

Spatial gradients in the characteristics of soil-carbon fractions are associated with abiotic features but not microbial communities – Sengupta – Biogeosciences

Water and extremophile microbiome

Diversity, Distribution, and Ecology of Fungi in the Seasonal Snow of Antarctica – Menezes – Microorganisms

Interaction and assembly processes of abundant and rare microbial communities during a diatom bloom process – Zhang – Environmental Microbiology

Built environment

Changes in the Bacterioplankton Community Structure from Southern Gulf of Mexico During a Simulated Crude Oil Spill at Mesocosm Scale – Valencia-Agami – Microorganisms

Increased loading leads to convergence of microbial communities and high methane yield in adapted anaerobic co-digesters – Wang – Water Research

Skeleton bones in museum indoor environments offer niches for fungi and are affected by weathering and deposition of secondary minerals – Pinzari – Environmental Microbiology

Bioinformatics

Species abundance information improves sequence taxonomy classification accuracy – Kaehler – Nature Communications

October 5, 2019

This weekend, read about how cooking food modifies the microbiome, how bacteria ‘strip off’ to evade antibiotics, and more. Check out an interesting pilot study looking at potential inclusion and exclusion criteria of donors for safe vaginal microbiota transplant. Enjoy!

Events

Bioinformatics for the Microbiome Symposium 2019, Stanford University, Monday October 28.
Some tickets are still available!

General microbiome

Mobile phones as fomites for potential pathogens in hospitals: microbiome analysis reveals hidden contaminants – Rebecca Simmonds – Journal of Hospital Infection

Review: Microbiomes as sources of emergent host phenotypes – J. B. Lynch and E. Y. Hsiao – Science

Vaginal microbiome

*Conceptual Design of a Universal Donor Screening Approach for Vaginal Microbiota Transplant – Kevin DeLong – Frontiers in Cellular and Infection Microbiology

Highly diverse anaerobe-predominant vaginal microbiota among HIV-infected pregnant women in Zambia – Joan T. Price – PlosOne

Urinary microbiome

*Possible role of L-form switching in recurrent urinary tract infection – Katarzyna M. Mickiewicz – Nature Communications

Aerococcus urinae and Globicatella sanguinis Persist in Polymicrobial Urethral Catheter Biofilms Examined in Longitudinal Profiles at the Proteomic Level – Yanbao Yu – Biochemistry Insights

Gut microbiome

*Cooking shapes the structure and function of the gut microbiome – Rachel N. Carmody – Nature Microbiology

Integrated paired-end enhancer profiling and whole-genome sequencing reveals recurrent CCNE1 and IGF2 enhancer hijacking in primary gastric adenocarcinoma – Wen Fong Ooi – Gut

Effects of Low-FODMAP Diet on Symptoms, Fecal Microbiome, and Markers of Inflammation in Patients With Quiescent Inflammatory Bowel Disease in a Randomized Trial – Selina R.Cox – Gastroenterology

Water microbiome

Trophic networks improve the performance of microbial anodes treating wastewater – Christin Koch – npj Biofilms and Microbiomes

Application of a novel molecular technique to characterise the effect of settling on microbial community composition of activated sludge – Luong N.Nguyen – Journal of Environmental Management

Bacterial diversity in Icelandic cold spring sources and in relation to the groundwater amphipod Crangonyx islandicus – Ragnhildur Guðmundsdóttir – PlosOne

Animal microbiome

Looking like the locals – gut microbiome changes post-release in an endangered species – Rowena Chong – Animal microbiome

Animal experiment

Letrozole treatment of pubertal female mice results in activational effects on reproduction, metabolism and the gut microbiome – Pablo Arroyo – PlosOne

Microbiota of MR1 deficient mice confer resistance against Clostridium difficile infection – Ashley D. Smith – PlosOne

Exploring the microbiota of upper respiratory tract during the development of pneumonia in a mouse model – Yoshitomo Morinaga – PlosOne

Plant microbiome

Microbiome profiling of the onion thrips, Thrips tabaci Lindeman (Thysanoptera: Thripidae) – Suresh J. Gawande – PlosOne

Food

Comparison of the microbial composition of African fermented foods using amplicon sequencing – Maria Diaz – Scientific Reports

The impact of grape processing and carbonic maceration on the microbiota of early stages of winemaking – Raffaele Guzzon – Journal of Applied Microbiology

Fungi

Phyllosphere Fungal Communities of Plum and Antifungal Activity of Indigenous Phenazine-Producing Pseudomonas synxantha Against Monilinia laxa – Tamara Janakiev – Frontiers in Microbiology

Microbial communities associated with the black morel Morchella sextelata cultivated in greenhouses – Gian Maria Niccolò Benucci – PeerJ

Viruses

The gut virome in inflammatory bowel disease pathogenesis: From metagenomics to novel therapeutic approaches – Federica Ungaro – United European Gastroenterology Journal

Association of the Eukaryotic Vaginal Virome with Prophylactic Antibiotic Exposure and Reproductive Outcomes in a Subfertile Population Undergoing In Vitro Fertilization: A Prospective Exploratory Study – Ashley M. Eskew – Obstetrics and Gynaecology

Bioinformatics

ProphET, prophage estimation tool: A stand-alone prophage sequence prediction tool with self-updating reference database – João L. Reis-Cunha – PlosOne

September 23, 2019

This Monday, check out the largest ever study of neonatal microbiomes, the study where researchers alter mouse gut microbiomes by feeding good bacteria their preferred fibers, and the study about the significant effect of antibiotics, antivirals and cofactors on the gut microbiome. Happy reading!

Pregnancy and early life

*Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth – Yan Shao – Nature

Gut microbiome

*Interspecies Competition Impacts Targeted Manipulation of Human Gut Bacteria by Fiber-Derived Glycans – Michael Patnode – Cell

*Distinct impact of antibiotics on the gut microbiome and resistome: a longitudinal multicenter cohort study – Matthias Willmann – BMC Biology

Identification of gut microbiome markers for schizophrenia delineates a potential role of Streptococcus – Feng Zhu – bioRxiv

Fecal Microbiotas of Indonesian and New Zealand Children Differ in Complexity and Bifidobacterial Taxa during the First Year of Life – Blair Lawley – Applied and Environmental Microbiology

Light-entrained and brain-tuned circadian circuits regulate ILC3s and gut homeostasis – Cristina Godinho-Silva – Nature

Baseline human gut microbiota profile in healthy people and standard reporting template – Charles H. King – PlosOne

Oral microbiome

Taste perception and oral microbiota are associated with obesity in children and adolescents – Chiara Mameli – PlosOne

Urinary microbiome

The urobiome of continent adult women: a cross-sectional study – Travis Price – Obstetrics & Gynaecology

The Urinary Microbiota in Relation to the Reproductive Tract Microbiota – Fei Li – bioRxiv

Respiratory microbiome

The effects of e-cigarette vapor exposure on the transcriptome and virulence of Streptococcus pneumoniae – Kamal Bagale – bioRxiv

Water microbiome

Diversity patterns of marine heterotrophic culturable bacteria along vertical and latitudinal gradients – Isabel Sanz-Sáez – bioRxiv

Laundry wastewater and domestic sewage pilot-scale anaerobic treatment: Microbial community resilience regarding sulfide production – A.G.L. Moura – Journal of Environmental Management

Distinct responses from bacterial, archaeal and fungal streambed communities to severe hydrological disturbances – G. Gionchetta – Scientific reports

Metagenome of a polluted river reveals a reservoir of metabolic and antibiotic resistance genes – Parul Mittal – Environmental Microbiome

Plant/root/soil microbiome

Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root Microbiome – Xiaoxuan Guo – Plant Communications

Metatranscriptomics reveals climate change effects on the rhizosphere microbiomes in European grassland – Qicheng Bei – Soil Biology and Biochemistry

Phages and viruses

Beyond cells – The virome in the human holobiont – Rodrigo García-López – Microbial cells

ViraMiner: Deep learning on raw DNA sequences for identifying viral genomes in human samples – Ardi Tampu – PlosOne

Bioinformatics

Review: The signal and the noise – characteristics of antisense RNA in complex microbial communities – Thomas Yssing Michaelsen – bioRxiv

SuRF: a New Method for Sparse Variable Selection, with Application in Microbiome Data Analysis – Lihui Liu – arXiv

September 3, 2019

Happy Tuesday and best of luck to those headed back to school! In today’s Digest, you’ll find the virome of the mosquito gut, leveraging blood metabolomics to predict gut alpha diversity, and a comparison of bacterial taxa consumed in organic vs. conventional apples.

General microbiome
Changes in microbial community structure during dark fermentative hydrogen production – Guang Yang – International Journal of Hydrogen Energy

Pregnancy and early life
Effect of the vaginal microbiome on the pregnancy rate in women receiving assisted reproductive treatment – Andrea Bernabeu – Journal of Assisted Reproduction and Genetics

Maturation of the infant rhesus macaque gut microbiome and its role in the development of diarrheal disease – Nicholas Rhoades – Genome Biology

Human gut microbiome
Blood metabolome predicts gut microbiome α-diversity in humans – Nature Biotechnology – Tomasz Wilmanski

B cell superantigens in the human intestinal microbiota – Jeffrey J. Bunker – Science Translational Medicine

Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut – Yoshihiko Suzuki – Microbiome

Microbiome of death
Preprint: Manner of death and demographic effects on microbial community composition in organs of the human cadaver – Holly L Lutz – bioRxiv

Animal experiments
Diet-induced remission in chronic enteropathy is associated with altered microbial community structure and synthesis of secondary bile acids – Shuai Wang – Microbiome

Animal microbiome
Testing the relationship between microbiome composition and flux of carbon and nutrients in Caribbean coral reef sponges – Shelby E. Gantt – Microbiome

Plant, root, and soil microbiome
A new family of uncultivated bacteria involved in methanogenesis from the ubiquitous osmolyte glycine betaine in coastal saltmarsh sediments – Helen J. Jones – Microbiome

Top-down Enrichment Guides in Formation of Synthetic Microbial Consortia for Biomass Degradation – Sean P. Gilmore – ACS Synthetic Biology

Microbial community response to environmental changes in a technosol historically contaminated by the burning of chemical ammunitions – Hugues Thouin – Science of the Total Environment

Preprint: Intra-genus metabolic diversity facilitates co-occurrence of multiple Ferrovum species at an acid mine drainage site – Christen L Grettenberger – bioRxiv

Water and extremophile microbiome
Exploring the effects of operational mode and microbial interactions on bacterial community assembly in a one-stage partial-nitritation anammox reactor using integrated multi-omics – Yulin Wang – Microbiome

Fungi in salterns – Dawoon Chung – Journal of Microbiology

Distinct temporal dynamics of planktonic archaeal and bacterial assemblages in the bays of the Yellow Sea – Jong-Geol Kim – Plos One

Food microbiology
An Apple a Day: Which Bacteria Do We Eat With Organic and Conventional Apples? – Birgit Wassermann – Frontiers in Microbiology

Preprint: Molecular characterization of bacterial communities in sheep cheese through 16S rRNA gene sequencing – Creciana Maria Endres – bioRxiv

Phages and viruses
Stable distinct core eukaryotic viromes in different mosquito species from Guadeloupe, using single mosquito viral metagenomics – Chenyan Shi – Microbiome

The virome of cerebrospinal fluid: viruses where we once thought there were none – Chandrabali Ghose – Frontiers in Microbiology

Detecting viral sequences in NGS data – Paul G. Cantalupo – Current Opinion in Virology

Bioinformatics
Identification of discriminatory antibiotic resistance genes among environmental resistomes using extremely randomized tree algorithm – Suraj Gupta – Microbiome

August 28, 2019

Today’s digest features interesting review articles about different aspects of human gut microbiome,  metaproteomics approach in microbiota, new study to tackle antibiotic resistance and updates on microbiome business.

General Microbiome

The long-term consequences of antibiotic therapy: Role of colonic short-chain fatty acids (SCFA) system and intestinal barrier integrity – Yuliia Holota – Plos One

Factors affecting the composition of the gut microbiota, and its modulation – Nihal Hasan – Peer Journal

The Microbiota and Malnutrition: Impact of Nutritional Status During Early Life – Carlos Gómez-Gallego – Annual review of Nutrition

The necessity to revise Koch’s postulates and its application to infectious and non-infectious diseases: a mini-review – Hasan Hosainzadegan – European Journal of Clinical Microbiology & Infectious Diseases

Pancreas–Microbiota Cross Talk in Health and Disease – Timon E. Adolph – Annual Review of Nutrition

Does Soil Contribute to the Human Gut Microbiome? – Winfried E.H. Blum – Microorganisms

Impact of the Microbiome on the Human Genome – Thiviya Jeyakumar – Trends in Parasitology

Problems with the concept of gut microbiota dysbiosis – Harald Brüssow – Microbial Biotechnology

Human microbiome

Lactulose Improves Cognition, Quality of Life and Gut Microbiota in Minimal Hepatic Encephalopathy: A Multi‐Center, Randomized Controlled Trial – Ji Yao Wang – Journal of Digestive Diseases

Microbial Profiles of Cirrhosis in the Human Small Intestine – Tien S. Dong – Current Gastroenterology Reports

Crosstalk between vaginal microbiome and female health: A review – Shagun Gupta – Microbial Pathogenesis

Animal experiments

Metformin and Dipeptidase Peptidyl-4 Inhibitor Differentially Modulate the Intestinal Microbiota and Plasma Metabolome of Metabolically Dysfunctional Mice – Ryan PM – Canadian Journal of Diabetes

The gut microbiome derived from anorexia nervosa patients impairs weight gain and behavioral performance in female mice – Tomokazu Hata – Endocrinology

Microbiota-derived lantibiotic restores resistance against vancomycin-resistant Enterococcus – Sohn G. Kim – Nature

Probiotics and prebiotics 

Developments in understanding and applying prebiotics in research and practice – an ISAPP conference paper – Karen P Scott – Journal of Applied Microbiology

Techniques

An automated ‘cells-to-peptides’ sample preparation workflow for high-throughput, quantitative proteomic assays of microbes – Yan Chen – Journal of Proteome Research

Comparison of metaproteomics workflows for deciphering the functions of gut microbiota in an animal model of obesity – Maria Guirro – Journal of Proteomics

An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data – Chenhao Li – Microbiome

Microbes in the news

‘A holistic approach’: EU-backed project taps microbiome to optimise food production – Food navigator.com

Remodeling unhealthful gut microbiomes to fight disease – Science daily

The microbiome and the effect of antimicrobials in food production – New Food

Researchers propose new technique to remodel the gut microbiome – News Atlas

Microbes and the market

Global Human Microbiome Market 2019 Research Analysis of Players:- Merck, DuPont, MicroBiome Therapeutics, Osel – Global Market News 24

Microbiome Sequencing Market Forecast by Biolog Inc., CosmosID Inc., Illumina Inc., Metabiomics and Oxford Nanopore Technologies Ltd to 2024 – SocioHerald

 

August 24, 2019

This weekend, read about the microbial index of skin health for children with eczema, gut microbiome of koalas, and interactions between the gut bacterial microbiome and virome of rhesus monkey. Happy reading!

General microbiome

Why we need a small data paradigm – Eric B. Hekler – BMC Medicine

Correspondence: The importance of genome sequence quality to microbial comparative genomics – Theo H. M. Smits – BMC Genomics

The applications of Big Data in molecular diagnostics – Yin Kwan Evelyn Wong – Expert Review of Molecular Diagnostics

Tiny Hidden Genes within Our Microbiome – Karin Mittelman & David Burstein – Cell

Skin microbiome

*A Microbiome-Based Index for Assessing Skin Health and Treatment Effects for Atopic Dermatitis in Children – Zheng Sun – mSystems

Gut microbiome

Reproducible changes in the gut microbiome suggest a shift in microbial and host metabolism during spaceflight – Peng Jiang – Microbiome

Review: Gut Microbiota, Dietary Phytochemicals, and Benefits to Human Health – Ran Yin – Current Pharmacology Reports

Mild cognitive impairment has similar alterations as Alzheimer’s disease in gut microbiota – Binyin Li – Alzheimer’s & Dementia

Design of synthetic microbial consortia for gut microbiota modulation – Jorge F. Vázquez-Castellanos – Current Opinion in Pharmacology

Intestinal microbiota and colorectal cancer: changes in the intestinal microenvironment and their relation to the disease – Sandra Aparecida dos Reis – Journal of Medical Microbiology

Review: Celiac disease: a comprehensive current review – Giacomo Caio – BMC Medicine

Pregnancy and early life

Maternal IgA protects against the development of necrotizing enterocolitis in preterm infants – Kathyayini P. Gopalakrishna – Nature Medicine

Oral microbiome

Oral Microbiome and Cancer Therapy-Induced Oral Mucositis – Jean-Luc C Mougeot – JNCI Monographs

Respiratory microbiome

Deciphering the Ecology of Cystic Fibrosis Bacterial Communities: Towards Systems-Level Integration – Annamaria Bevivino – Trends in Molecular Medicine

Water and extremophile microbiome

Effects of water recirculation rate on the microbial community and water quality in relation to the growth and survival of white shrimp (Litopenaeus vannamei) – Zhao Chen – BMC Microbiology

Pseudomethylobacillus aquaticus gen. nov., sp. nov., a new member of the family Methylophilaceae isolated from an artificial reservoir – Ceshing Sheu – International Journal of Systematic and Evolutionary Microbiology

Bacterial Communities from Extreme Environments: Vulcano Island – Camilla Fagorzi – Diversity

Diversity and biogeography of SAR11 bacteria from the Arctic Ocean – Susanne Kraemer – bioRxiv

Review: Metal and organic pollutants bioremediation by extremophile microorganisms – Patricia Giovanella – Journal of Hazardous Material

Animal microbiome

*Faecal inoculations alter the gastrointestinal microbiome and allow dietary expansion in a wild specialist herbivore, the koala – Michaela D. J. Blyton – Animal microbiome

Impact of pine leaf biochar amendment on bacterial dynamics and correlation of environmental factors during pig manure composting – Jiao Li – Bioresource Technology

Animal experiment

Potential roles of gut microbiome and metabolites in modulating ALS in mice – Eran Blacher – Nature

Plant microbiome

Shared mycorrhizae but distinct communities of other root-associated microbes on co-occurring native and invasive maples – Tonia DeBellis – PeerJ

Non-target Effects of Trichoderma on Plants and Soil Microbial Communities – Monika Jangi – Plant Microbe Interface

Inhibitory and nutrient use phenotypes among co‐existing Fusarium and Streptomyces populations suggest local coevolutionary interactions in soil – Adil Essarioui – Environmental Microbiology

Phages and viruses

*The altered gut virome community in rhesus monkeys is correlated with the gut bacterial microbiome and associated metabolites – Heng Li – Virology Journal

August 19, 2019

Monday’s digest is about microbiota as biomarker in diverse human diseases such as alopecia areata and bladder cancer, how arabinoxylan and grape pomace affects microbiota in rodents and microbial characterization of multi-strain probiotic VSL3 .

General microbiome

What Pediatricians Should Know Before Studying Gut Microbiota – Lorenzo Drago – Journal of Clinical Medicine

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

Human microbiome

The sex-specific interaction of the microbiome in neurodegenerative diseases – Laura M. Cox – Brain Research

Analysis of the gut microbiota in alopecia areata: identification of bacterial biomarkers – Oscar M. Moreno-Arrenos – Journal of the European Academy of Dermatology and Venereology

The dynamics of the oral microbiome and oral health among patients receiving clear aligner orthodontic treatment – Rui Zhao – Oral Diseases

Urinary microbiota – a potential biomarker and therapeutic target for bladder cancer – Hai Bi – Journal of Medical Microbiology

Animal experiments

Effect of arabinoxylan on colonic bacterial metabolites and mucosal barrier in high‐fat diet‐induced rats – Shanshan Li – Food Science and Nutrition

The Signature Microbiota Driving Rumen Function Shifts in Goat Kids Introduced Solid Diet Regimes – Xiaokang Lv – BioRxiv

Effects of grape pomace and seed polyphenol extracts on the recovery of gut microbiota after antibiotic treatment in high‐fat diet‐fed mice – Feng Lu – Food Science and Nutrition

Microbiota-driven gut vascular barrier disruption is a prerequisite for non-alcoholic steatohepatitis development – Juliette Mouries – Journal of Hepatology

Identification of rumen microbial biomarkers linked to methane emission in Holstein dairy cows – Yuliaxis Ramayo‐Caldas – Journal of Animal Breeding and Genetics

The gastrointestinal fate of limonin and its effect on gut microbiota in mice – Min Gu – Food and Function

Plant, root, soil microbiome

Environmental pollution effects on plant microbiota: the case study of poplar bacterial-fungal response to silver nanoparticles – Francesco Vitali – Applied Microbiology and Biotechnology

Salinity-induced changes in the rhizosphere microbiome improve salt tolerance of Hibiscus hamabo – Yongge Yuan – Plant and Soil

Water and extremophile microbiome

Metagenomic characterization of creek sediment microbial communities from a major agricultural region in Salinas, California – Brittany J. Suttner – BioRxiv

Probiotics

Development of omics-based protocols for the microbiological characterization of multi-strain formulations marketed as probiotics: the case of VSL#3 – Diego Mora – Microbial Biotechnology

Fecal microbiome and metabolome of infants fed bovine MFGM supplemented formula or standard formula with breast-fed infants as reference: a randomized controlled trial – Xuan He – Scientific Reports

Probiotic L. gasseri strain (LG21) for the upper gastrointestinal tract acting through improvement of indigenous microbiota – Yasuhiro Koga – BMJ Open Gastroenterology

Non Microbiology Picks

First cells may have emerged because building blocks of proteins stabilized membranes – Science Daily