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

Built-environment

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

Techniques

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

October 21, 2019

Good Morning! Highlights of today’s digest include malaria parasite control by a symbiont: investigation of a host immune response and mosquito development in responds to the mosquito symbiont Asaia. On a relating note, please also check out Parasite Microbiome Project, which aims to provide interactive centralized platform and resources for researchers to dissect complex interactions between parasites, hosts and their respective microbiota. Finally, a plant-microbe interactions study aimed to define a core microbiota of wheat crop and a possibility to use certain microbial taxa for management of stripe rust, a widely occuring wheat leaf disease.

General microbiome
*Asaia Activates Immune Genes in Mosquito Eliciting an Anti-Plasmodium Response: Implications in Malaria Control – Cappelli et al. – Frontiers in Genetics

*Opinion: Parasite microbiome project: Grand challenges – Dheilly et al. – PLOS PATHOGENS

Human oral microbiome
Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules – Baker et al. – bioRxiv

Human gut microbiome
Review: Is there any association between gut microbiota and type 1 diabetes? A systematic review – Jamshidi et al. – Gut Pathogens

Differential Effects of Typical Korean Versus American-Style Diets on Gut Microbial Composition and Metabolic Profile in Healthy Overweight Koreans: A Randomized Crossover Trial – Shin et al. – Nutrients

Animal experiments
Colonic Microbiota and Metabolites Response to Different Dietary Protein Sources in a Piglet Model – Li et al. – Frontiers in Nutrition

Antibiotics and Host-Tailored Probiotics Similarly Modulate Effects on the Developing Avian Microbiome, Mycobiome, and Host Gene Expression – Ward et al. – mBio

Evaluation of the bacterial ocular surface microbiome in clinically normal cats before and after treatment with topical erythromycin – Darden et al. – PLOS ONE

Animal microbiome
Effects of Nutritional Deprivation and Re-Alimentation on the Feed Efficiency, Blood Biochemistry, and Rumen Microflora in Yaks (Bos grunniens) – Zou et al. – MDPI Animals

Plant, root and soil microbiome
* Wheat‐associated microbiota and their correlation with stripe rust reaction – Dai et al. – Journal of Applied Microbiology

Prophage induction mediated by quorum sensing signals alters soil bacterial community structure – Liang et al. – bioRxiv

Water and extremophile microbiome
Chemical and biological dispersants differently affect the bacterial communities of uncontaminated and oil-contaminated marine water – de Almeida Couto et al. – Brazilian Journal of Microbiology

Shift of Sediments Bacterial Community in the Black-Odor Urban River during In Situ Remediation by Comprehensive Measures – Zhang et al. – MDPI Water

Built environment
Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach – Hendriksen et al. – PLOS ONE

October 7, 2019

Good Morning! Highlights of today’s digest include investigation about early childhood microbiota assembly in mother-infant participants from the Tsimane indigenous population from Amazon and with findings suggesting that socioeconomic changes may be altering interactions of highly abundant members of the microbiota in the host. Results from a gut-brain axis rat model showed possibility of novel biomarkers development for stress response based on abundance of genes in microbiomes. Finally, another study is aiming to access biologically active small molecules with antibacterial activity derived from human microbiota by sequencing of metagenomes and the use of computational and synthetic biology methods.

Pregnancy and early life
Prenatal and postnatal contributions of the maternal microbiome on offspring programming – Jasarevic and Bale – Frontiers in Neuroendocrinology

Multi-site human microbiome
*Microbiota Assembly, Structure, and Dynamics Among Tsimane Horticulturalists of the Bolivian Amazon – Sprockett et al. – bioRxiv

Human vaginal microbiome
Oncogenic Virome Benefits from the Different Vaginal Microbiome-Immune Axes – Campisciano et al. – MDPI Microorganisms

Non-optimal vaginal microbiota after azithromycin treatment for Chlamydia trachomatis infection – Tamarelle et al. – The Journal of Infectious Diseases

Human nearly-sterile sites
Targeted High-Throughput Sequencing Identifies Predominantly Fungal Pathogens in Patients with Clinically Infectious, Culture-Negative Endophthalmitis in South India – Gandhi et al. – MDPI Microorganisms

Human gut microbiome
Review: Synthetic ecology of the human gut microbiota – Vrancken et al. – Nature Reviews Microbiology

Review: The interaction between gut microbiome and nutrients on development of human disease through epigenetic mechanisms – Ho-Sun Lee – Genomics & Informatics

Adaptation of Syntenic Xyloglucan Utilization Loci of Human Gut Bacteroidetes to Polysaccharide Side Chain Diversity – Dejean et al. – Applied and Environmental Microbiology

Pre‐and post‐serial metagenomic analysis of gut microbiota as a prognostic factor in patients undergoing haematopoietic stem cell transplantation – Kusakabe et al. – British Journal of Haematology

Animal experiments
Experimental evidence for adaptation to species-specific gut microbiota in house mice – Moeller et al. – mSphere

Low‐calcium diet in mice leads to reduced gut colonization by Enterococcus faecium – Top et al. – MicrobiologyOpen

Letrozole treatment of pubertal female mice results in activational effects on reproduction, metabolism and the gut microbiome – Arroyo et al. – PLOS ONE

Transplanting Fecal Virus-Like Particles Reduces High-Fat Diet-Induced Small Intestinal Bacterial Overgrowth in Mice – Lin et al. – Frontiers in Cellular and Infection Microbiology

*Metabolome and microbiome profiling of a stress-sensitive rat model of gut-brain axis dysfunction – Bassett et al. – Nature Scientific Reports

Animal microbiome
The composition and stability of the faecal microbiota of Merino sheep – Al Mamun et al. – Journal of Applied Microbiology

Faecal microbiota and functional capacity associated with weaning weight in meat rabbits – Fang et al. – Microbial Biotechnology

Review: Feline Virome—A Review of Novel Enteric Viruses Detected in Cats – Martino et al. – MDPI Viruses

Phylogeography and ecological niche shape the cichlid fish gut microbiota in Central American and African lakes – Baldo et al. – Frontiers in Microbiology

Plant, root and soil microbiome
Biocontrol activities of rhizobacteria associated with apple, apricot and kiwi rhizosphere against bacterial canker caused by Clavibacter michiganensis – Gautam et al. – Indian Phytopathology

Distinct Drivers of Core and Accessory Components of Soil Microbial Community Functional Diversity under Environmental Changes – Zhang et al. – mSystems

Antarctic tundra soil metagenome as useful natural resources of cold-active lignocelluolytic enzymes – Oh et al. – Journal of Microbiology

Microbial communities in bioswale soils and their relationships to soil properties, plant species, and plant physiology – Brodsky et al. – Frontiers in Microbiology

Soil prokaryotes associated with decreasing pathogen density during anaerobic soil disinfestation – Lee et al. – bioRxiv

Water and extremophile microbiome
Bacterial Communities of Microbial Mats of the White Sea Supralittoral and of the Littoral of the Lakes Separated from the Sea – Burganskaya et al. – Microbiology

Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom – Bhatnagar et al. – bioRxiv

Bioinformatics
*A metagenomic strategy for harnessing the chemical repertoire of the human microbiome – Sugimoto et al. – Science

Techniques
Protocol: Open-Source Software Tools, Databases, and Resources for Single-Cell and Single-Cell-Type Metabolomics – Biswapriya B. Misra – Single Cell Metabolism

An Entropy-Based Graph Construction Method for Representing and Clustering Biological Data – Ariza-Jimenez et al. – Latin American Conference on Biomedical Engineering

Microbes in the news
Artificial gut aims to expose the elusive microbiome – Anne McGovern – MIT PHYS.ORG

September 9, 2019

Good Morning! Many research articles are posted! Highlights include a study describing hyper targeted phages in the human gut and a virome database, and construction of a pathway in a heterologus organism to pruduce secondary bile molecules for efforts to engineer and control bacterial metabolites in diseases. Happy readings!

Human oral microbiota
Identification of Initial Colonizing Bacteria in Dental Plaques from Young Adults Using Full-Length 16S rRNA Gene Sequencing – Ihara et al. – mSystems

Human vaginal microbiome
Life history recorded in the vagino-cervical microbiome – Jie et al. – bioRvix

Human gut microbiome
*A metabolic pathway for bile acid dehydroxylation by the gut microbiome – Funabashi et al. – bioRxiv

Probiotics for Gastrointestinal Symptoms and Quality of Life in Autism: A Placebo-Controlled Pilot Trial – Arnold et al. – Journal of Child and Adolescent Psychopharmacology

Animal experiments
The characteristics of gut microbiota and commensal Enterobacteriaceae isolates in tree shrew (Tupaia belangeri) – Gu et al. – BMC Microbiology

Modulation of high fat diet-induced microbiome changes, but not behaviour, by minocycline – Hasebe et al. – Brain, Behavior, and Immunity

Batch effect exerts a bigger influence on the rat urinary metabolome and gut microbiota than uraemia: a cautionary tale – Randall et al. – Microbiome

Animal microbiome
Linking pollen foraging of megachilid bees to their nest bacterial microbiota – Voulgari-Kokota et al. – Ecology and Evolution

Plant, root and soil microbiome
Consequences of microbial diversity in forest nitrogen cycling: diverse ammonifiers and specialized ammonia oxidizers – Isobe et al. – The ISME Journal

Historical Drought Affects Microbial Population Dynamics and Activity During Soil Drying and Re-Wet – Veach and Zeglin – Microbial Ecology

Stable Microbial Community and Specific Beneficial Taxa Associated with Natural Healthy Banana Rhizosphere – Europe PMC Journal of Microbiology and Biotechnology

Copepod carcasses in the subtropical convergence zone of the Sargasso Sea: implications for microbial community composition, system respiration and carbon flux – Tang et al. – Journal of Plankton Research

Predominance of soil vs root effect in rhizosphere microbiota reassembly – Zhao et al. – FEMS Microbiology Ecology

Bacterial rhizosphere community profile at different growth stages of Umorok (Capsicum chinense) and its response to the root exudates – Devi et al. – International Microbiology

The Burning of Sugarcane Plantation in the Tropics Modifies the Microbial and Enzymatic Processes in Soil and Rhizosphere – Trujillo-Narcia et al. – Journal of Soil Science and Plant Nutrition

Biocontrol and plant growth-promoting ability of plant-associated bacteria from tomato (Lycopersicum esculentum) under field condition – Amaresan et al. – Microbial Pathogenesis

Time-series analysis of phosphorus-depleted microbial communities in carbon/nitrogen-amended soils – Mise et al. – Applied Soil Ecology

The Bacterial Microbiome Associated with Arid Biocrusts and the Biogeochemical Influence of Biocrusts upon the underlying Soil – Moreira-Grez et al. – Frontiers in Microbiology

The Origin, Succession, and Predicted Metabolism of Bacterial Communities Associated with Leaf Decomposition – Jackrel et al. – mBio

Water and extremophile microbiome
Copepod carcasses in the subtropical convergence zone of the Sargasso Sea: implications for microbial community composition, system respiration and carbon flux – Tang et al. – Journal of Plankton Research

Built-environment
Genome-centered omics insight into the competition and niche differentiation of Ca. Jettenia and Ca. Brocadia affiliated to anammox bacteria – Zhao et al. – Applied Microbiology and Biotechnology

Food microbiology
Modeling and regulation of higher alcohol production through the combined effects of the C/N ratio and microbial interaction – Jiang et al. – Journal of Agricultural and Food Chemistry

Phages and viruses
*CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog – Cell Host & Microbe

Bioinformatics
MITRE: inferring features from microbiota time-series data linked to host status – Bogart et al. – BMC Genome Biology

Phylogenetic Tree-based Microbiome Association Test – Kim et al. – Bioinformatics

September 2, 2019

Good Morning! Highlights of today’s digest include an investigation with childern’s oral microbiota to show that consumption of licorice lollipop effectively reduces dental caries risk, another study showed the use of lantibiotic-producing colon commensal, Blautia producta BPSCSK, as a better probiotic agent against vancomycin-resistant gut pathogen Enterococcus faecium, and finally, to help reduce indoor air pollution, formaldehyde removal was measured to determine effectiveness of a plant-microbe technology with cultured microbes.

General Microbiology
Formation of the Francisella tularensis Biofilm is Affected by Cell Surface Glycosylation, Growth Medium, and a Glucan Exopolysaccharide – Champion et al. – Nature Research Scientific Reports

Gene expression of Porphyromonas gingivalis ATCC 33277 when growing in an in vitro multispecies biofilm – Romero-Lastra et al. – PLOS ONE

General microbiome
MiniReview: The necessity to revise Koch’s postulates and its application to infectious and non-infectious diseases: a mini-review – Hosainzadegan et al. – European Journal of Clinical Microbiology & Infectious diseases

Biofilm formation inhibition and dispersal of multi-species communities containing ammonia-oxidising bacteria – Keshvardoust et al. – Biofilms and Microbiomes

Human oral microbiome
*Lollipop containing Glycyrrhiza uralensis extract reduces Streptococcus mutans colonization and maintains oral microbial diversity in Chinese preschool children – Chen et al. – PLOS ONE

Human gut microbiome
Review: Therapeutic Opportunities in Inflammatory Bowel Disease: Mechanistic Dissection of Host-Microbiome Relationships – Plichta et al. – Cell

Age-dependent association of gut bacteria with coronary atherosclerosis: Tampere Sudden Death Study – Tuomisto et al. – PLOS ONE

Pathobiome driven gut inflammation in Pakistani children with Environmental Enteric Dysfunction – Iqbal et al. – PLOS ONE

Animal experiments
Gut microbiota from NLRP3-deficient mice ameliorates depressive-like behaviors by regulating astrocyte dysfunction via circHIPK2 – Zhang et al. – Microbiome

Chronic wound microbiome colonization on mouse model following cryogenic preservation – Tipton et al. – PLOS ONE

Ozone-induced changes in the serum metabolome: Role of the microbiome – Cho et al. – PLOS ONE

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

*Microbiota-derived lantibiotic restores resistance against vancomycin-resistant Enterococcus – Kim et al. – Nature

Plant, root and soil microbiome
Metabolome and microbiome signatures in the roots of citrus affected by Huanglongbing – Padhi et al. – Phytopathology

*An efficient plant–microbe phytoremediation method to remove formaldehyde from air – Yang et al. – Environmental Chemistry Letters

Built-environment (subways, indoor surfaces)
Review: From one species to another: A review on the interaction of chemistry and microbiology in relation to cleaning in the built environment – Velazquez et al. – Indoor Air

Phages and viruses
Analyses of virus/viroid communities in nectarine trees by next-generation sequencing and insight into viral synergisms implication in host disease symptoms – Xu et al. – Nature Research Scientific Reports

Characterization of the viral genomes present in commercial batches of horse serum obtained by high-throughput sequencing – Paim et al. – Biologicals

Myoviridae Phage PDX Kills Enteroaggregative Escherichia coli without Human Microbiome Dysbiosis – Cepko et al. – bioRxiv

Phylogenetics
The number of domains in the ribosomal protein S1 as a hallmark of the phylogenetic grouping of bacteria – Machulin et al. – PLOS ONE

TreeCluster: Clustering biological sequences using phylogenetic trees – Balaban et al. – PLOS ONE

Techniques
Bayesian hierarchical negative binomial models for multivariable analyses with applications to human microbiome count data – Pendegraft et al. – PLOS ONE

Automated “Cells-To-Peptides” Sample Preparation Workflow for High-Throughput, Quantitative Proteomic Assays of Microbes – Chen et al. – J. Proteome Res.

Variations of gut microbiome profile under different storage conditions and preservation periods: A multi-dimensional evaluation – Ma et al. – bioRxiv

Microbes in the news
Depression researchers rethink popular mouse swim tests – S. Reardon – Nature News

August 26, 2019

Good Morning! Highlights of today’s digest include two spearate studies on carrions, one analyzed microbial community of carcasses at Grassy Mountain region of Utah and the second quantified cytotoxicity of carcasses along ocean beaches to determine risk associated peak points for threatened iconic scavenger animals. And, a study characterized taxonomic diversity of less known marine fungi associated with a seagrass in the Bodega Bay. Finally, many reviews are posted! Check out the Research Review on plasmid-based tools for your favorite host microorganisms!

General Microbiology
Evolution of resistance in vitro reveals a novel mechanism of artemisinin activity in Toxoplasma gondii – Rozenberg et al. – biorxiv

General microbiome
Review: Microbiota-Nourishing Immunity: A Guide to Understanding Our Microbial Self – Litvak and Baumler – Immunity

Human gut microbiome
Review: Pursuing Human-Relevant Gut Microbiota-Immune Interactions – Spencer et al. – Immunity

Gut Microbiome Biomarkers in Adolescent Obesity:a Regional Study – Gao et al. – biorxiv

Animal experiments
Review: Commensal microbiota regulate vertebrate innate immunity – insights from the zebrafish – Murdoch and Rawls – Frontiers in Immunology

Animal microbiome
*Succession of bacterial communities on carrion is independent of vertebrate scavengers – Dangerfield et al. – biorxiv

*Not all rotten fish stink: Microbial changes in decaying carcasses increase cytotoxicity and potential risks to animal scavengers – Blandford et al. – Estuarine, Coastal and Shelf Science

Plant, root and soil microbiome
*Characterization of the mycobiome of the seagrass, Zostera marina, reveals putative 2 associations with marine chytrids – Ettinger and Eisen – bioRxiv

Built-environment
The occurrence of Listeria monocytogenes is associated with built environment microbiota in three tree fruit processing facilities – Tan et al. – Microbiome

Bioinformatics
The importance of genome sequence quality to microbial comparative genomics – Smits – BMC Genomics

Techniques
*Research Review: Recent advances in plasmid-based tools for establishing novel microbial chassis – Czamanski Nora et al. – Biotechnology Advances

High-throughput multi-parallel enteropathogen quantification via nano-liter qPCR – Grembi et al. – biorxiv

Longitudinal bioluminescent imaging of HIV-1 infection during antiretroviral therapy and treatment interruption in humanized mice – Ventura et al. – biorxiv

CRISPR-Cas9 mediated genome editing in vancomycin resistant Enterococcus faecium – de Maat et al. – biorxiv

August 5, 2019

Good Morning! Highlights of today’s digest include a comprehensive analysis of biosynthetic gene clusters from Bacillus amyloliquifaciens that synthesize a lipopeptide with anticancer activity, another study conducted with African-origin adults confirms association of the oral and gut microbiota to cardiometabolic risks, a review about future applications of probiotics focusing on the characteristics of Bacteroides fragilis and an editorial article on environmental bacteriophages highlighting exciting future applications such as antibacterial therapies for antibiotic-resistant pathogens.

General Microbiology

* A comprehensive genomic and growth proteomic analysis of antitumor lipopeptide bacillomycin Lb biosynthesis in Bacillus amyloliquefaciens X030 – Jiao Yang Lu et al. – Applied Microbiology and Technology

Pregnancy and early life

Patterned progression of gut microbiota associated with necrotizing enterocolitis and late onset sepsis in preterm infants: a prospective study in a Chinese neonatal intensive care unit – Jiayi Liu et al. – PeerJ

Multi-site human microbiome

*The human microbiota is associated with cardiometabolic risk across the epidemiologic transition – Na Fei et al. – PLOS ONE

Human vaginal microbiome

The effect of antiretroviral therapy initiation on the vaginal microbiome in HIV-infected women – Cindy M Liu et al. – Open Forum Infectious Diseases

Competition among Gardnerella subgroups from the human vaginal microbiome – Salahuddin Khan et al. – bioRxiv

Human gut microbiome

Exposure to parasitic protists and helminths changes the intestinal community structure of bacterial microbiota but not of eukaryotes in a cohort of mother-child binomial from a semi-rural setting in Mexico – Oswaldo Partida-Rodriguez et al. – bioRxiv

Animal experiments

Metagenomic analysis of the effects of toll-like receptors on bacterial infection in the peritoneal cavity following cecum ligation and puncture in mice – Pao-Jen Kuo et al. – PLOS ONE

Animal microbiome

Social interactions across groups of colobus monkeys (Colobus vellerosus) explain similarities in their gut microbiomes – bioRxiv

Plant, root and soil microbiome

Phosphorus Input Alters the Assembly of Rice (Oryza sativa L.) Root-Associated Communities – Xi-En Long et al. – Microbial Ecology

Water and extremophile microbiome

Review: Microbial Diversity of Saline Habitats: An Overview of Biotechnological Applications – Shubhrima Ghosh et at. – Microorganisms in Saline Environments: Strategies and Functions

Built-environment microbiome

Rapid metagenomics analysis of EMS vehicles for monitoring pathogen load using nanopore DNA sequencing – Taylor Sheahan et al. – PLOS ONE

Food microbiology

Characterization and comparison of metaproteomes in traditional and commercial dajiang, a fermented soybean paste in northeast China – Mengxi Xie et al. – Food Chemistry

Probiotics / peribiotics

*Review: A potential species of next-generation probiotics? The dark and light sides of Bacteroides fragilis in health – X Li et al. – Food Research International

Phages and viruses

*Editorial: Environmental Bacteriophages: from Biological Control Applications to Directed Bacterial Evolution – Robert Czajkowski et al. – Frontiers in Microbiology

Techniques

Quantitative Stable Isotope Probing with H218O to Measure Taxon-Specific Microbial Growth – Alicia M. Purcell et al. – ACSESS Metods of Soil Analysis

Linking process performances and core microbial community structures in anaerobic membrane bioreactor with rotatory disk (ARMBR) system fed with high-strength food waste recycling wastewater – Hyunduk Seo et al. – Bioresource Technology

Nanopore sequencing for fast determination of plasmids, phages, virulence markers, and antimicrobial resistance genes in Shiga toxin-producing Escherichia coli – Narjol Gonzalez-Escalona et al. – PLOS ONE

Microbes in the news

Poop transplants can help prematurely old mice live longer – Eva Freserick – Science Magazine