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

Advertisements

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

July 29, 2019

Good Morning! Highlights of today’s digest include a revisited study that showed a significant alterations in the gut microbiome by the consumption of low/no-calorie sweeteners (LNCS), such as Splenda, and raising safety concerns, another work tells us development of Burkholderia-free host plant model to show how Burkholderia helps plant development, and finally a study finds a mechanistic link between the gut microbiome and early childhood asthma as shown with highthened expression of bacterial genes that make 12,13-diHOME which alters immune response.

Human gut microbiome

***Revisited: Assessing the in vivo data on low/no-calorie sweeteners and the gut microbiota – Susan S. Schiffman et al. – Food and Chemical Toxicology

A structured weight loss program increases gut microbiota phylogenetic diversity and reduces levels of Collinsella in obese type 2 diabetics: A pilot study – Fabian Frost et al. – PLOS ONE

Human respiratory microbiome

Chronic obstructive pulmonary disease upper airway microbiome is associated with select clinical characteristics – Alexa A. Pragman et al. – PLOS ONE

Animal experiments

***Elevated faecal 12,13-diHOME concentration in neonates at high risk for asthma is produced by gut bacteria and impedes immune tolerance – Sophia R. Levan et al. – Nature Microbiology

Effect of live yeast Saccharomyces cerevisiae supplementation on the performance and cecum microbial profile of suckling piglets – Tadele G. Kiros et al. – PLOS ONE

Low-dose inoculation of Escherichia coli achieves robust vaginal colonization and results in ascending infection accompanied by severe uterine inflammation in mice – Valerie P. O’Brien – PLOS ONE

Probiotic strains improve high-fat diet-induced hypercholesterolemia through modulating gut microbiota in ways different from atorvastatin – Dun Su et al. – bioRxiv

Host Genotype-shaped Gut Microbiome Modulate Atherosclerosis Development in Mice – Kazuyuki Kasahara et al. – Arteriosclerosis, Thrombosis, and Vascular Biology

Animal microbiome

Fecal microbiota of different reproductive stages of the central population of the lesser-long nosed bat, Leptonycteris yerbabuenae – Osiris Gaona et al. – PLOS ONE

Taxon appearance from extraction and amplification steps demonstrates the value of multiple controls in tick microbiome analysis – Emilie Lejal et al. – bioRxiv

Characterization of the gastrointestinal bacterial microbiome of farmed juvenile and adult white Cachama (Piaractus brachypomus) – Victor Alfonso et al. – Aquaculture

Biosynthesis and Characterization, Antioxidant and Antimicrobial Activities
of Selenium Nanoparticles from Ethanol Extract of Bee Propolis
– Shubharani R. et al. – Journal of Nanomedicine & Nanotechnology

Plant, root and soil microbiome

The role of inoculum dispersal and plant species identity in the assembly of leaf endophytic fungal communities – Kevin D. Ricks et al. – PLOS ONE

***Is the bacterial leaf nodule symbiosis obligate for Psychotria umbellata? The development of a Burkholderia-free host plant – Arne Sinnesael et al. – PLOS ONE

AOA and AOB communities respond differently to changes of soil pH under long-term fertilization – Rubio Sun et al. – Soil Ecology Letters

***Negative plant-microbiome feedback limits productivity in aquaponics – Jessica A. Day et al. – bioRxiv

Do plant–microbe interactions and aluminum tolerance influence
alpine sedge species’ responses to nitrogen deposition?
– Teal S. Potter et al. – Ecosphere

Plant diversity and fertilizer management shape the belowground microbiome of native grass bioenergy feedstocks – Daniel Revillini et al. – Frontiers in Plant Science

Microbial taxonomical composition in spruce phyllosphere, but not community functional structure, varies by geographical location – Yunshi Li et al. – PeerJ

Responses of plant growth, physiological, gas exchange parameters of super and non-super rice to rhizosphere temperature at the tillering stage – Shuying Li at al. – Nature Scientific Reports

Influence of introduced arbuscular mycorrhizal fungi and phosphorus sources on plant traits, soil properties, and rhizosphere microbial communities in organic legume-flax rotation – Yunliang Li et al. – Plant and Soil

Effects of arbuscular mycorrhizal fungi on inoculated seedling growth and rhizosphere soil aggregates – Zhongfeng Zhang et al. – Soil and Tillage Research

Properties of bacterial community in the rhizosphere soils of Achyranthes bidentata tolerant to consecutive monoculture – Juanying Wang et al. – Plant Growth Regulation

The role of volatile organic compounds and rhizosphere competence in the mode of action of the non-pathogenic Fusarium oxysporum FO12 towards Verticillium wilt – Mulero-Aparicio et al. – Frontiers in Microbiology

Dynamic changes in soil chemical properties and microbial community structure in response to different nitrogen fertilizers in an acidified celery soil – Yuping Wu et al. – Soil Ecology Letters

Improved rhizoremediation for decabromodiphenyl ether (BDE-209) in E-waste contaminated soils – Jiayin Feng et al. – Soil Ecology Letters

Review: Soil biofilms: microbial interactions, challenges, and advanced techniques for ex-situ characterization – Peng Cai et al. – Soil Ecology Letters

Organic amendment effects on nematode distribution within aggregate fractions in agricultural soils – Xiaoke Zhang et al. – Soil Ecology Letters

Water and extermophile microbiome

Book chapter: New Perspectives on the Distribution and Roles of Thermophilic Fungi – Miriam I. Hutchinson et al. – Fungi in Extreme Environments: Ecological Role and Biotechnological Significance

Diversity and biogeography of eukaryotic microorganism in the deepsea sediment of the Eastern Indian Ocean – Xiaoxia Ma et al. – International Journal of Science

Phages and viruses

Phage composition of a fermented milk and colostrum product assessed by microbiome array; putative role of open reading frames – Stefania Pacini et al. – bioRxiv

Techniques

Modelling approaches for studying the microbiome – Manish Kumar et al. – Nature Microbiology

Guest Editorial: Beyond sequencing: fast and easy microbiome profiling by flow cytometry – Charlotte Esser at al. – Archives of Toxicology

View Point: Opportunities at the Intersection of Synthetic Biology, Machine Learning, and Automation – Pablo Carbonell et al. – ACS Synthetic Biology

Microbes in the News

***Elevated Concentration of Lipid in Neonatal Microbiome Predicts Later Risk for Asthma, Allergy – Allison Inserro – AJMC Newsroom

July 8, 2019

Good Morning! Highlights of today’s digest include several AACR Cancer Research meeting abstracts on microbiome profiling which are promising for development of early detection cancer or treatment-associated-toxicity biomarkers and novel probiotics that can prevent HPV infections-associated cancers and oropharyngeal cancers, development of non-invasive health monitoring tools for endangered humpback whales from East Australia, and re-assemblage of rhizosphere microbiome of medicinal Chinese ginseng or Sanqi. Finally, check out the news about development of a food supplement, expected to be commercialized by 2021 and suggested only to be used as a complementary approach -not a replacement of appropriate dietary habits, that involves a probiotic gut bacterium Akkermansia muciniphila to improve metabolism and metabolic factors in obesity, type II diabetes and inflammatory bowel diseases.

Human oral microbiome

Meeting Abstract: Mucositis, candidiasis, and associations with the oral microbiome in treatment naive patients with oropharyngeal cancer – Pierce et al. – AACR Cancer Research

Multi-site human microbiome

Meeting Abstract: The microbiota associated to cervical and anal HPV infections in a Hispanic population – Vazquez-Sanchez et al. – AACR Cancer Research

Animal microbiome

Review: Coral microbiome dynamics, functions and design in a changing world – van Oppen et al. – Nature Reviews Microbiology

Interannual comparison of core taxa and community composition of the blow microbiota from East Australian humpback whales – Vendl et al. – FEMS Microbiology Ecology

Plant, root and soil microbiome

Ecological Processes Shaping Bulk Soil and Rhizosphere Microbiome Assembly in a Long-Term Amazon Forest-to-Agriculture Conversion – Goss-Souza et al. – Microbial Ecology

Mycorrhizal frequency, physiological parameters, and yield of strawberry plants inoculated with endomycorrhizal fungi and rhizosphere bacteria – Mikiciuk et al. – Mycorrhiza

Negative plant-soil feedback driven by re-assemblage of the rhizosphere microbiome with the growth of Panax notoginseng – Zhu et al. – Frontiers in Microbiology

Water and extermophile microbiome

Microbial communities in a flow-through fish farm for lumpfish (Cyclopterus lumpus L.) during healthy rearing conditions – Roalkvam et al. – Frontiers in Microbiology

Probiotics / prebiotics

Dietary Resistant Potato Starch Alters Intestinal Microbial Communities and Their Metabolites, and Markers of Immune Regulation and Barrier Function in Swine – Trachsel et al. – Frontiers in Immunology

Phages and viruses

Virome capture sequencing does not identify active viral infection in unicentric and idiopathic multicentric Castleman disease – Nabel et al. – PLOS ONE

Wide distribution of phage that infect freshwater SAR11 bacteria – Chen et al. – BioRxiv

Techniques

Meeting Abstract: Microbial sequencing using a single-pool target enrichment of multiple variable regions of the 16S rRNA gene, the nuclear ribosomal internal transcribed spacer (ITS) region, and antimicrobial resistance genes – Peck et al. – AACR Cancer Research

Microbes in the news

Microbiome Food Supplement Improves Metabolic Syndrome in Overweight People – Smith – Labiotech.eu Newsletter

June 3, 2019

Good Morning! Highlights from Monday’s digest include understanding the evolution of the E. coli chemosensory machinery from an ancient form with a stress response pathway function, curriculum design and evaluation tool for developing bioinformatics competencies and strain-dependent induction of gastric dysbiosis and gastric cancers investigated in the animal model, Mongolian gerbil.

General microbiology

Repurposing a macromolecular machine: Architecture and evolution of the F7 chemosensory system – Ortega et al. – BioRxiv

Microbiome science

** Perspectives – Moving Microbiome Science from the Bench to the Bedside: a Physician-Scientist Perspective – Surana – mSystems

Training in bioinformatics

The Mastery Rubric for Bioinformatics: supporting design and evaluation of career-spanning education and training – Tractenberg et al. – BioRxiv

Human gut microbiome

Mucin O-glycans facilitate symbiosynthesis to maintain gut immune homeostasis – Yamada et al. – BioRxiv

Animal experiments

Modification of the Gastric Mucosal Microbiota by a Strain-Specific Helicobacter pylori Oncoprotein and Carcinogenic Histologic Phenotype – Noto et al. – mBio

Metformin and DPP-4 Inhibitor Differentially Modulate the Intestinal Microbiota and Plasma Metabolome of Metabolically Dysfunctional Mice – Ryan et al. – Canadian Journal of Diabetes

Plant, root and soil microbiome

Changes in soil taxonomic and functional diversity resulting from gamma irradiation – Ogwu et al. – Scientific Reports

Chestnuts bred for blight resistance depart nursery with distinct fungal rhizobiomes – Reazin et al. – Mycorrhiza

Potential links between wood‐inhabiting and soil fungal communities: Evidence from high‐throughput sequencing – Purahong et al. – MicrobiologyOpen

Phages and Viruses

** Review – Viroids-First—A Model for Life on Earth, Mars and Exoplanets – Moelling et al. – Geosciences

Metagenomic exploration of viral diversity and virus-host interactions in a deep freshwater lake – Okazaki et al. – BioRxiv

Tecniques

Triplicate PCR reactions for 16S rRNA gene amplicon sequencing are unnecessary – Marotz et al. – BioTechniques

Microbes in the news

Gut Bacteria Linked To Autism Symptoms, Mice Study Shows – Carlos – Tech Times

Autism Mouse Models for the Microbiome? – Lowe – Science Translational Medicine

Microbes on the market

Global Microbiome Therapeutics Market Report Forecast by Development, Trends, and Forecast (2019 – 2024) – The Scripps Voice