May 24, 2019

Today we have a short Digest before the Memorial Day weekend in America. Highlights include a comparative metabolomic study on Mycobacterium tuberculosis and a live attenuated strain as a potential vaccine, a report on oral cavity resistome worldwide and last but not least, fossils of early fungi that are about 1 billion years old!

General microbiology

Quorum Sensing Circuits in the Communicating Mechanisms of Bacteria and Its Implication in the Biosynthesis of Bacteriocins by Lactic Acid Bacteria: a Review – Ourdia Kareb & Mohammed Aïder – Probiotics and Antimicrobial Proteins

** Early fungi from the Proterozoic era in Arctic Canada – Corentin C. Loron et al. – Nature

Antimicrobial resistance

** Preprint: Abundance and diversity of resistomes differ between healthy human oral cavities and gut – Victoria R. Carr et al. – bioRxiv

Human skin microbiome

Skin Microbiome Differences in Atopic Dermatitis and Healthy Controls in Egyptian Children and Adults, and Association with Serum Immunoglobulin E – Mohammed Ramadan et al. – OMICS: A Journal of Integrative Biology

Review: Microbiome and skin biology – Lunjani, Nonhlanhla et al. – Current opinion in allergy and clinical immunology

Human oral microbiome

Intra‐oral single site comparisons of periodontal and peri‐implant microbiota in health and disease – Xiao‐Lin Yu et al. – Clinical Oral Implants Research

Built environment microbiome

Spatial Gradients of Fungal Abundance and Ecology throughout a Damp Building – Bridget Hegarty et al. – Environmental Science & Technology Letters

Metabolomics

** COMPARATIVE METABOLOMICS BETWEEN Mycobacterium tuberculosis AND THE MTBVAC VACCINE CANDIDATE – Caridad Díaz Navarro et al. – ACS Infectious Diseases

Animal microbiome

The Role of Tissue Type, Sampling and Nucleic Acid Purification Methodology on the Inferred Composition of Pacific Oyster (Crassostrea gigas) Microbiome – Erandi Pathirana et al. – Journal of Applied Microbiology

Plant, root and soil microbiome

Vertical distribution of microbial communities in chromium-contaminated soil and isolation of Cr(Ⅵ)-Reducing strains – Bang Liu & Guirong Su et al. – Ecotoxicology and Environmental Safety

Preprint: Root development is maintained by specific bacteria-bacteria interactions within a complex microbiome – Omri M. Finkel et al. – bioRxiv

Microbes in the news

Microbiome: Small Organisms Play Big Shots in Plants – Soumya Kumar Sahoo et al. – Biomolecule Reports

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May 23, 2019

Composition of the human mucosa-associated microbiota, changes in gut microbial diversity with social rank in cichlid fish, microbes supporting sustainable rice production, the effects of tweeting on article engagement in medical education.

General microbiome

Global change microbiology — big questions about small life for our future – Antje Boetius – Nature Reviews Microbiology

Human oral microbiome

Review: The Structure of Dental Plaque Microbial Communities in the Transition from Health to Dental Caries and Periodontal Disease – Alex M Valm – Journal of Molecular Biology

Human gut microbiome

Within-host evolution of Helicobacter pylori shaped by niche-specific adaptation, intragastric migrations and selective sweeps – Florent Ailloud – Nature Communications

Pre-print: Complete genome assembly of clinical multidrug resistant Bacteroides fragilis isolates enables comprehensive identification of antimicrobial resistance genes and plasmids – Thomas V Syndenham – bioRxiv

Composition of the mucosa-associated microbiota along the entire gastrointestinal tract of human individuals – FER Vuik – United European Gastroenterology Journal

Animal experiments

Loss of function dysbiosis associated with antibiotics and high fat, high sugar diet – Aaron W Miller – The ISME Journal

Saccharomyces boulardii CNCM I-745 changes lipidemic profile and gut microbiota in a hamster hypercholesterolemic model – F Briand – Beneficial Microbes

Animal microbiome

Gut microbial diversity increases with social rank in the African cichlid fish, Astatotilapia burtoni – Avehi Singh – Animal Behaviour

Amphibian Host and Skin Microbiota Response to a Common Agricultural Antimicrobial and Internal Parasite – Obed Hernández-Gómez – Microbial Ecology

Pre-print: Space, time, and captivity: quantifying the factors influencing the fecal microbiome of an alpine ungulate – Sarah E Haworth – bioRxiv

Plant, root, and soil microbiome

Interaction between root hairs and soil phosphorus on rhizosphere priming of soil organic matter – Gabriel Boilard – Soil Biology and Biochemistry

Green manures of Indian mustard and wild rocket enhance cucumber resistance to Fusarium wilt through modulating rhizosphere bacterial community composition – Xue Jin – Plant and Soil

Ozone dose-response relationships for soil microbial dynamics of winter wheat in North China – Enzhu Hu – Atmospheric Environment

Water and extremophile microbiome

Filamentous calcareous alga provides substrate for coral-competitive macroalgae in the degraded lagoon of Dongsha Atoll, Taiwan – Carolin Nieder – PLOS ONE

Food microbiology

Roles of microbes in supporting sustainable rice production using the system of rice intensification – Febri Doni – Applied Microbiology and Biotechnology

Microbes in the news

Airway microbiome appears altered in severe asthma linked to neutrophils – EurekAlert

Coffee Consumption Alters Microbiome and Improves Gut Motility – Genetic Engineering & Biotechnology News

Researchers receive $1.94 million to study connection between autism, microbiome – EurekAlert

Novel Autonomous Biosampler Will Foster In Situ Aquatic Microbiome Monitoring – Eunice Sousa – Science Trends

Meta-study suggests anxiety can be reduced by altering gut bacteria, but not with probiotics – Rich Haridy – New Atlas

Science, career, and publishing

Pre-print: To Tweet or Not to Tweet, That is the Question: A Randomized Trial of Twitter Effects on Article Engagement in Medical Education – Lauren A Maggio – bioRxiv

May 22, 2019

Today’s Digest is full of new perspectives on appropriate models and techniques, including the future of gnotobiotics and using unbiased metagenomics to find RNA viruses. There are also several plant, root, and soil papers, particularly examining the interplay between bacterial and fungal communities. Finally, enjoy a preprint about the cartography of antibiotic resistance genes in a hospital, a study examining the microbiota in larval mosquito vectors of malaria, and a paper about the microeukaryotes associated with coral reefs.

General Microbiome
Review: Antibiotics versus biofilm: an emerging battleground in microbial communities – Divakar Sharma – Antimicrobial Resistance & Infection Control

Review: Gnotobiotics: Past, present and future – Marijana Basic – Laboratory Animals

Review: The use of non-rodent model species in microbiota studies – Aaron C. Ericsson – Laboratory Animals

Pregnancy and Early Life
Influence of a Serratia marcescens outbreak on the gut microbiota establishment process in low-weight preterm neonates – Esperanza Escribano – PLoS One

Human Vaginal Microbiome
Vaginal microbiota and mucosal pharmacokinetics of tenofovir in healthy women using tenofovir and tenofovir/levonorgestrel vaginal rings – Andrea Ries Thurman – PLoS One

Human Oral Microbiome
Aerodigestive sampling reveals altered microbial exchange between lung, oropharyngeal, and gastric microbiomes in children with impaired swallow function – Claire Duvallet – PLoS One

Animal Microbiome
Color morphology of Diaphorina citri influences interactions with its bacterial endosymbionts and ‘Candidatus Liberibacter asiaticus’ – Saeed Hosseinzadeh – PLoS One

Conspecific coprophagy stimulates normal development in a germ-free model invertebrate – Benjamin C. Jahnes – PeerJ

Malaria vector species in Amazonian Peru co-occur in larval habitats but have distinct larval microbial communities – Catharine Prussing – PLoS Neglected Tropical Diseases

Animal Experiments
Gut and immune effects of bioactive milk factors in preterm pigs exposed to prenatal inflammation – Shuqiang Ren – American Journal of Physiology-Gastrointestinal and Liver Physiology

Effects of oregano essential oil on the ruminal pH and microbial population of sheep – Rui Zhou – PLoS One

Plant, Root, and Soil Microbiome
Characterizing the intra-vineyard variation of soil bacterial and fungal communities – Hebin Liang – Frontiers in Microbiology

The role of fungi in heterogeneous sediment microbial networks – Jenny Marie Booth – Scientific Reports

Altering N2O emissions by manipulating wheat root bacterial community – Alla Usyskin-Tonne – Scientific Reports

Sphingomonas sp. Cra20 Increases Plant Growth Rate and Alters Rhizosphere Microbial Community Structure of Arabidopsis Thaliana Under Drought Stress – Yang Luo – Frontiers in Microbiology

Enrichment of soil rare bacteria in root by an invasive plant Ageratina adenophora – Lin Chen – Science of the Total Environment

Effect of rhizospheric and endophytic bacteria with multiple plant growth promoting traits on wheat growth – Somayeh Emami – Environmental Science and Pollution Research

Water and Extremophile Microbiome
A comparison of microeukaryote communities inhabiting sponges and seawater in a Taiwanese coral reef system – Daniel Francis Richard Cleary – Annals of Microbiology

An integrated insight into the response of bacterial communities to anthropogenic contaminants in a river: A case study of the Wonderfonteinspruit catchment area, South Africa – K. Jordaan – PLoS One

Built Environment
Preprint: Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment – Kern Rei Chng – bioRxiv

Fungal community composition analysis of 24 different urban parks in Shanghai, China – Jing Zhang – Urban Ecosystems

Techniques
Expanding the RNA Virosphere by Unbiased Metagenomics – Yong-Zhen Zhang – Annual Review of Virology

Preprint: Next-generation sequencing of double stranded RNA is greatly improved by treatment with the inexpensive denaturing reagent DMSO – Alexander H. Wilcox – bioRxiv

Development of an autonomous biosampler to capture in situ aquatic microbiomes – Hugo Ribeiro – PLoS One

May 21, 2019

Today’s digest is short and sweet but includes interesting articles. A brilliant essay on multidisciplinarity in microbiome research 🥰

General Microbiome

ESSAY: Multidisciplinarity in Microbiome Research: A Challenge and Opportunity to Rethink Causation, Variability, and Scale. KR Amato – BioEssays

REVIEW:Contribution of the Mucosal Microbiota to Bovine Respiratory HealthM Zeineldin. Trends in Microbiology

Characterization of a novel salt-, xylose-and alkali-tolerant GH43 bifunctional β-xylosidase/α-l-arabinofuranosidase from the gut bacterial genome. B Xu. Journal of Bioscience and Bioengineering

Gut Microbiome

Circulating Microbiota-Based Metagenomic Signature for Detection of Hepatocellular CarcinomaEJ Cho. Scientific Reports

The bacterial communities of the small intestine and stool in children with short bowel syndrome. SL Zeichner. PLOS ONE

Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approachesGA Lugli. BMC Genome Biology

Plant, Soil, and Water Microbiome

Microbial production and consumption of dissolved organic matter in glacial ecosystems on the Tibetan PlateauL Zhou. Water Research

Engineering banana endosphere microbiome to improve Fusarium wilt resistance in banana. Y Liu.Microbiome
Toxic responses of metabolites, organelles and gut microorganisms of Eisenia fetida in a soil with chromium contaminationR Tang. Environmental Pollution

Roles of microbes in supporting sustainable rice production using the system of rice intensificationF Doni. Applied Microbiology and Biotechnology

Cover crop species have contrasting influence upon soil structural genesis and microbial community phenotype.A Bacq-Labreuil. Scientific Reports

Preprint

Treatment-Specific Composition of Gut Microbiota Is Associated with Disease Remission in a Pediatric Crohn’s Disease Cohort . Daniel Sprockett. bioRxiv posted 19 May 2019

May 20, 2019

This Monday, read about the stability within gut resident clonal populations of Enterobacteriaceae, significance of microbiome in personalized medicine, and impacts of intermittent supply on the drinking water microbiome. Happy reading!

General microbiome

Defining Microbiome Health through a Host Lens – Sean M. Gibbonsa – mSystems

*Review: The significance of microbiome in personalized medicine – Ava Behrouzi – Clinical and Translational Medicine

Moving towards a Robust Definition for a “Healthy” Indoor Microbiome – Karen C. Dannemiller – mSystems

Gut microbiome

*Rethinking gut microbiome residency and the Enterobacteriaceae in healthy human adults – Jonathan N. V. Martinson – ISME Journal

Rectal swabs in critically-ill patients provide discordant representations of the gut microbiome compared to stool samples: a brief methodologic report – Katherine Fair – bioRxiv

Development of a Covalent Inhibitor of Gut Bacterial Bile Salt Hydrolases – Arijit A. Adhikari – bioRxiv

Temporal Gut Microbial Changes Predict Recurrent Clostridium difficile in Patients with and without Ulcerative Colitis – Allen A. Lee – boRxiv

Alteration of Gut Microbiome in Lung Cancer Patients – Li Ming – bioRxiv

Respiratory microbiome

Microbiome disturbance and resilience dynamics of the upper respiratory tract in response to influenza A virus infection in humans and ferrets – Drishti Kaul – bioRxiv

High mortality from viral pneumonia in patients with cancer – Youn-Jung Ki – Infectious Diseases

Water microbiome

Global diversity and biogeography of bacterial communities in wastewater treatment plants – Linwei Wu – Nature Microbiology

*Understanding the impacts of intermittent supply on the drinking water microbiome – Quyen Melina Bautista-de los Santos – Current Opinion in Biotechnology

Animal microbiome

Exploration of the rumen microbial diversity and carbohydrate active enzyme profile of black Bengal goat using metagenomic approach – Prashant R. Suryawanshi – Animal Biotechnology

Assessing key microbial communities determining nitrogen transformation in composting of cow manure using illumina high-throughput sequencing – Yu Sun – Waste Management

Plant/root/soil microbiome

Root microbiota assembly and adaptive differentiation among European Arabidopsis populations – Thorsten Thiergart – bioRxiv

Response of Microbial Communities and Their Metabolic Functions to Drying–Rewetting Stress in a Temperate Forest Soil – Dong Liu – Microorganisms

Review: Rhizosphere size and shape: Temporal dynamics and spatial stationarity – Yakov Kuzyakov & Bahar S. Razavi – Soil Biology and Biochemistry

Phages and viruses

Production and characterization of novel ssRNA bacteriophage virus-like particles from metagenomic sequencing data – Ilva Lieknina – Journal of Nanobiotechnology

Techniques

PhenoGMM: Gaussian mixture modelling of microbial cytometry data enables efficient predictions of biodiversity – Peter Rubbens – bioRxiv

May 17, 2019

Today’s digest featuring a detailed contribution of the human microbiome to carcinogenesis, some interesting research, and reviews focusing on the microbial role in combat neurodegeneration, neuroimmune alterations, metabolism of lipids and N-ε-Carboxymethyllysine and an antibiotic resistome from healthy pig metagenome. Enjoy reading.

General microbiome

International Cancer Microbiome Consortium consensus statement on the role of the human microbiome in carcinogenesis – Alasdair J Scott – Gut

Exploring the impacts of raw materials and environments on the microbiota in Chinese Daqu starter – HaiDu – International Journal of Food Microbiology

Review: The Use of Defined Microbial Communities To Model Host-Microbe Interactions in the Human Gut – Janneke Elzinga – Microbiology and Molecular Biology Reviews

Gut microbiome

The bacterial communities of the small intestine and stool in children with short bowel syndrome – Steven L. Zeichner – PLOS ONE

Review: Modification of the gut microbiome to combat neurodegeneration – Andrew Octavian Sasmita Reviews in the Neurosciences

Markers of dysbiosis in patients with ulcerative colitis and Crohn’s disease – Danilova NA – Terapevticheskiĭ Arkhiv

Mid-life microbiota crises: middle age is associated with pervasive neuroimmune alterations that are reversed by targeting the gut microbiome – Marcus Boehme – Molecular Psychiatry

Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease Almut Heinken – Microbiome

Anaerobic Degradation of N-ε-Carboxymethyllysine, A Major Glycation End Product, By Human Intestinal Bacteria – Thi Phuong Nam Bui – Journal of Agricultural and Food Chemistry

Letter: Lipopolysaccharide from Gut Microbiota Modulates α-Synuclein Aggregation and Alters Its Biological Function – Dipita Bhattacharyya – ACS Chemical Neuroscience

Respiratory microbiome

Competition among Nasal Bacteria Suggests a Role for Siderophore-Mediated Interactions in Shaping the Human Nasal Microbiota – Reed M. Stubbendieck – Applied and Environmental Microbiology

Could the Sputum Microbiota Be a Biomarker That Predicts Mortality after Acute Exacerbations of Chronic Obstructive Pulmonary Disease?Jun-Chieh J. Tsay – American Journal of Respiratory and Critical Care Medicine

Skin microbiome

Amphibian Host and Skin Microbiota Response to a Common Agricultural Antimicrobial and Internal Parasite – Obed Hernández-Gómez – Microbial Ecology

Plant microbiome

Engineering banana endosphere microbiome to improve Fusarium wilt resistance in banana – Yupei Liu – Microbiome

Review: Ecology and Evolution of Plant Microbiomes – Viviane Cordovez – Annual Review of Microbiology

Animal microbiome / Animal experiments

Does MHC heterozygosity influence microbiota form and function? – M. A. Wadud Khan – PLOS ONE

Faecal microbiota shift during weaning transition in piglets and evaluation of AO blood types as shaping factor for the bacterial community profile – Vincenzo Motta – PLOS ONE

CD1d Modulates Colonic Inflammation in NOD2−/− Mice by Altering the Intestinal Microbial Composition Comprising Acetatifactor murisChansu Lee – Journal of Chron’s and Colitis

Switching on the light: using metagenomic shotgun sequencing to characterize the intestinal microbiome of Atlantic cod – Even Sannes Riiser – Environmental Microbiology

Predicting residual feed intake status using rumen microbial profiles in ewe lambs – Melinda J Ellison – Journal of Animal Science

Antibiotic resistomes of healthy pig faecal metagenomes Aoife Joyce – Microbial Genomics

Extract of ice plant (Mesembryanthemum crystallinum) ameliorates hyperglycemia and modulates the gut microbiota composition in type 2 diabetic Goto-Kakizaki rats – Chengcheng Zhang – Food and Function

Absence of gut microbiota during early life affects anxiolytic Behaviors and monoamine neurotransmitters system in the hippocampal of mice – Jun-Xi Pan – Journal of the Neurological Science

Gut microbiota characterization and lipid metabolism disorder found in PCB77-treated female mice – YulangChi – Toxicology

Fecal Viral Diversity of Captive and Wild Tasmanian Devils Characterized Using Virion-Enriched Metagenomics and Metatranscriptomics – Rowena Chong – Journal of Virology

Depression Promotes the Onset of Irritable Bowel Syndrome through Unique Dysbiosis in Rats – Takeshi Takajo – Gut and Liver

Hepatic progenitor cell activation is induced by the depletion of the gut microbiome in mice – Fei Wang – MicrobiologyOpen

Prebiotics/Probiotics

Saccharomyces boulardii CNCM I-745 changes lipidemic profile and gut microbiota in a hamster hypercholesterolemic model – F. Briand – Beneficial Microbes

May 16, 2019

Today’s digest includes the microbial communities of fruit peels, bacterial crude oil degradation, and the gut microbiome of sea cucumbers. Enjoy!

Pregnancy and early life

Preprint: Interactions between the gut microbiome and mucosal immunoglobulins A, M and G in the developing infant gut – Janzon – BioRxiv

Human gut microbiome

Evolution of the gut microbiome following acute HIV-1 infection – Rocafort – Microbiome

Animal microbiome

Evaluation of the Function of Wild Animal Gut Microbiomes Using Next-Generation Sequencing and Bioinformatics and its Relevance to Animal Conservation – Yao – Evolutionary Bioinformatics

High-throughput sequencing of 16S rRNA amplicons characterizes gut microbiota shift of juvenile sea cucumber Apostichopus japonicus feeding with three antibiotics – Zhao – Journal of Oceanology and Limnology

Plant, root, and soil microbiome

Contrasting patterns and drivers of soil fungal communities in subtropical deciduous and evergreen broadleaved forests – Chen – Applied Microbiology and Biotechnology

Evaluation of microbial communities in peels of Brazilian tropical fruits by amplicon sequence analysis – Cruz – Brazilian Journal of Microbiology

Assembly mechanisms of soil bacterial communities in subalpine coniferous forests on the Loess Plateau, China – Zhao – Journal of Microbiology

Evaluating the effects of canine urine on urban soil microbial communities – Lee – Urban Ecosystems

Methane emission and soil microbial communities in early rice paddy as influenced by urea-N fertilization – Liu – Plant and Soil

Rhizosphere carbon supply accelerates soil organic matter decomposition in the presence of fresh organic substrates – Jackson – Plant and Soil

The relative contributions of pH, organic anions, and phosphatase to rhizosphere soil phosphorus mobilization and crop phosphorus uptake in maize/alfalfa polyculture – Sun – Plant and Soil

Diversity of anammox bacteria and abundance of functional genes for nitrogen cycling in the rhizosphere of submerged macrophytes in a freshwater lake in summer – Zhao – Journal of Soils and Sediments

Direct and indirect effects of elevated CO2 and nitrogen addition on soil microbial communities in the rhizosphere of Bothriochloa ischaemum – Xiao – Journal of Soils and Sediments

Rhizocompartments and environmental factors affect microbial composition and variation in native plants – Kang – Journal of Microbiology

The inhibitory effect of cadmium and/or mercury on soil enzyme activity, basal respiration, and microbial community structure in coal mine–affected agricultural soil – Zheng – Annals of Microbiology

Water and extremophile microbiome

Preprint: Metabolic Architecture of the Deep Ocean Microbiome – Acinas – BioRxiv

Production of Current by Syntrophy Between Exoelectrogenic and Fermentative Hyperthermophilic Microorganisms in Heterotrophic Biofilm from a Deep-Sea Hydrothermal Chimney – Pillot – Microbial Ecology

A glimpse of the prokaryotic diversity of the Large Aral Sea reveals novel extremophilic bacterial and archaeal groups – Shurigin – MicrobiologyOpen

Molecular analyses of bacterioplankton communities with highly abundant Vibrio clades: a case study in Bohai Sea coastal waters – Wang – Journal of Oceanology and Limnology

Archaeal communities in the deep-sea sediments of the South China Sea revealed by Illumina high-throughput sequencing – Li – Annals of Microbiology

Bacterial succession and co‐occurrence patterns of an enriched marine microbial community during light crude oil degradation in a batch reactor – Uribe‐Flores – Journal of Applied Microbiology

Microbial assemblages reflect environmental heterogeneity in alpine streams – Hotaling – Global Change Biology

Food microbiology

Bacterial community dynamics in lait caillé, a traditional product of spontaneous fermentation from Senegal – Groenenboom – PLoS One