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

Biomarker discovery in inflammatory bowel diseases using network-based feature selection – Abbas et al. – PLOS ONE

Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing – Srivathsan et al. – BMC Biology

December 2, 2019

Good Morning! Highlights of today’s digest include investigation of microbial communities from ground water sources to develop bioremediation strategies for removal of contaminating micropollutants for production of drinking water, another study with whole-virome analysis identifies changes in the human gut virome in inflammatory bowl diseases with a hope to develop biomarkers and therapeutics. Also, take a look at cool techniques such as Photo-PCR with gold nanorods and irradiation that shortens time for cell lysis and termocycling allowing rapid detection of bacteria as a point-of-care diagnostic tool. Enjoy!

Human skin microbiome
Review: Revealing the secret life of skin With the microbiome you never walk alone – Sfriso et al. – International Journal of Cosmetic Science

Human urinary tract microbiome

Human gut microbiome
In silico Identification of Riboswitches in the Human Gut Microbiome for
Therapeutic Applications
– Kumari and Som – Journal of RNA and Genomics

Animal microbiome
Age, gut location and diet impact the gut microbiome of a tropical herbivorous surgeonfish – Parata et al. – FEMS Microbial Ecology

Microbial signatures of protected and impacted Northern Caribbean reefs: changes from Cuba to the Florida Keys – Weber et al. – Environmental Microbiology

Geographically isolated Colorado potato beetle mediating distinct defense responses in potato is associated with the alteration of gut microbiota – Wang et al. – Journal of Pest Science

Plant, root and soil microbiome
Dynamics of bacterial community in litter and soil along a chronosequence of Robinia pseudoacacia plantations – Xu et al. – Science of The Total Environment

Influence of invasion by Sosnowsky’s hogweed on nematode communities and microbial activity in forest and grassland ecosystems – Cerevkova et al. – Global Ecology and Conservation

Water and extremophile microbiome
*Exploring groundwater microbial communities for natural attenuation potential of micropollutants – Aldas-Vargas et al. – bioRxiv

Shifts in dimethylated sulfur concentrations and microbiome composition in the red-tide causing dinoflagellate Alexandrium minutum during a simulated marine heatwave – Deschaseaux et al. – Biogeosciences

Artificial light at night erases positive interactions across trophic levels – Maggi et al. – Functional Ecology

Review: Linking metagenomics to aquatic microbial ecology and biogeochemical cycles – Grossart et al. – Limnology and Oceanography

Anaerobic microbial communities can influence algal growth and nutrient removal from anaerobic digestate – Bankston and Higgins – Bioresource Technology

Analysis of microbial communities involved in organic matter and nitrogen removal in a full-scale moving bed biofilm reactor located near the Polar Arctic Circle – Rodriguez-Sanchez et al. – International Biodeterioration & Biodegradation

Enhanced volatile fatty acid production and microbial population analysis in anaerobic treatment of high strength wastewater – Lim et al. – Journal of Water Process Engineering

Rainfall Influences on Microbial Community Dynamics in an Urban Watershed – Banka et al. – Journal of Student-Scientists’ Research

Management of water bodies in show caves – A microbial approach – Moldovan et al. – Tourism Management

Continental-scale microbiome study reveals different environmental characteristics determining microbial richness and composition/quantity in hotel rooms – Fu et al. – bioRxiv

Food microbiology
Integrated Meta-omics Approaches To Understand the Microbiome of Spontaneous Fermentation of Traditional Chinese Pu-erh Tea – Zhao et al. – mSystems

Phages and viruses
*Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease – Clooney et al. – Cell Host & Microbe

Metagenomics of the faecal virome indicate a cumulative effect of enterovirus and gluten amount on the risk of coeliac disease autoimmunity in genetically at risk children: the TEDDY study – Lindfors et al. – BMJ Gut

Detecting contamination in viromes using ViromeQC – Zolfo et al. – Nature Biotechnology

Review: Metagenomics: Is it a powerful tool to obtain lipases for application in biocatalysis? – Almeida et al. – Biochimica et Biophysica Acta (BBA) – Proteins and Proteomics

In-depth serum virome analysis in patients with acute liver failure with indeterminate etiology – Ren et al. – Archives of Virology

Visualization of viral infection dynamics in a unicellular eukaryote and quantification of viral production using VirusFISH – Castillo et al. – bioRxiv

High-efficiency multi-site genomic editing (HEMSE) of Pseudomonas putida through thermoinducible ssDNA recombineering – Aparicio et al. – bioRxiv

A user guide to environmental protistology: primers, metabarcoding, sequencing, and analyses – Geisen et al. – bioRxiv

MiniReview: Next-Generation Sequencing Coupled With in situ Hybridization: A Novel Diagnostic Platform to Investigate Swine Emerging Pathogens and New Variants of Endemic Viruses – Resende et al. – Frontiers in Veterinary Science

*Gold Nanorod-based Photo-PCR System for One-Step, Rapid Detection of Bacteria – Kim et al. – Nanotheranostics

Science career
Using a Systems Change Framework to Evaluate Academic Equity & Climate Efforts in a Graduate Program – Wallace and York – bioRxiv

November 17, 2019

Good Morning! Highlights of today’s digest include a promising probiotic effect of Lactobaccillus helveticus on acute liver failure as shown in an animal model study. Findings from another study about soil sterilization and how it leads to healthier soil microbiome and plant growth by modulating promotion of plant and beneficial microbes associations. Finally, check out an investigation aiming to generate a standardized approach for microbiome profiling by evaluating a series of hypervariable regions of 16S gene and estimating community richness across diverse sample types. Many review articles are also posted. Enjoy!

Pregnancy and early life

Acquisition and Development of the Extremely Preterm Infant Microbiota Across Multiple Anatomical Sites – Young et al. – J of Pediatric Gastroebterology and Nutrition

Multi-site human microbiome

Review: Urobiome: In Sickness and in Health – Wojciuk et al. – Microorganisms

Review: The Skin and Gut Microbiome and Its Role in Common Dermatologic Conditions – Ellis et al. – Microorganisms

Human oral microbiome

Analysis of the human oral microbiome from modern and historical samples with SPARSE and EToKi – Achtman and Zhou – bioRxiv

Human vaginal microbiome

HIV infection is associated with preterm delivery independent of vaginal microbiota in pregnant African women – Gudza-Mugabe et al. – The Journal of Infectious Diseases

Human gut microbiome

Review: Microbial Phenolic Metabolites: Which Molecules Actually Have an Effect on Human Health? – Marhuenda-Munoz et al. – Nutrients

Microbial succession during wheat bran fermentation and colonisation by human faecal microbiota as a result of niche diversification – Paepe et al. – ISME

Bifidogenic and butyrogenic effects of young barely leaf extract in an in vitro human colonic microbiota model – Sasaki et al. – AMB Express

Animal experiments

Dietary energy and protein levels influenced the growth performance, ruminal morphology and fermentation and microbial diversity of lambs – Cui et al. – Scientific Reports

*Lactobacillus helveticus R0052 alleviates liver injury by modulating gut microbiome and metabolome in d-galactosamine-treated rats – Wang et al. – Applied Microbiology and Biotechnology

Plant, root and soil microbiome

Evaluation of the ecological restoration of a coal mine dump by exploring the characteristics of microbial communities – Chen et al. – Applied Soil Ecology

*Soil sterilization leads to re-colonization of a healthier rhizosphere microbiome – Li et al. – Rhizosphere

Water and extremophile microbiome

Microbial composition and variability of natural marine planktonic and biofouling communities from the Bay of Bengal – Angelova et al. – Frontiers in Microbiology

Changes to the microbial communities within groundwater in response to a large crustal earthquake in Kumamoto, southern Japan – Morimura et al. – Journal of Hydrology

Increasing oxygen defciency changes rare and moderately abundant bacterial communities in coastal soft sediments – Sinkko et al. – Scientific Reports Nature Research

Probiotics / peribiotics

Review: Recent systems biology approaches for probiotics use in health aspects: a review – Yadave and Shukla – 3 Biotech


A phylogenetic model for the recruitment of species into microbial communities and application to studies of the human microbiome – Darcy et al. – bioRxiv

Developing a Reproducible Microbiome Data Analysis Pipeline Using the Amazon Web Services Cloud for a Cancer Research Group: Proof-of-Concept Study – Bai et al. – JMIR Medical Informatics


*Evaluation of primer pairs for microbiome profiling across a food chain from soils to humans within the One Health framework – Wasimuddin et al. – bioRxiv

Rapid, selective and single cell electrical detection of antibiotic resistant bacteria – Kumar et al. – bioRxiv

Droplet Digital PCR Technology for Detection of Ilyonectria liriodendri from Grapevine Environmental Samples – Martinez Diz et al. – APS Publications

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

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

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

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

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

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

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

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

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

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

*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


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