Category Archives: Animal microbiome

July 04, 2018

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Today’s Digest is about association of the microbiome at various mucosal sites with different diseases in humans, germ-free chicken and microbial community in anoxic inter-tidal zone of Earth to study Lacustrine system of Mars. You can also read about BacStalk- software to analyze bacterial images, Chinese baby project and how air pollution is contributing to incidence of diabetes.

General microbiome

Review: Gut associated bacteria are critical to metabolism, inflammation and health – Philip Newsholme – Current Opinion in Clinical Nutrition and Metabolic Care

Review: The Microbiome and Acute Kidney Injury – H Rabb – Nephron

Multi-site human microbiome

Review: Cariogenic microbiome and microbiota of the early primary dentition: a contemporary overview – Kausar Sadia Fakhruddin – Oral Diseases

Dysbiosis of oral microbiota and its association with salivary immunological biomarkers in autoimmune liver disease – Kazumichi Abe – PlosOne

Human respiratory microbiome

Severe Obstructive Sleep Apnea is Associated with Alterations in the Nasal Microbiome and Increase in Inflammation – Benjamin G Wu – American Journal of Respiratory and Critical Care Medicine

Microbiota Composition and the Integration of Exogenous and Endogenous Signals in Reactive Nasal Inflammation – Francesco Antonio Salzano – Journal of Immunology Research

Human skin microbiome

Inflammatory cytokines and biofilm production sustain Staphylococcus aureus outgrowth and persistence: a pivotal interplay in the pathogenesis of Atopic Dermatitis – E.G.Di Domenico – Scientific reports

Human vaginal microbiome

Complex ecological interactions of Staphylococcus aureus in tampons during menstruation – Isaline Jacquemond – Scientific Reports

Human gut microbiome

Altered Intestinal Microbiota with Increased Abundance of Prevotella Is Associated with High Risk of Diarrhea-Predominant Irritable Bowel Syndrome – Tingting Su – Gastroenterology Research and Practice

The presence of genetic risk variants within PTPN2 and PTPN22 is associated with intestinal microbiota alterations in Swiss IBD cohort patients – Bahtiyar Yilmaz – PlosOne

Animal experiments 

Gut Microbial succession during conventionalization of germfree chicken – Thomas Milton – bioRxiv

Early-life antibiotics attenuate regulatory T cell generation and increase the severity of murine house dust mite-induced asthma – Alexander J. Adami – Pediatric Research

Changes in intestinal gene expression and microbiota composition during late pregnancy are mouse strain dependent – Marlies Elderman – Scientific Reports

Critical Roles for Microbiota-Mediated Regulation of the Immune System in a Prenatal Immune Activation Model of Autism – Catherine R. Lammert – The Journal of Immunology

Plant, root, and soil microbiome

Cascading effects of elevated ozone on wheat rhizosphere microbial communities depend on temperature and cultivar sensitivity – F. Changey – Environmental Pollution

Litter quality drives the differentiation of microbial communities in the litter horizon across an alpine treeline ecotone in the eastern Tibetan Plateau – Haifeng Zheng – Scientific Reports

Identification of a Novel Feruloyl Esterase by Functional Screening of a Soil Metagenomic Library – Xuanxuan Li – Applied Biochemistry and Biotechnology

Water and extremophile microbiome

Quorum sensing and iron regulate a two-for-one siderophore gene cluster in Vibrio harveyi – Darcy L. McRose – PNAS

Identifying labile DOM components in a coastal ocean through depleted bacterial transcripts and chemical signals – Alexey Vorobev – Environmental Microbiology

Metabolic potential of microbial communities from ferruginous sediments – Aurele Vuillemin – Environmental Microbiology

Microbes in space

The Microbial Community of a Terrestrial Anoxic Inter-Tidal Zone: A Model for Laboratory-Based Studies of Potentially Habitable Ancient Lacustrine Systems on Mars – Elliot Curtis-Harper – Microorganisms

Phages and viruses

Development of a high-throughput assay to detect antibody inhibition of low pH induced conformational changes of influenza virus hemagglutinin – Jessica F. Trost – PlosOne

Techniques

Review: Errors during Gene Expression: Single-Cell Heterogeneity, Stress Resistance, and Microbe-Host Interactions – Christpher R. Evans – mBio

BacStalk: a comprehensive and interactive image analysis software tool for bacterial cell biology – Raimo Hartmann – bioRxiv

Assessing the Mouse Intestinal Microbiota in Settings of Type-2 Immune Responses – Mei San Tang – Type 2 Immunity

Microbes in the news

Bacteria can ‘divide and conquer’ to vanquish their enemies – Science Daily

Gigantic study of Chinese babies yields slew of health data – Nature News

Non-microbiology picks

The 2016 global and national burden of diabetes mellitus attributable to PM2·5 air pollution – Benjamin Bowe – The Lancet Planetary Health

July 02, 2018

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Good morning! Today’s Microbiome Digest will cover the general microbiome, HIV infection and multi-site bacterial microbiota, crucial role of lung microbiome in asthma, gut microbiome in type 1 diabetes, Link between diet and metabolic syndrome, Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes, HmmUFOtu: a tool for taxonomic assignment and OTU picking and a news on plastic eating bacteria …

Events and jobs

Post-Doctoral Research Position, Oregon State University, with Dr. Stephen Giovannoni

Postdoctoral Researcher Position Characterizing Microbial Candidate Phlya at Stanford University

General microbiome

Issue: The microbiome: more than a gut reaction – John R. Wingard – Blood

Evaluation at scale of microbiome-derived metabolites as biomarker of flavan-3-ol intake in epidemiological studies – Javier I. Ottaviani – Scientific Reports

All disease begins in the gut: Influence of gastrointestinal disorders and surgery on oral drug performance – Grace B. Hatton – International Journal of Pharmaceutics

Designing microbial consortia with defined social interactions – Wentao Kong – Nature Chemical Biology

Multi-site human microbiome

HPV infection and bacterial microbiota in the placenta, uterine cervix and oral mucosa – Heidi Tuominen – Scientific Reports

Human respiratory microbiome

State of the Art: Does lung microbiome play a causal or casual role in asthma? – Maria Di Cicco – Pediatric Pulmonology

Human vaginal microbiome

Increased richness and diversity of the vaginal microbiota and spontaneous preterm birth – Aline C. Freitas – Microbiome

Human gut microbiome

Review: Gut microbiome in type 1 diabetes: A comprehensive review – Zheng P – Diabetes Metab Res Rev

Review: Altered Gut Microbiota: A Link Between Diet and the Metabolic Syndrome – Velasquez Manuel T – Metabolic Syndrome and Related Disorders

Chapter: Microbiota, Obesity and NAFLD – Louis H. S. Lau – Obesity, Fatty Liver and Liver Cancer

Chapter: The Influence of Gut Microbial Metabolism on the Development and Progression of Non-alcoholic Fatty Liver Disease – Wei Jia – Obesity, Fatty Liver and Liver Cancer

Method: Assessing the Mouse Intestinal Microbiota in Settings of Type-2 Immune Responses – Mei San Tang – Type 2 Immunity

Ancient Thali Diet: Gut Microbiota, Immunity, and Health – Kaitlyn Shondelmyer – Yale Journal of Biology & Medicine

Altered gut microbiome composition in children with refractory epilepsy after ketogenic diet – Yunjian Zhang – Epilepsy Research

The Stringent Response Determines the Ability of a Commensal Bacterium to Survive Starvation and to Persist in the Gut – Whitman B. Schofield – Cell Host & Microbe

Review: Update on the Gastrointestinal Microbiome in Systemic Sclerosis – Chiara Bellocchi – Current Rheumatology Reports

Review: The Gut Microbiome Alterations and Inflammation-Driven Pathogenesis of Alzheimer’s Disease—a Critical Review – Marta Sochocka – Molecular Neurobiology

The controversial role of Enterococcus faecalis in colorectal cancer – Carolina Vieira de Almeida – Therapeutic Advances in Gastroenterology

Animal experiments

Pea-protein alginate encapsulation adversely effects development of clinical signs of Citrobacter rodentium-induced colitis in mice treated with probiotics – Natallia Varankovich – Canadian Journal of Microbiology

Maternal Soluble Fiber Diet during Pregnancy Changes the Intestinal Microbiota, Improves Growth Performance, and Reduces Intestinal Permeability in Piglets – Chuanshang Cheng – Applied and Environmental Microbiology

Overlapping community composition of gut and fecal microbiomes in lab-reared and field-collected German cockroaches – Madhavi L. Kakumanu – Applied and Environmental Microbiology

TRIF deficiency protects non-obese diabetic mice from type 1 diabetes by modulating the gut microbiota and dendritic cells – Elke Gülden – Journal of Autoimmunity

Mucosal homeostasis is altered in the ileum of gnotobiotic mice – Chasen J. Greig – Journal of Surgical Research

Animal microbiome

Factors influencing bacterial microbiome composition in a wild non-human primate community in Taï National Park, Côte d’Ivoire – Jan F. Gogarten – The ISME Journal

Characterization of Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes – Pablo Tsukayama – mSystems

Genetic variability and ontogeny predict microbiome structure in a disease-challenged montane amphibian – Sarah M. Griffiths – The ISME Journal

Plant, root, and soil microbiome

Review: Multifaceted Impacts of Bacteriophages in the Plant Microbiome – Britt Koskella – Annual Review of Phytopathology

‘Concord’ grapevine nutritional status and chlorosis rank associated with fungal and bacterial root zone microbiomes – R.W.Lewis – Plant Physiology and Biochemistry

Draft Genome Sequences of Two Novel Cellulolytic Streptomyces Strains Isolated from South African Rhizosphere Soil – Mobolaji F. Adegboye – Genome Announcements

Differences in microbial key players in anaerobic degradation between biogas and sewage treatment plants – Christian Buettner – International Biodeterioration & Biodegradation

Water and extremophile microbiome

The impact of the Deepwater Horizon blowout on historic shipwreck-associated sediment microbiomes in the northern Gulf of Mexico – Leila J. Hamdan – Scientific Reports

Stoichio-Metagenomics of ocean waters: a molecular evolution approach to trace the dynamics of nitrogen conservation in natural communities – Hannes Dittberner – Frontiers in Microbiology

 Probiotics / prebiotics

Review: Impact of Prebiotics on Poultry Production and Food Safety – Steven C. Ricke – Yale Journal of Biology & Medicine

Isolation and Partial Characterization of Lactic Acid Bacteria from the Gut Microbiota of Marine Fishes for Potential Application as Probiotics in Aquaculture – Sergio Alonso – Probiotics and Antimicrobial Proteins

Effects of Prebiotics vs a Diet Low in Fodmaps in Patients with Functional Gut Disorder – Jose-Walter Huaman – Gastroenterology

Bioinformatics

HmmUFOtu: An HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies – Qi Zheng – Genome Biology

Techniques

Review: Culturing the human microbiota and culturomics – Jean-Christophe Lagier – Nature Reviews Microbiology

Microbes in the news

Plastic-eating bacteria discovered by student could help solve global pollution crisis

Sewage microbes make a fuel booster

Our intestinal microbiome influences metabolism — through the immune system

 

Ashok’s non-microbiology picks

Efficacy and Safety of Dupilumab in Glucocorticoid-Dependent Severe Asthma – Klaus F. Rabe – The NEW ENGLAND JOURNAL of Medicine

June 29, 2018

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A variety of reviews on the human skin and gut microbiota, effects of probiotics on depressive behaviors, microbiota changes in deer populations in China.

Human skin microbiome

Review: Microbiome in the Gut-Skin Axis in Atopic Dermatitis – So-Yeon Lee – Allergy and Asthma Immunology Research

Human gut microbiome

Pre-print: The Genetic Basis for the Cooperative Bioactivation of Plant Lignans by a Human Gut Bacterial Consortium – Elizabeth N Bess – bioRxiv

Review: Mechanistic Insights in the Success of Fecal Microbiota Transplants for the Treatment of Clostridium difficile Infections – Amoe Baktash – Frontiers in Microbiology

Review: Reciprocal Interactions Between Gut Microbiota and Host Social Behavior – Emmanuelle Münger – Frontiers in Integrative Neuroscience

Review: Gut microbiota bile acid metabolism controls cancer immunosurveillance – Anna Dart – Nature Reviews Microbiology

Animal experiments

Pulmonary Arterial Hypertension Affects the Rat Gut Microbiome – María Callejo – Scientific Reports

Animal microbiome

Comparative Analysis of Gut Microbiota Changes in Père David’s Deer Populations in Beijing Milu Park and Shishou, Hubei Province in China – Meishan Zhang – Frontiers in Microbiology

Ixodes scapularis does not harbor a stable midgut microbiome – Benjamin D Ross – The ISME Journal

Plant, root, and soil microbiome

Different Height Forms of Spartina alterniflora Might Select Their Own Rhizospheric Bacterial Communities in Southern Coast of China – Li’an Lin – Microbial Ecology

Survey of sediment oxygenation in rhizospheres of the saltmarsh grass – Spartina anglica – Ketil Koop-Jakobsen – Science of the Total Environment

Probiotics/prebiotics

Probiotics decrease depressive behaviors induced by constipation via activating the AKT signaling pathway – Nana Xu – Metabolic Brain Disease

Phages and viruses

Pre-print: Seroprevalence of fourteen human polyomaviruses determined in blood donors – Sergio S Kamminga – bioRxiv

Bioinformatics

A distinct abundant group of microbial rhodopsins discovered using functional metagenomics – Alina Pushkarev – Nature

Techniques

Selection of validated hypervariable regions is crucial in 16S-based microbiota studies of the female genital tract – Simon Graspeuntner – Scientific Reports

More microbes

Cryo-EM structure of an essential Plasmodium vivax invasion complex – Jakub Gruszczyk – Nature

Microbes in the news

Genetically modified bacteria enlisted in fight against disease – Sara Reardon – Nature

A short course of laxatives has long-lasting effects on microbiome – Nature

June 28, 2018

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Microbial adaptation to snake and spider venom, a 1.5-year study of fungi in space at the International Space Station, US National Postdoc Survey results.

General microbiome

Quantitative assessment of individual populations within polymicrobial biofilms – Susana Patrícia Lopes – Scientific Reports

Human nearly-sterile sites

Streptococcus mutans in Umbilical Cord Blood, Peripheral Blood, and Saliva from Healthy Mothers – Marcelly Milhomem Mendes – Current Microbiology

Animal microbiome

Pre-print: Microbial adaptation to venom is common in snakes and spiders – E Esmaeilishirazifard – bioRxiv

Plant, root, and soil microbiome

Colonisation dynamics of arbuscular mycorrhizal fungi and dark septate endophytes in the sugarcane crop cycle – Anders Claassens – Rhizosphere

Response Surface Modelling through Box-Behnken approach to optimize bacterial quorum sensing inhibitory action of Tribulus terrestris root extract – Kayeen Vadakkan – Rhizosphere

Multi ‘omics comparison reveals metabolome biochemistry, not microbiome composition or gene expression, corresponds to elevated biogeochemical function in the hyporheic zone – Emily B Graham – Science of the Total Environment

Pre-print: Co-culture of soil biofilm isolates enables the discovery of novel antibiotics – Chun-Hui Gao – bioRxiv

Pre-print: Microbial interkingdom interactions in roots promote Arabidopsis survival – Paloma Duran – bioRxiv

Water and extremophile microbiome

Persisting responses of salt marsh fungal communities to the Deepwater Horizon oil spill – Candice Y Lumibao – Science of the Total Environment

Microbes in space

Integrity of the DNA and Cellular Ultrastructure of Cryptoendolithic Fungi in Space or Mars Conditions: A 1.5-Year Study at the International Space Station – Silvano Onofri – Life

Food microbiology

Influence of lactate and acetate removal on the microbiota of French fresh pork sausages – Agnès Bouju-Albert – Food Microbiology

Probiotics/prebiotics

The anxiolytic effect of probiotics: A systematic review and meta-analysis of the clinical and preclinical literature – Daniel J Reis – PLOS ONE

Phages and viruses

Pre-print: Megaphage infect Prevotella and variants are widespread in gut microbiomes – Audra E Devoto – bioRxiv

Bacteria art

Fifty Percent Human – how art brings us in touch with our microbial cohabitants – Sonja Bäumel – Microbial Biotechnology

Scottish fashion student who grows dresses from tea brews up storm in fashion world – Daily Record

artist reimagines the human microbiome as an intricately cut paper coral reef – design bloom

The next big home design trend? Bacteria – Co.Design

Science, career, and publishing

Pre-print: Career Choice, Gender, and Mentor Impact: Results of the U.S. National Postdoc Survey – Sean C McConnell – bioRxiv

June 27, 2018

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In today’s Microbiome Digest you can read about: cyanobacterial blooms by J. Huisman, designer microbial consortia by W. Kong,  the significance of the intestinal microbiome for vaccinology by Vanessa C. Harris, indigenous microbes residing in oil sands by Xiaoxuan Yu, effects of sliver nanoparticles on soil microbiome by J.Y. Xu,  WHAM!: a web-based visualization tool for metagenomics by J.C. Devlin. Yet another interesting read you can find in Science & Publishing  –> “Death of scientific journals after 350 years” by S. Silver. Enjoy!

General microbiome

Designing microbial consortia with defined social interactions –  Wentao Kong – Nature Chemical Biology

Pregnancy and early life

Antibiotics in early life: dysbiosis and the damage done – Hadar Neuman – FEMS Microbiology Reviews

Human ear microbiota

The unsolved problem of otitis media in indigenous populations: A systematic review of upper respiratory and middle ear microbiota in indigenous children – Andrea Coleman – bioRxiv

Human respiratory microbiome

Does lung microbiome play a causal or casual role in asthma? – Maria Di Cicco – Pediatric Pulmonology

Human gut microbiome

Alterations in the gut bacterial microbiome in fungal Keratitis patients – Sama Kalyana Chakravarthy – PLOS One

Altered intestinal microbiota composition, antibiotic therapy and intestinal inflammation in children and adolescents with cystic fibrosis – Maiara Brusco de Freitas – PLOS One

Nonaplex PCR using Cliffhanger primers to identify diarrhoeagenic Escherichia coli from crude lysates of human faecal samples – Uffe Vest Schneider – PLOS One

Review: The Significance of the Intestinal Microbiome for Vaccinology: From Correlations to Therapeutic Applications – Vanessa C. Harris – Drugs

Review: Update on the Gastrointestinal Microbiome in Systemic Sclerosis – Chiara Bellocchi – Current Rheumatology Reports

Gut microbiota components are associated with fixed airway obstruction in asthmatic patients living in the tropics – Emiro Buendía – Scientific Reports

Role of Microbiota and Tryptophan Metabolites in the Remote Effect of Intestinal Inflammation on Brain and Depression – Barbora Waclawiková – Pharmaceuticals

The study of bacteria in biopsies from Slovak colorectal adenoma and carcinoma patients – L. Wachsmannova-  Neoplasma

Amplification of Antimicrobial Resistance in Gut Flora of Patients Treated with Ceftriaxone – J. Meletiadis – Antimicrobial Agents and Chemotherapy

Animal experiments 

Metabolome disruption of pregnant rats and their offspring resulting from repeated exposure to a pesticide mixture representative of environmental contamination in Brittany – Nathalie Bonvallot – PLOS One

Dietary supplementation with raspberry extracts modifies the fecal microbiotain obese diabetic db/db mice –    Jose F. Garcia-Mazcorro – Journal of Microbiology and Biotechnology

Effects of dietary yeast nucleotides supplementation on intestinal barrier function, intestinal microbiota, and humoral immunity in specific pathogen-free chickens – Che Wu – Poultry Science

Magnesium lithospermate B improves the gut microbiome and bile acid metabolic profiles in a mouse model of diabetic nephropathy – Jing Zhao – Acta Pharmacologica Sinica

Animal microbiome

Evaluation of the impact of dental prophylaxis on the oral microbiota of dogs – Rebecca Flancman – PLOS One

Improving the standards for gut microbiome analysis of fecal samples: insights from the field biology of Japanese macaques on Yakushima Island – Takashi Hayakawa – Primates

Plant, root, and soil microbiome

Indigenous microorganisms residing in oil sands tailings biodegrade residual bitumen – Xiaoxuan Yu – Chemosphere

Interactive effects of Magnaporthe inoculation and nitrogen doses on the plant enzyme machinery and phyllosphere microbiome of resistant and susceptible rice cultivars – Shobit Thapa – Archives of Microbiology

Large-scale replicated field study of maize rhizosphere identifies heritable microbes – William A. Walters – PNAS

Long-term effects of sliver nanoparticles on the abundance and activity of soil microbiome – Jing Yang Xu – Journal of Environmental Sciences

Long-term effects of environmentally relevant concentrations of silver nanoparticles on microbial biomass, enzyme activity, and functional genes involved in the nitrogen cycle of loamy soil – Anna-Lena Grün – Journal of Environmental Sciences

Sphingomonas tabacisoli sp. nov., a member of the genus Sphingomonas, isolated from rhizosphere soil of Nicotiana tabacum L. – Xing-Kui Zhou – International Journal of Systematic and Evolutionary Microbiology

Effects of Bacillus subtilis and nanohydroxyapatite on the metal accumulation and microbial diversity of rapeseed (Brassica campestris L.) for the remediation of cadmium-contaminated soil – Wei Liu – Environmental Science and Pollution Research

Interactive effects of Magnaporthe inoculation and nitrogen doses on the plant enzyme machinery and phyllosphere microbiome of resistant and susceptible rice cultivars – Shobit Thapa – Archives of Microbiology

Water and extremophile microbiome

Heliorhodopsins are absent in diderm (Gram-negative) bacteria: Some thoughts and possible implications for activity – Jose Flores-Uribe – bioRxiv

Comparative genomics analyses indicate differential methylated amine utilisation trait within the member of the genus Gemmobacter – Eileen Kröber – bioRxiv

Functional annotation of hypothetical proteins from the Exiguobacterium antarcticum strain B7 reveals proteins involved in adaptation to extreme environments, including high arsenic resistance – Wana Lailan Oliveira da Costa – PLOS One

Factors affecting infection of corals and larval oysters by Vibrio coralliilyticus – Blake Ushijima – PLOS One

“Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell ‘omics” –  Xyrus X Maurer-Alcalá – Genome Biology and Evolution

Integrated methodological approach reveals microbial diversity and functions in aerobic groundwater microcosms adapted to vinyl chloride – Xikun Liu – FEMS Microbiology Ecology

Specialized proteomic responses and an ancient photoprotection mechanism sustain marine green algal growth during phosphate limitation – Jian Guo –  Nature Microbiology

Warming and oligotrophication cause shifts in freshwater phytoplankton communities – Laura Verbeek – Global Change Biology

Review: Cyanobacterial blooms – Jef Huisman – Nature Reviews Microbiology

Research letter: Airborne Microbes Contribute to N2 Fixation in Surface Water of the Northern Red Sea – Eyal Rahav – Geophysical Research Letters

Bloom of a denitrifying methanotroph, “Candidatus Methylomirabilis limnetica”, in a deep stratified lake – Jon S. Graf – Environmental Microbiology

Extensive nitrification and active ammonia oxidizers in two contrasting coastal systems of the Baltic Sea – Elisabeth Happel – Environmental Microbiology

Microbial life under ice: Metagenome diversity and in situ activity of Verrucomicrobia in seasonally ice‐covered lakes – Patricia Tran – Environmental Microbiology

Rapid thermal adaptation in a marine diatom reveals constraints and tradeoffs – Daniel R. O’Donnell – Global Change Biology

A Virus Infecting Marine Photoheterotrophic Alphaproteobacteria (Citromicrobium spp.) Defines a New Lineage of ssDNA Viruses – Qiang Zheng – Frontiers in Microbiology / Virology

Built environment 

Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales – Mikayla A. Borton – PNAS

Phages and viruses

Two point mutations in the Hantaan virus glycoproteins afford the generation of a highly infectious recombinant vesicular stomatitis virus vector – Megan M Slough – bioRxiv

ΦCrAss001, a member of the most abundant bacteriophage family in the human gut, infects Bacteroides – Andrey Shkoporov – bioRxiv

In silico characterisation of the two-component system regulators of Streptococcus pyogenes – Sean J. Buckley- PLOS One

Host-microbiome interactions

Opinion: Classic Models for New Perspectives: Delving into Helminth–Microbiota–Immune System Interactions – Alba Cortés – Trends in Parasitology

Review: Helminth–Bacterial Interactions: Cause and Consequence – Alexis Rapin – Trends in Immunology

Bioinformatics

WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data – Joseph C. Devlin – BMC Genomics

MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples – Ehsaneddin Asgari – Bioinformatics

Science, publishing, and career 

The Impact of Grant Funding on the Publication Activity of Awarded Applicants: A Systematic Review of Comparative Studies and Meta-analytical Estimates – Ruslan Saygitov – bioRxiv

Death of scientific journals after 350 years – Simon Silver – FEMS Microbiology Letters

June 26, 2018

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Today’s Microbiome Digest cover the topics on bioinformatics; methods and models; trials and therapies; infection and immunity; microbiome of human gut, human vagina, insect, animals, plant, marine; food and nutrition; bioremediation and metabolomics.

 

EVENTS- JOBS – PhD POSITIONS:

Event – Organoids: Modelling Organ Development and Disease in 3D Culture – EMBO| EMBL Symposia

 

NEWS and VIEWS:

Pairing off: a bottom-up approach to the human gut microbiome– Clare Abreu – Molecular Systems Biology

 

BIOINFORMATICS:
Zero-inflated generalized Dirichlet multinomial regression model for microbiome compositional data analysis – Tang ZZ – Biostatistics

 

METHODS and MODELS:

Book Chapter – Methods for Microbiota Analysis: Sample Collection and Laboratory Methods – Saleh Ibrahim – The Microbiome in Rheumatic Diseases and Infection

Review: Culturing the human microbiota and culturomics – Lagier JC – Nature Reviews Microbiology

Using glycolysis enzyme sequences to inform Lactobacillus phylogeny – Katelyn Brandt – Microbial Genomics

Multicenter study establishing the clinical validity of a nucleic-acid amplification-based assay for the diagnosis of bacterial vaginosis – Cartwright CP – Diagnostics Microbiology and Infectious Disease.

PATENT – SYSTEM AND METHODS FOR DEVELOPING AND USING A MICROBIOME-BASED ACTION COMPONENT FOR PATIENT HEALTH – Warren Tracy, Jantzen Tammi Gregory Katherine

 

TRIALS and THERAPIES:

Antimicrobial photodynamic therapy as a new approach for the treatment of vulvovaginal candidiasis: preliminary results – Aline Silva Sousa – Lasers in Medical Science

Review – Prevention of Cystitis: Travelling between the Imaginary and Reality – Vecchio M – Annals of Nutrition and Metabolism

 

INFECTIONS and IMMUNITY:

Book Chapter – The Impact of Infections on Reproduction and Fertility – VE Jones – Clinical Reproductive Science

Intestinal barrier disruption and dysregulated mucosal immunity contribute to kidney fibrosis in chronic kidney disease – Yang J – Nephrology Dialysis Transplantation

In Press: Treatment and Prevention of Recurrent Lower Urinary Tract Infections in Women: A Rapid Review with Practice Recommendations – Ariana l Smith – The Journal of Urology

Book Chapter – Immunology of the Microbiome: Implications for Rheumatoid Arthritis and Other Autoimmune Diseases – Daniel M Altmann – The Microbiome in Rheumatic Diseases and Infection

 

VAGINAL MICROBIOME:

Description of three new Peptoniphilus species cultured in the vaginal fluid of a woman diagnosed with bacterial vaginosis: Peptoniphilus pacaensis sp. nov., Peptoniphilus raoultii sp. nov., and Peptoniphilus vaginalis sp. nov. – Diop K – Microbiology Open

 

GUT MICROBIOME: 

Preview – Gut microbiota as a missing link between nutrients and traits of human – Hea-Jong Chung – Frontiers in Microbiology

Preview – The gut-brain axis, the human gut microbiota and their integration in the development of obesity – Edward S Bliss – Frontiers in Microbiology

Review – The Gut Microbiome as a Target for the Treatment of Type 2 Diabetes – Ömrüm Aydin – Current Diabetes reports

Beneficial metabolic effects of 2’, 3’, 5’-tri-acetyl-N6-(3-hydroxylaniline) adenosine in multiple biological matrices and intestinal flora of hyperlipidemic hamsters– Tianqi Li – Journal of Proteome Research

 

ANIMAL MICROBIOME:

Preview – Dynamics of gut microbiota diversity during the early development of an avian host: evidence from a cross-foster experiment – Aimeric Teyssier – Frontiers in Microbiology

Enterococcus faecium WEFA23 from infant lessens high-fat-diet-induced hyperlipidemia via cholesterol 7-alpha-hydroxylase gene by altering the composition of gut microbiota in rats – Fuqing Huang – ScienceDirect

Evaluation of the impact of dental prophylaxis on the oral microbiota of dogs – Flancman R – PloS One

Microbial diversity and community composition of caecal microbiota in commercial and indigenous Indian chickens determined using 16s rDNA amplicon sequencing – Ramesh J Pandit – Microbiome

 

GENERAL MICROBIOME:

Review – Role of nutrition, infection, and the microbiota in the efficacy of oral vaccines – Amrita Bhattacharjee – Clinical Science

Commensal Microbiota Enhance Both Osteoclast and Osteoblast Activities – Yoko Uchida – Molecules

 

PLANT/ROOT/SOIL MICROBIOME:

Editorial – The contribution of plant microbiota to economy growth – Angela Sessitsch – Microbial Biotechnology

Colonization cues of leaf- and root-inhabiting bacterial microbiota of Atractylodes lancea derived in vitro and in vivo – Yong Jia – Plant and Soil

Preview – Complete Genome Sequence of Industrial Biocontrol Strain Paenibacillus polymyxa HY96-2 and Further Analysis of Its Biocontrol Mechanism – Yuanchan Luo – – Frontiers in Microbiology

Genome Sequence of Bacillus megaterium Strain YC4-R4, a Plant Growth-Promoting Rhizobacterium Isolated from a HighSalinity Environment – Juan Ignacio Vílchez – GenomeAnnouncements

 

INSECT MICROBIOME:

Exposure of soil collembolans to microplastics perturbs their gut microbiota and alters their isotopic composition – DongZhu – Soil Biology and Biochemistry

 

SKIN MICROBIOME:

Book Chapter – Psoriasis and Psoriatic Arthritis – Madhura Castelino – The Microbiome in Rheumatic Diseases and Infection

 

MARINE MICROBIOME:
Metagenomics Sheds Light on the Ecology of Marine Microbes and Their Viruses – Felipe Hernandes Coutinho – Trends in Microbiology

 

NEONATAL/INFANT MICROBIOME:

Communication – Maternal Intrapartum Antibiotic Administration and Infantile Colic: Is there a Connection? – Leppälehto E – Neonatology

Review – Intrauterine Inflammation, Epigenetics, and Microbiome Influences on Preterm Infant Health – Lu L – Current Pathobiology Reports

 

CROSS – POPULATION MICROBIOME:
Similarities and differences in gut microbiome composition correlate with dietary patterns of Indian and Chinese adults – Abhishek Jain – AMB Express

 

PHAGES/VIRUSES:

Genome Sequence of the Pseudomonas protegens Phage GP100 – Jordan Vacheron – GenomeAnnouncements

 

FOOD and NUTRITION:

Plasma and urine metabolite profiling reveals the protective effect of Clinacanthus nutans in an ovalbumin-induced anaphylaxis model: 1H-NMR metabolomics approach – Leng Wei Khoo – Journal of Pharmaceutical and Biomedical Analysis

Drivers that establish and assembly the lactic acid bacteria biota in cheeses – Marco Gobbetti – Trends in Food Science & Technology

The food safety of DP-356Ø43 soybeans on SD rats reflected by physiological variables and fecal microbiota during a 90-day feeding study – Zou S – Regul Toxicol Pharmacol

Fermented Soybean Suppresses Visceral Fat Accumulation in Mice – Kushida M – Molecular Nutrition and Food Research

Combined Use of C. butyricum Sx-01 and L. salivarius C-1-3 Improves Intestinal Health and Reduces the Amount of Lipids in Serum via Modulation of Gut Microbiota in Mice – Long M – Nutrients

Review – Dietary polyphenols: A novel strategy to modulate microbiota-gut-brain axis – Diana Serra – Trends in Food Science & Technology

 

METABOLOMICS:

Non-invasive urinary metabolomic profiles discriminate biliary atresia from infantile hepatitis syndrome – Wei-Wei Li – Metabolomics

Metabolomics of the amniotic fluid: Is it a feasible approach to evaluate the safety of Chinese medicine during pregnancy? – Jinjun Shan – Journal of Applied Toxicology

Article – A validated, fast method for quantification of sterols and gut microbiome derived 5α/β-stanols in human faeces by isotope dilution LC-high resolution MS – Schoett HF – Analytical Chemistry

 

BIOREMEDIATION:

Bioprospecting for microbes with potential hydrocarbon remediation activity on the northwest coast of the Yucatan Peninsula, Mexico, using DNA sequencing – Mariela Beatriz Reyes-Sosa – Science of The Total Environment

 

ANTIBIOTIC SUSCEPTIBILITY:
Skin and nasal vestibule colonisation by Staphylococcus aureus and its susceptibility to drugs in atopic dermatitis patients – Wrobel J – Annals of Agriculture and Environmental Medicine

 

 

June 25, 2018

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Today’s Microbiome Digest features the sea turtle microbiome, the bacteria responsible for degrading bioplastics, a new clinical center for phage therapy, the gut-microbiome-brain axis in an Alzheimer’s Disease model, and a preprint about image duplication in scientific publishing.

Pregnancy and early life

Late-onset Sepsis in Preterm Infants Can Be Detected Preclinically by Fecal Volatile Organic Compound Analysis: A Prospective, Multicenter Cohort Study. – Daniel J C Berkhout- Clinical Infectious Diseases

Human vaginal microbiome

Abnormal vaginal microbioma is associated with severity of localized provoked vulvodynia. Role of aerobic vaginitis and Candida in the pathogenesis of vulvodynia. – Gilbert G. G. Donders- European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

* Gut microbiota regulates maturation of the adult enteric nervous system via enteric serotonin networks – Filipe De Vadder – PNAS

Linking the Gut Microbiota to a Brain Neurotransmitter – Kelly G. Jameson – Trends in Neurosciences

Can epilepsy be treated by antibiotics? – Hilde M. H. Braakman – Journal of Neurology

* Changes in intestinal microbiota in HIV-1-infected subjects following cART initiation: influence of CD4+ T cell count – Yongjia Ji – Emerging Microbes & Infections

Review: Human gut microbiome: hopes, threats and promises – Patrice D Cani – Gut

Review: New treatments and therapeutic targets for IBS and other functional bowel disorders – Magnus Simrén – Nature Reviews Gastroenterology & Hepatology

Animal experiments

Effects of chronic noise exposure on the microbiome-gut-brain axis in senescence-accelerated prone mice: implications for Alzheimer’s disease – Bo Cui – Journal of Neuroinflammation

Bacterial methionine metabolism genes influence Drosophila melanogaster starvation resistance – Alec M. Judd – Applied and Environmental Microbiology

The benign helminth Hymenolepis diminuta ameliorates chemically induced colitis in a rat model system – Kateřina Jirků Pomajbíková – Parasitology

Protective role of commensal bacteria in Sjögren Syndrome – Mahira Zaheer – Journal of Autoimmunity

Lactobacillus murinus HF12 colonizes neonatal gut and protects rats from necrotizing enterocolitis. – Mubina Isani – PLOS One

Animal microbiome

Identification of bacteria present in ulcerative stomatitis lesions of captive sea turtles Chelonia mydas – D. X. Vega-Manriquez – Veterinary Research Communications

Characterization of the Microbiota of Oyster Larvae (Crassostrea virginica) and Tank Water from an Aquaculture System with High and Low Larval Survival Rates – Padmini Ramachandran – Genome Announcements

Early colonisation and temporal dynamics of the gut microbial ecosystem in Standardbred foals – S. Quercia – Equine Veterinary Journal

Plant, root, and soil microbiome

Microbial communities responsible for the degradation of poly(lactic acid)/poly(3-hydroxybutyrate) blend mulches in soil burial respirometric tests – Lenka Jeszeová – World Journal of Microbiology and Biotechnology

Phylogenetic diversity and investigation of plant growth-promoting traits of actinobacteria in coastal salt marsh plant rhizospheres from Jiangsu, China – Yuan Gong – Systematic and Applied Microbiology

Dynamics of soil microbial recovery from cropland to orchard along a 20-year chronosequence in a degraded karst ecosystem. – Hongkai Liao – Science of The Total Environment

Investigation of viable taxa in the deep terrestrial biosphere suggests high rates of nutrient recycling. – Margarita Lopez-Fernandez – FEMS Microbial Ecology

Distinct impacts of reductive soil disinfestation and chemical soil disinfestation on soil fungal communities and memberships. – Jun Zhao – Applied Microbiology and Biotechnology

* Dispersal-competition tradeoff in microbiomes in the quest for land colonization – Francisco Dini-Andreote – Scientific Reports

Water and extremophile microbiome

Linking patterns of net community production and marine microbial community structure in the western North Atlantic. – Seaver Wang – The ISME Journal

Probiotics/Prebiotics

Composition and metabolism of fecal microbiota from normal and overweight children are differentially affected by melibiose, raffinose and raffinose-derived fructans. – Kaarel Adamberg – Anaerobe

Review: Nutraceuticals in Colorectal Cancer: A Mechanistic Approach – Marco Rossi – European Journal of Pharmacology

Science, publishing, and career

* Analysis and Correction of Inappropriate Image Duplication: The Molecular and Cellular Biology Experience – Arturo Casadevall – bioRxiv

Microbes in the news

U.S. center will fight infections with viruses – Kelly Servick – Science

Alyson’s non-microbiology pick

Neanderthal brain organoids come to life – Jon Cohen – Science

June 21, 2018

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Have a good Thursday! Today: Gut microbiome and brain injury, position statement from the European STI Guidelines Editorial Board about microbial pathogen testing, age-dependent patterns in obesity, bats microbiome changes by diet,  analysis of primate microbiome changes by different diets, and more…

 

Human and General Microbiome

Review: A Review of Traumatic Brain Injury and the Gut Microbiome: Insights into Novel Mechanisms of Secondary Brain Injury and Promising Targets for Neuroprotection –  Caroline S. Zhu – Brain Sciences

Review: Should we be testing for urogenital Mycoplasma hominis, Ureaplasma parvum and U. urealyticum in men and women? – a Position Statement from the European STI Guidelines Editorial Board –  P Horner – JEADV

Preview: What Came First: The Microbiota or the Tr(egg) Cells? – Tal Gefen – Immunity

Colorectal cancer mutational profiles correlate with defined microbial communities in the tumor microenvironment – Michael B. Burns – PLoS Genetics

Microbiome and Bile Acid Profiles in Duodenal Aspirates from Cirrhotics: The Microbiome, Microbial Markers and Liver Disease Study – Jonathan P. Jacobs – Hepatology Research

Phospholipase A2 of Microbiota as Pathogenetic Determinant to Induce Inflammatory States in Ulcerative Colitis: Therapeutic Implications of Phospholipase A2 Inhibitors – Stremmel W – Inflammatory Intestinal Diseases

Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns – Federica Del Chierico – Frontiers in Microbiology

In Vitro Modeling of Bile Acid Processing by the Human Fecal Microbiota – Glynn Martin – Frontiers in Microbiology

Leishmania, microbiota and sand fly immunity – Erich Loza Telleria – Parasitology

 

Animal Microbiome

Intestinal microbial and metabolic profiling of mice fed with high-glucose and high-fructose diets – João C.P. Silva – Journal of Proteome Research

Protective Effects of Salvianolic Acid A against Dextran Sodium Sulfate-Induced Acute Colitis in Rats – Kai Wang – Nutrients

Changes in bacterial diversity and composition in the faeces and colon of weaned piglets after feeding fermented soybean meal –  Jia-jia Zhu – Journal of Medical Microbiology

Fecal Bacteriome and Mycobiome in Bats with Diverse Diets in South China – Juan Li – Current Microbiology

Gut Microbiome Composition in Non-human Primates Consuming a Western or Mediterranean Diet – Ravinder Nagpal – Frontiers in Nutrition

Dietary Deoxynivalenol Contamination and Oral Lipopolysaccharide Challenge Alters the Cecal Microbiota of Broiler Chickens – Annegret Lucke – Frontiers in Microbiology

Microbiome niche modification drives diurnal rumen community assembly, overpowering individual variability and diet effects – Yoav Shaani – The ISME Journal

Metabolomic signatures distinguish the impact of formula carbohydrates on disease outcome in a preterm piglet model of NEC – Lee Call – Microbiome

 

Environmental Microbiome

Dissecting Community Structure in Wild Blueberry Root and Soil Microbiome – Svetlana N. Yurgel – Frontiers in Microbiology

 

Plant Microbiome

Review: Belowground Microbiota and the Health of Tree Crops – Jesús Mercado-Blanco – Frontiers in Microbiology

 

Other papers

Aspergillus fumigatus Inhibits Pseudomonas aeruginosa in Co-culture: Implications of a Mutually Antagonistic Relationship on Virulence and Inflammation in the CF Airway – Emma Reece – Frontiers in Microbiology

Absolute quantitation of microbiota abundance in environmental samples – Andrzej Tkacz – Microbiome

June 20, 2018

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This digest has a study on the human hair microbiome, lots of animal studies and experiments, the normal long list of soil/plant publications, some water/extremophile studies, and a few interesting bioinformatics articles.  Enjoy!

Events and jobs

There were some very cool events to check out from my employer, GENEWIZ, this past month.  Every year here there is a celebration with a number of different events called GENEWIZ Week.  Check out this past set of events below:

GENEWIZ Week

GENEWIZ Webinars – definitely check these cool talks out.  You can access past talks, like mine on Metagenomics from 2017, at GENEWIZ Webinars Archive and my past webinar here: Metagenomics for Biomarker Discovery: Precision Medicine Applications

GENEWIZ DNA Award Winners

GENEWIZ Scientist of the Day

General microbiome

[pre-print] Free-living Bacterial Communities Are Mostly Dominated by Oligotrophs – Yingnan Gao – bioxRiv

Pregnancy and early life

Pilot assessment of probiotics for pregnant women in Rwanda – Amy McMillan – PLOS ONE

Human respiratory microbiome

* The respiratory virome in chronic obstructive pulmonary disease – Marian Garcia-Nuñez – Future Medicine

TRANSPLANTING THE PULMONARY VIROME: DYNAMICS OF TRANSIENT POPULATIONS – Alicia B Mitchell – The Journal of Heart and Lung Transplantation

Human skin microbiome

** Spatial and Environmental Variation of the Human Hair Microbiota – Lauren Brinkac – Scientific Reports

Human oral microbiome

Denture-Associated Oral Microbiome and Periodontal Disease Causing an Anaerobic Pyogenic Liver Abscess in an Immunocompetent Patient: A Case report and Review of the Literature – Muhammad Bader Hammami – Gastroenterology Research

Human gut microbiome

Changes in Gastric Microbiota during Gastric Carcinogenesis – Sun-Young Lee – KoreaMed Synapse

ADTU-05 Gut microbial composition in the migrant south-asian IBD population in UK – Mohammed Quraishi – BMJ Journals (Gut)

Gut Microbiota Dysbiosis and Diarrhea in Kidney Transplant Recipients – Lee JR – American Journal of Transplantation

The microbiome in autoimmune diseases – Fabrizio De Luca – Clinical and Experimental Immunology

Suppression of IL-17F, but not of IL-17A, provides protection against colitis by inducing Treg cells through modification of the intestinal microbiota – Ce Tang – Nature Immunology

* Characteristics of the bacterial microbiome in association with common intestinal parasites in irritable bowel syndrome – Laura Rindom Krogsgaard – Clinical and Translational Gastroenterology

Fecal microbiota transplantation for recurrent Clostridium difficile infection – Susy S. Hota – CMAJ

(not just human) The Expensive-Tissue Hypothesis in Vertebrates: Gut Microbiota Effect, a Review – Chun Hua Huang – International Journal of Molecular Sciences

Mediterranean Diet Score: Associations with Metabolic Products of the Intestinal Microbiome, Carotid Plaque Burden, and Renal Function – Michael Pignanelli – Nutrients

Animal experiments

Rumen Microbial Community of Saanen Goats Adapted to a High‐Fiber Diet in the Northeast of Iran – S.H. Ebrahimi – Iranian Journal of Applied Animal Science

Humic substances alter ammonia production and the microbial populations within a RUSITEC fed a mixed hay – concentrate diet – Stephanie A. Terry – Frontiers in Microbiology

Intestinal Microbiota Ecological Response to Oral Administrations of Hydrogen-Rich Water and Lactulose in Female Piglets Fed a Fusarium Toxin-Contaminated Diet – Weijiang Zheng – Toxins

Animal microbiome

Archaeal and bacterial diversity and community composition from 18 phylogenetically divergent sponge species in Vietnam – Ton That Huu Dat​ – PeerJ Microbiology

Gut bacterial and fungal communities of the domesticated silkworm (Bombyx mori) and wild mulberry-feeding relatives – Bosheng Chen – The ISME Journal

Gut bacterial and fungal communities of the domesticated silkworm (Bombyx mori) and wild mulberry-feeding relatives – Bosheng Chen – The ISME Journal

Aetiological Characterization of the Cutaneous Ulcer Syndrome in Papua New Guinea using Shotgun Metagenomics – Marc Noguera-Julian – Clinical Infectious Diseases

Inter-population variation in the Atlantic salmon microbiome reflects environmental and genetic diversity – Tamsyn M. Uren Webster – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Influence of Belowground Herbivory on The Dynamics of Root and Rhizosphere Microbial Communities – Morgane Ourry – Frontiers of Ecological Evolution

* Plant species and heavy metals affect biodiversity of microbial communities associated with metal-tolerant plants in metalliferous soils – Sławomir Borymski – Frontiers in Microbiology

Functional Microbial Features Driving Community Assembly During Seed Germination and Emergence – Torres-Cortés Gloria – Frontiers in Plant Science

Influence of the Chemical Form of Antimony on Soil Microbial Community Structure and Arsenite Oxidation Activity – Kataoka T – Europe PMC

Recognizing Patterns: Spatial Analysis of Observed Microbial Colonization on Root Surfaces – Hannes Schmidt – Frontiers in Environmental Science

Microbial diversity of tobacco rhizosphere soil in different growth stages of marigold-tobacco intercropping system –  Xia TiYuan – Editorial Department of Southwest China Journal of Agricultural Sciences

Differences in rice rhizosphere bacterial community structure by application of lignocellulolytic plant-probiotic bacteria with rapid composting traits – Thounaojam Nevita – Ecological Engineering

Data on molecular identification, phylogeny and in vitro characterization of bacteria isolated from maize rhizosphere in Cameroon – Tchuisseu Tchakounté Gylaine Vanissa – Data in Brief

[pre-print] A comprehensive mycofloral diversity of pedosphere, phyllosphere and aerosphere of Som. (Persea bombycina Kost.) -Manjit Kumar Ray  – bioRxiv

Rhizosphere Microbiomes Modulated by Pre-crops Assisted Plants in Defense Against Plant-Parasitic Nematodes – Ahmed Elhady – Frontiers in Microbiology

The culturable endophytic fungal communities of switchgrass grown on a coal-mining site and their effects on plant growth – Ye Xia – PLOS ONE

Arbuscular mycorrhizal fungi stimulate organic phosphate mobilization associated with changing bacterial community structure under field conditions – Lin Zhang – Environmental Microbiology

Water and extremophile microbiome 

Metagenomic insights into diazotrophic communities across Arctic glacier forefields – Maisie V. Nash – FEMS Microbiology Ecology

Microbial community shifts in response to acid mine drainage pollution within a natural wetland ecosystem – Oscar E. Aguinaga – Frontiers in Microbiology

Heterogeneity of interactions of microbial communities in regions of Taihu Lake with different nutrient loadings: A network analysis – Xinyi Cao – Scientific Reports

Diversity and functionality of archaeal, bacterial and fungal communities in deep Archaean bedrock groundwater – Lotta Purkamo – FEMS Microbial Ecology

Reduced arsenic availability and plant uptake and improved soil microbial diversity through combined addition of ferrihydrite and Trichoderma asperellum SM-12F1 – Hongxiang Zhang – Environmental Science and Pollution Research

Fungi from Admiralty Bay (King George Island, Antarctica) Soils and Marine Sediments – Lia Costa Pinto Wentzel – Microbial Ecology

Bioinformatics

When old metagenomic data meet newly sequenced genomes, a case study – Xin Li – PLOS ONE

PERFect: PERmutation Filtering test for microbiome data – Ekaterina Smirnova – Biostatistics

Ed’s non-microbiology picks

Photochemistry beyond the red limit in chlorophyll f–containing photosystems –  Dennis J. Nürnberg – Science

Research Finds Tipping Point for Large-scale Social Change

LACK OF PAID SICK LEAVE INCREASES POVERTY

Toxic toads could devastate Madagascar’s biodiversity – Science

Effects of 8-hour time restricted feeding on body weight and metabolic disease risk factors in obese adults: A pilot study – Kelsey Gabel – Nutrition and Healthy Aging

Forget in a Flash: A Further Investigation of the Photo-Taking-Impairment Effect – Julia S. Soares – Journal of Applied Research in Memory and Cognition

New discovery about the brain’s water system may prove beneficial in stroke

DNA repair processes are critical mediators of p53-dependent tumor suppression – Ana Janic – Nature Medicine

Astronomers find a galaxy unchanged since the early universe

June 19, 2018

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In today’s digest you can read about: the field of CRISPR-CAS antimicrobials by E. Pursey, “microbiota influencers” by G. Rizzatti, bioplastic producing bacterial communities by V. Kumar, mixotrophic behavior of the harmful benthic dinoflagellate by B. Lee and many many diverse and interesting articles. Enjoy!

General microbiome

CRISPR-Cas antimicrobials: Challenges and future prospects – Elizabeth Pursey – PLOS Pathogens

Considering Microbial CO2 during Microbe-Plant Cocultivation – Birgit Piechulla – Plant Physiology

Metabolic model-based analysis of the emergence of bacterial cross-feeding via extensive gene loss – Colin P. McNally  – BMC Systems Biology

Pregnancy and early life

Prevalence of antibiotic resistance in commensal Escherichia coli among the children in rural hill communities of Northeast India – Ashish Kumar Singh – PLOS One

Shared and Distinct Features of Human Milk and Infant Stool Viromes – Pia S. Pannaraj – Frontiers in Microbiology

Preterm infant gut microbial patterns related to the development of necrotizing enterocolitis – Tristan P. Lindberg – The Journal of Maternal-Fetal & Neonatal Medicine

Human respiratory microbiome

Multi-omic profiling to assess the effect of iron starvation in Streptococcus pneumoniae TIGR4 – Irene Jiménez-Munguía – PeerJ

Human gut microbiome

Addendum: “I will survive”: A tale of bacteriophage-bacteria coevolution in the gut – Luisa De Sordi – Gut Microbes

The Gut-Associated Microbiome of the Eastern Spruce Budworm Does Not Influence Larval Growth or Survival – Melbert T Schwarz – bioRxiv

Prioritizing and modelling of putative drug target proteins of Candida albicans by systems biology approach – Tariq Ismail – Acta Biochimica Polonica

Antibiotic and Modulation of Microbiota: A New Paradigm? – Gianenrico Rizzatti – Journal of Clinical Gastroenterology

Streptomyces, shared microbiome member of soil and gut, as “old friends” against colon cancer – Alireza Bolourian – FEMS Microbiology Ecology

Gut Microbial-related Choline Metabolite Trimethylamine-N-oxide is Associated with Progression of Carotid Artery Atherosclerosis in HIV Infection – Zhilei Shan – The Journal of Infectious Diseases

Role of Microbiota in Sexually Dimorphic Immunity – Marlies Elderman – Frontiers in Immunology

Early results of fecal microbial transplantation protocol implementation at a community-based university hospital – Rodrigo Duarte-Chavez – Journal of Global Infectious Diseases

Gut microbiota modulate neurobehavior through changes in brain insulin sensitivity and metabolism – Marion Soto – Molecular Psychiatry

The Rise and Rise of Eosinophilic Gut Diseases Including Eosinophilic Esophagitis Is Probably Not Explained by the Disappearance of Helicobacter pylori, so Who or What’s to Blame? – Nicholas J. Talley – The American Journal of Gastroenterology

Effect of administration of a probiotic preparation on gut microbiota and immune response in healthy women in India: an open-label, single-arm pilot study – Ankita Singh – BMC Gastroenterology

Animal experiments

Toxin-positive Clostridium difficile latently infect mouse colonies and protect against highly pathogenic C. difficile – Lucie Etienne-Mesmin – Gut microbiome

Animal microbiome

A comparative analysis of microbial profile of Guinea fowl and chicken using metagenomic approach – Sarayu Bhogoju – PLOS One

Tracking sources of Clostridium botulinum type E contamination in seal meat – Daniel Leclair – International Journal of Circumpolar Health

Plant, root, and soil microbiome

Applying predictive models to decipher rhizobacterial modifications in common reed die-back affected populations – Giovanni Bacci – Science of The Total Environment

Bioplastic reservoir of diverse bacterial communities revealed along altitude gradient of Pangi-Chamba trans-Himalayan region – Vijay Kumar – FEMS Microbiology Letters

Antagonism and antibiotic resistance drive a species-specific plant microbiota differentiation in Echinacea spp – Valentina Maggini – FEMS Microbiology Ecology

Divergent Responses of the Diazotrophic Microbiome to Elevated CO2 in Two Rice Cultivars – Yongjie Yu – Frontiers in Microbiology

Synthesis and detoxification of nitric oxide in the plant beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 and its effect on biofilm formation – Xiaoyan Dong – Biochemical and Biophysical Research Communications

Understanding the Strategies to Overcome Phosphorus–Deficiency and Aluminum–Toxicity by Ryegrass Endophytic and Rhizosphere Phosphobacteria – Patricio J. Barra – Frontiers in Microbiology

Soil viruses are underexplored players in ecosystem carbon processing – Gareth Trubl – bioRxiv

Dispersal limitation and thermodynamic constraints govern spatial structure of permafrost microbial communities –  Eric M Bottos – FEMS Microbiology Ecology

Changes of soil microbial and enzyme activities are linked to soil C, N and P stoichiometry in afforested ecosystems – F.Z. Zhao – Forest Ecology and Management

Responses of soil microbial communities to nutrient limitation in the desert-grassland ecological transition zone – Cui Y – The Science of the Total Environment

Observed metabolic asymmetry within soybean root nodules reflects unexpected complexity in rhizobacteria-legume metabolite exchange – Dušan Veličković – The ISME Journal

Antibacterial activity of soil bacteria isolated from Kochi, India and their molecular identification – Davis Gislin – Journal of Genetic Engineering and Biotechnology

Brassica napus Growth in Lead-Polluted Soil: Bioaccumulation in Plant Organs at Different Ontogenetic Stages and Lead Fractionation in Soil – Gisele V. Ferreyroa – Water, Air, & Soil Pollution

Editorial: “Plant-Microbe-Insect Interaction: Source for Bio-fertilizers, Bio-medicines and Agent Research” – Gero Benckiser – Frontiers in Plant Science

Broad-spectrum antimicrobial activity by Burkholderia cenocepacia TAtl-371, a strain isolated from the tomato rhizosphere – Fernando Uriel Rojas-Rojas – Microbiology

Improvement of Ni phytoextraction by Alyssum murale and its rhizosphere microbial activities by applying nitrogen fertilizer – Ali Kanso – Ecological Research

Water and extremophile microbiome

Abundance determines the functional role of bacterial phylotypes in complex communities – Damian W. Rivett  – Nature Microbiology

Metabolic Diversity within the Globally Abundant Marine Group II Euryarchaea Drives Ecological Patterns – Benjamin J Tully – bioRxiv

Diversity of bacterial communities and dissolved organic matter in a temperate estuary – Helena Osterholz – FEMS Microbiology Ecology

Clean Low-Biomass Procedures and Their Application to Ancient Ice Core Microorganisms – Zhi-Ping Zhong – Frontiers in Microbiology

Genetic diversity and co-occurrence patterns of marine cyanopodoviruses and picocyanobacteria – Yingting Sun – Applied and Environmental Microbiology

Proteome response of a metabolically flexible anoxygenic phototroph to Fe(II) oxidation – Casey Bryce – Applied and Environmental Microbiology

Genome rearrangement shapes Prochlorococcus ecological adaptation – Wei Yan – Applied and Environmental Microbiology

High CO2 Under Nutrient Fertilization Increases Primary Production and Biomass in Subtropical Phytoplankton Communities: A Mesocosm Approach – Nauzet Hernández-Hernández – Frontiers in Microbiology

Genetic Analyses of the rbcL and psaA Genes From Single Cells Demonstrate a Rhodophyte Origin of the Prey in the Toxic Benthic Dinoflagellate Ostreopsis – Bora Lee – Frontiers in Marine Science

Ubiquitous abundance distribution of non-dominant plankton across the global ocean – Enrico Ser-Giacomi – Nature Ecology & Evolution

Copiotrophic marine bacteria are associated with strong iron‐binding ligand production during phytoplankton blooms – Shane L. Hogle – Limnology and Oceanography

Dynamics and interactions of highly resolved marine plankton via automated high-frequency sampling – David M. Needham – The ISME Journal

Distinct patterns and processes of abundant and rare eukaryotic plankton communities following a reservoir cyanobacterial bloom – Yuanyuan Xue – The ISME Journal

Coral Microbiomes as Bioindicators of Reef Health – Sofia Roitman – Population Genomics

Microbial community structure and functional potential along a hypersaline gradient – Jeffrey A. Kimbrel – Frontiers in Microbiology

Comparative genomics of Pseudomonas sp. strain SI-3 associated with macroalga Ulva prolifera, the causative species for green tide in the Yellow Sea – Huihui Fu – Frontiers in Microbiology

Probiotics / prebiotics

Pilot assessment of probiotics for pregnant women in Rwanda – Amy McMillan – PLOS One

Phages and viruses

Low spatial structure and selection against secreted virulence factors attenuates pathogenicity in Pseudomonas aeruginosa – Elisa T Granato – bioRxiv

Identification of anti-norovirus genes in mouse and human cells using genome-wide CRISPR activation screening –  Robert Orchard – bioRxiv

Biotechnology

Simultaneous autotrophic removal of sulphate and nitrate at different voltages in a bioelectrochemical reactor (BER): Evaluation of degradation efficiency and characterization of microbial communities – Hao Xua – Bioresource Technology

Evaluation of A Novel Split-Feeding Anaerobic/Oxic Baffled Reactor (A/OBR) For Foodwaste Anaerobic Digestate: Performance, Modeling and Bacterial Community – Shaojie Wang – Scientific Reports

Viewpoint: Synthetic Biology for Natural Compounds – Xinrui Zhao – Biochemistry

Bioinformatics

iMetaLab 1.0: A web platform for metaproteomics data analysis – Bo Liao – Bioinformatics

Taxonomy annotation and guide tree errors in 16S rRNA databases – Robert Edgar​ – PeerJ

The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level – Luis M Rodriguez-R – Nucleic Acids Research

Techniques

Whole-Cell MALDI-TOF MS Versus 16S rRNA Gene Analysis for Identification and Dereplication of Recurrent Bacterial Isolates – Michal Strejcek – Frontiers in Microbiology

Low-power portable devices for metagenomics analysis: Fog computing makes bioinformatics ready for the Internet of Things –  Ivan Merelli – Future Generation Computer Systems

Microbes in the news 

Unique microbe could thrive on Mars, help future manned missions

In a Warming World, Deadly Bacteria Are More Resistant to Antibiotics

Microbes on the market

Startup aims to make allies of human gut’s microbes

Department of Energy Announces $40 Million for Bio-Based Research

Tina’s non-microbiology picks

Towards an Evolutionary Perspective in Teaching and Popularizing Microbiology – Fernando Bueno Ferreira Fonseca de Fraga – Journal of  Microbiology & Biology Education