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

Advertisements

August 20, 2019

Today’s digest includes the gut microbiome of sea turtles, microbes on a guyot in the Pacific Ocean, and a review of microbiome animal models. Enjoy!

General microbiome

Review: Simple animal models for microbiome research – Douglas – Nature Reviews Microbiology

Review: An Ecological Loop: Host Microbiomes across Multitrophic Interactions – Liu – Trends in Ecology & Evolution

Review: The antibody/microbiota interface in health and disease – Sterlin – Mucosal Immunology

Pregnancy and early life

Early-life gut microbiome modulation reduces the abundance of antibiotic-resistant bacteria – Casaburi – Antimicrobial Resistance & Infection Control

Human skin microbiome

The prevalence of the culturable human skin aerobic bacteria in Riyadh, Saudi Arabia – Shami – BMC Microbiology

Animal experiments

Oral Administration of Clinically Relevant Antimalarial Drugs Does Not Modify the Murine Gut Microbiota – Denny & Schmidt – Scientific Reports

Animal microbiome

New insights into the gut microbiome in loggerhead sea turtles Caretta caretta stranded on the Mediterranean coast – Arizza – PLoS One

Outcomes of a low birth weight phenotype on piglet gut microbial composition and intestinal transcriptomic profile – Fouhse – Canadian Journal of Animal Science

Plant, root, and soil microbiome

Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia – Pérez-Jaramillo – Microbiome

Preprint: Exploring the microbial diversity in oil-contaminated mangrove sediments using 16S rRNA metagenomics – Ghanbari – BioRxiv

Plant-microorganisms interaction promotes removal of air pollutants in Milan (Italy) urban area – Franzetti – Journal of Hazardous Materials

Effects of natural vegetative restoration on soil fungal and bacterial communities in bare patches of the southern Taihang Mountains – Zhao – Ecology and Evolution

Water and extremophile microbiome

The differentiation of iron-reducing bacterial community and iron-reduction activity between riverine and marine sediments in the Yellow River estuary – Zhang – Marine Life Science & Technology

Bacterial Community on a Guyot in the Northwest Pacific Ocean Influenced by Physical Dynamics and Environmental Variables – Liu – JGR: Biogeosciences

Microdiversity ensures the maintenance of functional microbial communities under changing environmental conditions – García-García – ISME

Built environment

Seasonal diversity of the bacterial communities associated with petroglyphs sites from the Negev Desert, Israel – Nir – Annals of Microbiology

Antibiotic fermentation residue for biohydrogen production using different pretreated cultures: Performance evaluation and microbial community analysis – Yang – Bioresource Technology

Bioinformatics

Metagenomic approaches: effective tools for monitoring the structure and functionality of microbiomes in anaerobic digestion systems – Carabeo-Pérez – Applied Microbiology and Biotechnology

August 15, 2019

Have a nice Thursday! Today we have a set of papers showing randomized trials related to antibiotic use and alimentary interventions, metabolic networks associated with C. difficile infection, and analysis of E. coli isolates from human stool. Today, we also include a couple of protocol papers about the use of stable isotope probing in plant microbiome research.

 

Human and General Microbiome

Gut microbiome alteration in MORDOR I: a community-randomized trial of mass azithromycin distribution – T. Doan – Nature Medicine 

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

Antibiotic Resistance, Virulence Factors, Phenotyping, and Genotyping of E. coli Isolated from the Feces of Healthy Subjects – Stefano Raimondi – Microorganisms

Metabolomic networks connect host-microbiome processes to human Clostridioides difficile infections – John I. Robinson – The Journal of Clinical Investigation

Antibiotic exposure and ‘response failure’ for subsequent respiratory tract infections: an observational cohort study of UK preschool children in primary care – Oliver van Hecke – British Journal of General Practice 

Abnormal vaginal microbiome associated with vaginal mesh complications – Nikolaus Veit‐Rubin – Neurology and Urodynamics

Acceptability, Tolerability and Safety of Faecal Microbiota Transplantation in patients with active Ulcerative Colitis (AT&S Study) – Ajit Sood – Journal of Gastroenterology and Hepatology

The bacteriome of otitis media with effusion: Does it originate from the adenoid? – Oguz Ari – International Journal of Pediatric Otorhinolaryngology 

An Exploratory Analysis of Fecal Immunochemical Test Performance for Colorectal Cancer Screening in Nigeria – Gregory C. Knapp – World Journal of Surgery

Isolates from colonic spirochaetosis in humans show high genomic divergence and potential pathogenic features but are not detected using standard primers for the human microbiota – Kaisa Thorell – Journal of Bacteriology

Microbiota-derived Trimethylamine N-oxide Predicts Cardiovascular Risk After STEMI – Yasushi Matsuzawa – Scientific Reports

Review: Targeting Microbiota: What Do We Know about It at Present? – Aleksejs Derovs – Medicina

Tech News: Reproducibility: the search for microbiome standards – Joseph Martin – BioTechniques

 

Animal Microbiome

Intestinal microbial products from alcohol-fed mice contribute to intestinal permeability and peripheral immune activation – Derrick R. Samuelson – Alcoholism

Comparative metagenomic sequencing analysis of cecum microbiotal diversity and function in broilers and layers – Zhao Qi – 3 Biotech

Oligosaccharides Modulate Rotavirus-Associated Dysbiosis and TLR Gene Expression in Neonatal Rats – Ignasi Azagra-Boronat – Cells

Role of coprophagy in the cecal microbiome development of an herbivorous bird Japanese rock ptarmigan – Atsushi Kobayashi – Journal of Veterinary Medical Science

 

Beneficial compounds and microbes

Review: 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

Commentary: Microbiome, probiotics and dermatology – J.A. Cardenas‐de la Garza – British Journal of Dermatology

Cooked Red Lentils Dose-Dependently Modulate the Colonic Microenvironment in Healthy C57Bl/6 Male Mice – Daniela Graf – Nutrients

Health Benefits of Lactobacillus gasseri CP2305 Tablets in Young Adults Exposed to Chronic Stress: A Randomized, Double-Blind, Placebo-Controlled Study – Kensei Nishida – Nutrients 

Effect of coffee on the compositional shift of oral indigenous microbiota cultured in vitro – 

 

Food Microbiome

Microbial Transformations of Organically Fermented Foods – Ruma Raghuvanshi – Metabolites

 

Plant Microbiome

Protocol: Stable Isotope Probing of Microbiota Structure and Function in the Plant Rhizosphere – Wafa Achouak – Stable Isotope Probing (Methods in Molecular Biology)

Protocol: Targeted Metatranscriptomics of Soil Microbial Communities with Stable Isotope Probing – Ang Hu – Stable Isotope Probing (Methods in Molecular Biology)

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

August 13, 2019

Have a good Tuesday!  Today we have a brief digest, covering papers about Staphylococcus and Skin infections and the gut microbiome and Insomnia disorder, in addition with different studies in mice and a report showing genetic relationships between plants and bacterial community configuration. 

 

Human or General Microbiome

Review: Protective effect of the “food-microorganism-SCFAs” axis on colorectal cancer: from basic research to practical application – Han Shuwen – Journal of Cancer Research and Clinical Oncology

Strains of Staphylococcus aureus that Colonize and Infect Skin Harbor Mutations in Metabolic Genes – Karen P. Acker – IScience

Inflamm-aging micrornas may integrate signals from food and gut microbiota by modulating common signalling pathways – Laura Teodori – Mechanisms of Ageing and Development

Gut Microbiota as a Subjective Measurement for Auxiliary Diagnosis of Insomnia Disorder – Bingdong Liu – Frontiers in Microbiology

 

Animal Microbiome

Adhesive Bifidobacterium Induced Changes in Cecal Microbiome Alleviated Constipation in Mice – Linlin Wang – Frontiers in Microbiology

Short-term dietary restriction in old mice rejuvenates the aging-induced structural imbalance of gut microbiota – Ting Zeng – Biogerontology

Species-specific effects of arsenic on the soil collembolan gut microbiota – Yi-Fei Wang – Ecotoxicology and Environmental Safety

Fecal metabonomics combined with 16S rRNA gene sequencing to analyze the changes of gut microbiota in rats with kidney-yang deficiency syndrome and the intervention effect of You-gui pill – Ruiqun Chen – Journal of Ethnopharmacology

Age- and diet-specific effects of chronic exposure to chlorpyrifos on hormones, inflammation and gut microbiota in rats – Jin-Wang Li – Pesticide Biochemistry and Physiology

High-throughput 16S rRNA gene sequencing reveals that 6-hydroxydopamine affects gut microbial environment – Jin Gyu Choi – PLoS ONE

 

Plant Microbiome

Genome Sequences of a Plant Beneficial Synthetic Bacterial Community Reveal Genetic Features for Successful Plant Colonization – Rafael Soares Correa de Souza – Frontiers in Microbiology

 

Non-Microbiology Picks

Science–graphic art partnerships to increase research impact – Colin K. Khoury – Communications Biology

August 10, 2019

This weekend, read about the role that gut microbes play in inflammation, microbes in the placenta-maternal interface, BactMAP R package, and more. Happy reading!

General microbiome

High proportions of bacteria and archaea across most biomes remain uncultured – Andrew D. Steen – The ISME Journal

Isolation of an archaeon at the prokaryote-eukaryote interface – Hiroyuki Imachi – bioRxiv

Urinary microbiome

A Prospective Study of the Urinary and Gastrointestinal Microbiome in Prepubertal Males – Borna Kassir – Urology

Gut microbiome

*Review: The intestinal microbiota fuelling metabolic inflammation – Herbert Tilg – Nature Reviews Immunology

Long-term dietary intervention reveals resilience of the gut microbiota despite changes in diet and weight – Gabriela K Fragiadakis – bioRxiv

Recovery of the gut microbiota after antibiotics depends on host diet and environmental reservoirs – Katharine M. Ng – bioRxiv

Differential detection of Entamoeba species in stool samples collected from children in District Swat, Khyber Pakhtunkhwa Pakistan – Muhammad Iftikhar Khan – bioRxiv

Association network analysis identifies enzymatic components of gut microbiota that significantly differ between colorectal cancer patients and healthy controls – Dongmei Ai – PeerJ

Specific changes in faecal microbiota are associated with familial Mediterranean fever – Samuel Deshayes – Annals of the Rheumatic Diseases

Pregnancy and early life

*Functional characterization of Ralstonia insidiosa, a bona fide resident at the maternal-fetal interface – Lindsay A. Parnell – bioRxiv

The association between caesarean section delivery and later life obesity in 21-24 year olds in an Urban South African birth cohort – Eniola Sogunle – bioRxiv

Water and extremophile microbiome

Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments – Satoshi Hiraoka – bioRxiv

Metabolically-active obligate aerobes in anoxic (sulfidic) marine sediments – Sabyasachi Bhattacharya – bioRxiv

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

Bioinformatics

*BactMAP: an R package for integrating, analyzing and visualizing bacterial microscopy data – Renske van Raaphorst – bioRxiv

Podcast

The placental microbiome, and advances in artificial intelligence – Nick Howe and Noah Baker – Nature Podcast

August 3, 2019

Have a happy weekend! Today, in this Digest: an interesting study of the human placenta microbiome, papers showing associations between microbiome and pancreatic or lung cancer, and an update of the pathogenesis of bacterial vaginosis. In addition, a paper showing that the microbiome in primates has a different evolutionary pattern in comparison with the host.  Enjoy!

 

Human and General Microbiome

Human placenta has no microbiome but can contain potential pathogens – Marcus C. de Goffau – Nature

Microbial dysbiosis and polyamine metabolism as predictive markers for early detection of pancreatic cancer – Roberto Mendez – Carcinogenesis

Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints – Andres Gomez – mSphere

Whole genome sequencing revealed microbiome in lung adenocarcinomas presented as ground-glass nodules – Yijiu Ren – Translational Lung Cancer Research

An Updated Conceptual Model on the Pathogenesis of Bacterial Vaginosis – Christina A Muzny – The Journal of Infectious Diseases

Review: Gut microbes and metabolites as modulators of blood-brain barrier integrity and brain health – Aimeé Parker – Gut Microbes

Editorial: The only thing that stops a bad microbiome, is a good microbiome – Jessica R. Galloway-Peña – Haematologica

Review: Consumer Safety Considerations of Skin and Oral Microbiome Perturbation – Andrew J. McBain – Clinical Microbiology Reviews

News: Microbiome therapeutics go small molecule – Megan Cully – Nature Reviews Drug Discovery

Pharmacomicrobiomics informs clinical pharmacogenomics – Theodora Katsila – Future Medicine

Each Additional Day of Antibiotics is Associated with Lower Gut Anaerobes in Neonatal Intensive Care Unit Patients – Ashley M Rooney, BSc – Clinical Infectious Diseases

Prevention and treatment of recurrent Clostridioides difficile infection – Jae Shin – Current Opinion in Infectious Diseases

An integrated respiratory microbial gene catalogue to better understand the microbial aetiology of Mycoplasma pneumoniae pneumonia – Wenkui Dai – Gigascience

Review: Connection between gut microbiome and the development of obesity – Cuiting Zhi – European Journal of Clinical Microbiology & Infectious Diseases

Animal Microbiome

Hyperuricemia is associated with impaired intestinal permeability in mice – Daxing Xu – Gastrointestinal and Liver Physiology

 

Beneficial compounds and Foods

Prevention of Vascular Inflammation by Pterostilbene via Trimethylamine-N-Oxide Reduction and Mechanism of Microbiota Regulation – Yen‐Chun Koh – Molecular Nutrition and Food Research

Interactions of tea polyphenols with intestinal microbiota and their implication for cellular signal conditioning mechanism – Yongyong Li – Journal of Food Biochemistry

Hass Avocado Inclusion in a Weight-Loss Diet Supported Weight Loss and Altered Gut Microbiota: A 12-Week Randomized, Parallel-Controlled Trial – Susanne M Henning – Current Developments in Nutrition

 

Plant Microbiome

Host plant-dependent effects of microbes and phytochemistry on the insect immune response – Su’ad A. Yoon – Oecologia

Engineering transkingdom signalling in plants to control gene expression in rhizosphere bacteria – Barney A. Geddes – Nature Communications 

August 1, 2019

Happy Thursday! Today’s digest includes fungi abundance in paddy fields, the microbial quality of treated wastewater, and the oral microbiome of cats. Enjoy!

Animal microbiome

The feline cutaneous and oral microbiota are influenced by breed and environment – Older – PLoS One

Microbial community modulates growth of symbiotic fungus required for stingless bee metamorphosis – Paludo – PLoS One

Preprint: Effects of the copper IUD on composition of the vaginal microbiota in the olive baboon – Eastman – bioRxiv

Plant, root, and soil microbiome

Nitrogen fertilization altered arbuscular mycorrhizal fungi abundance and soil erosion of paddy fields in the Taihu Lake region of China – Zhang – Environmental Science and Pollution Research

Reconciling disparate responses to grazing in the arbuscular mycorrhizal symbiosis – van Der Heyde – Rhizosphere

Redox-driven shifts in soil microbial community structure in the drawdown zone after construction of the Three Gorges Dam – Wang – Soil Ecology Letters

Water and extremophile microbiome

Biomarker Profiling of Microbial Mats in the Geothermal Band of Cerro Caliente, Deception Island (Antarctica): Life at the Edge of Heat and cold – Lezcano – Astrobiology

Microbial diversity analysis and screening for novel xylanase enzymes from the sediment of the Lobios Hot Spring in Spain – Knapik – Scientific Reports

Built environment

How does urban wastewater treatment affect the microbial quality of treated wastewater? – Lopez – Process Safety and Environmental Protection

Identifying microbial community evolution in membrane bioreactors coupled with anaerobic side-stream reactor, packing carriers and ultrasonication for sludge reduction by linear discriminant analysis – Zheng – Bioresource Technology

Food microbiology

Preprint: Deep microbial community profiling along the fermentation process of pulque, a major biocultural resource of Mexico – Rocha-Arriaga – bioRxiv

Bioinformatics

Preprint: µbialSim: constraint-based dynamic simulation of complex microbiomes – Popp and Centler – bioRxiv