November 4, 2019

Good Morning! Highlights of today’s digest include a skin microbiome study in leprosy disease in Indian patients, another study shows findings from a mouse model and suggests vitamin B6 may have a therapeutic potential for treatment of chronic stress-induced gastritis. Finally, metagenomic sequencing and assembly of bacteria from different soils show how a soil type can influence genetic potential of bacteria for production of specialized metabolites such as antibiotics.

General microbiome

Review: Recent metabolomics and gene editing approaches for synthesis of microbial secondary metabolites for drug discovery and development – Sinha et al. – World Journal of Microbiology and Biotechnology

Human oral microbiome

Targeted polymerase chain reaction-based expression of putative halitogenic bacteria and volatile sulphur compound analysis among halitosis patients at a tertiary hospital in Nigeria – Adedapo et al. – Odontology

Human respiratory microbiome

The composition and functional protein subsystems of the human nasal microbiome in granulomatosis with polyangiitis: a pilot study – Wagner et al. – BMC Microbiome

Human skin microbiome

*16S rDNA based skin microbiome data of healthy individuals and leprosy patients from India – Bayal et al. – Nature Scientific Data

Human vaginal microbiome

Associations between the vaginal microbiome and Candida colonization in women of reproductive age – Tortelli et al. – American Journal of Obstetrics and Gynecology

Vaginal Biomarkers That Predict Cervical Length and Dominant Bacteria in the Vaginal Microbiomes of Pregnant Women – Witkin et al. – mBio

Human gut microbiome

Cohabitation is associated with a greater resemblance in gut microbiota which can impact cardiometabolic and inflammatory risk – Finnicum et al. – BMC Microbiology

Animal experiments

*Hydrogen sulfide‐mediated resistance against water avoidance stress‐induced gastritis by maintenance of gastric microbial homeostasis – Han et al. – MicrobiologyOpen

Animal microbiome

Bacterial communities associated with the midgut microbiota of wild Anopheles gambiae complex in Burkina Faso – Zoure et al. – Molecular Biology Reports

It’s what’s on the inside that counts: stress physiology and the bacterial microbiome of a wild urban mammal – Stothart et al. – Proceedings of the Royal Society B

Analysis of the Microbiota in the Fecal Material of Painted Turtles (Chrysemys picta) – Fugate et al. – Current Microbiology

Plant, root and soil microbiome

*Bacterial secondary metabolite biosynthetic potential in soil varies with phylum, depth, and vegetation type – Sharrar et al. – bioRxiv

Evidence for extensive anaerobic dechlorination and transformation of the pesticide chlordecone (C10Cl10O) by indigenous microbes in microcosms from Guadeloupe soil – Lomheim et al. – bioRxiv

Functional screening of a soil metagenome for DNA endonucleases by acquired resistance to bacteriophage infection – Mtimka et al. – Molecular Biology Reports

Exploring Actinobacteria Associated with Rhizosphere and Endosphere of the Native Alpine Medicinal Plant Leontopodium Nivale Subspecies Alpinum – Oberhofer et al. – Frontiers in Microbiology

Plant communities are more sensitive than soil microbial communities to multiple environmental changes in the Eurasian steppe – Zhou et al. – Global Ecology and Conservation

Floral organs act as environmental filters and interact with pollinators to structure the yellow monkeyflower (Mimulus guttatus) floral microbiome – Gomez and Ashman – Molecular Ecology

Characterization of Bacterial and Fungal Communities in Soils under Different Farming Systems. The Cacao Plantation in Sulawesi Island—Indonesia – Suwastika et al. – Eurasian Soil Science

Soil microbial biomass, activity and community structure as affected by mineral phosphorus fertilization in grasslands – She et al. – Applied Soil Ecology

Water and extremophile microbiome

Artificial substrata increase pond farming density of grass carp (Ctenopharyngodon idella) by increasing the bacteria that participate in nitrogen and phosphorus cycles in pond water – Li et al. – PeerJ

High-throughput sequencing revealed differences of microbial community structure and diversity between healthy and diseased Caulerpa lentillifera– Liang et al. – BMC MIcrobiology

Stochastic processes shape microeukaryotic community assembly in a subtropical river across wet and dry seasons – Chen et al. – BMC Microbiome


Prediction of microbial communities for urban metagenomics using neural network approach – Zhou et al. – Human Genomics

Food microbiology

Fermented cereal-based Munkoyo beverage: Processing practices, microbial diversity and aroma compounds – Phiri et al. – PLOS ONE

Phages and viruses

High Diversity and Novel Enteric Viruses in Fecal Viromes of Healthy Wild and Captive Thai Cynomolgus Macaques (Macaca fascicularis) – Sawaswong et al. – Viruses


HS-SPME-GC-MS approach for the analysis of volatile salivary metabolites and application in a case study for the indirect assessment of gut microbiota – Campanella et al. – Analytical and Bioanalytical Chemistry

Unraveling interspecies interactions across heterogeneities in complex biofilm communities – Roder et al. -2920.14834 – Environmental Microbiology

The microbiome during lung development

Perinatal maternal antibiotic exposure augments lung injury in experimental bronchopulmonary dysplasia – Willis et al – Am J Physiol Lung Cell Mol Physiol

Editorial: Maternal Antibiotics Augment Hyperoxia Induced Lung Injury in Neonatal Mice – Lal et al – Am J Physiol Lung Cell Mol Physiol

Effects of Hyperoxia on Alveolar and Pulmonary Vascular Development in Germ Free Mice – Dolma et al – Am J Physiol Lung Cell Mol Physiol

Editorial: Mice without a microbiome are partially protected from lung injury by hyperoxia – Willis et al – Am J Physiol Lung Cell Mol Physiol

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