Category Archives: Human skin

July 6, 2018

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Today’s digest includes the spleen microbiome of wild mammals, the microbial phylogenetic diversity of natural clay, and the effects of non-nutritive sweeteners on the mouse gut microbiome. It also includes Nature’s picks for June’s best science images.

Pregnancy and early life

Maternal diet during pregnancy is related with the infant stool microbiome in a delivery mode-dependent manner – Sara N. Lundgren – Microbiome

Human skin microbiome

Skin commensal bacteria S. epidermidis promote survival of melanocytes bearing UVB‐induced DNA damage, while bacteria P. acnes inhibit survival of melanocytes by increasing apoptosis – Zhenping Wang – Photodermatology, Photoimmunology, and Photomedicine

Human gut microbiome

Review: Gut microbiota‐immune‐brain interactions in chemotherapy‐associated behavioral comorbidities – Kelley R. Jordan – Cancer

Involvement of T helper 17 cells in inflammatory arthritis depends on the host intestinal microbiota – Heather Evans‐Marin – Arthritis and Rheumatology

Analysis of the Gut Microbiome of Rural and Urban Healthy Indians Living in Sea Level and High Altitude Areas – Bhabatosh Das – Scientific Reports

Animal experiments

Non-nutritive sweeteners possess a bacteriostatic effect and alter gut microbiota in mice – Qiao-Ping Wang – PLoS One

Effects of naturally-produced lovastatin on feed digestibility, rumen fermentation, microbiota and methane emissions in goats over a 12-week treatment period – Su Chui Len Candyrine – PLoS One

Perinatal short-chain fructooligosaccharides program intestinal microbiota and improve enteroinsular axis function and inflammatory status in high-fat diet-fed adult pigs – Cindy Le Bourgot – FASEB

Bifidobacterium bifidum TMC3115 Can Characteristically Influence Glucose and Lipid Profile and Intestinal Microbiota in the Middle-Aged and Elderly – Ke Wang – Probiotics and Antimicrobial Proteins

Isoquercetin and inulin synergistically modulate the gut microbiome to prevent development of the metabolic syndrome in mice fed a high fat diet – Si Tan – Scientific Reports

Animal microbiome

The spleen microbiota of small wild mammals reveals distinct patterns with tick-borne bacteria – Yan Ge – PLoS Neglected Tropical Diseases

Drosophila melanogaster establishes a species-specific mutualistic interaction with stable gut-colonizing bacteria – Inês S. Pais – PLoS Biology

Plant, root, and soil microbiome

Phylogenetic diversity and metabolic potential of microbiome of natural healing clay from Chamliyal (J&K) – Sakshi Sharma – Archives of Microbiology

Bioinformatics

Taxonomic and Functional Compositions Impacted by the Quality of Metatranscriptomic Assemblies – Maggie C. Y. Lau – Frontiers in Microbiology

Techniques

Development of outbred CD1 mouse colonies with distinct standardized gut microbiota profiles for use in complex microbiota targeted studies – Marcia L. Hart – Scientific Reports

Non-microbiology picks

Astronauts, atmospheres and axolotls — June’s best science images – Nature

July 5, 2018

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Today’s microbiology picks have articles on sampling source effect on the gut microbial diversity, whether resistant starch in mothers could benefit the offsprings, protective role of the gut bacteria of firebugs, microbial community shift during different stages in anaerobic membrane bioreactor, NanoAmpli-Seq as well as articles from plant-root-soil microbiome. Precision medicine, genetics of social interaction and isolation, “ethics dumping ” among our non-microbiology picks.

 

Events and jobs

John Maddox Prize 2018 nomination – Deadline: 13th August 2018 – Check their website for more details

General microbiome

Human-associated microbial populations as evidence in forensic casework – Frederike C.A. Quaak – Forensic Science International: Genetics

The Mammalian Intestinal Microbiome: Composition, Interaction with the Immune System, Significance for Vaccine Efficacy, and Potential for Disease Therapy.  – U Desselberger – MDPI

244 Analysis of microbiome prostatic secretion in depending of levels total testosterone in blood serum – M.I. Kogan – The Journal of Sexual Medicine

Triclosan and triclocarban exposure, infectious disease symptoms and antibiotic prescription in infants—A community-based randomized intervention – Catherine Ley – PLoS One

 

Human skin microbiome

Microbiome analysis of forehead skin in patients with atopic dermatitis and healthy subjects: Implication of Staphylococcus and Corynebacterium –  Masutaka Furue – The Journal of Dermatology

Human vaginal microbiome

Trichomonas vaginalis: Pathogenesis, Symbiont Interactions, and Host Cell Immune Responses – Frances Mercer – Trends in Parasitology

Human gut microbiome

More of the Gut in the Lung: How Two Microbiomes Meet in ARDS – Samiran Mukherjee – Yale Journal of Biology and Medicine

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

Severe Defects in the Macrophage Barrier to Gut Microflora in Inflammatory Bowel Disease and Colon Cancer. – Carlos A. Rubiro – Anticancer Research

Animal experiments 

Feeding sows resistant starch during gestation and lactation impacts their faecal microbiota and milk composition but shows limited effects on their progeny – Julie Leblois – PLoS One

Animal microbiome

The cotton stainer’s gut microbiota suppresses infection of a co‐transmitted trypanosomatid parasite – Thomas O Onchuru – Molecular Ecology

Gut microbial diversity in two insectivorous bats: Insights into the effect of different sampling sources – Haonan Wu – Microbiology Open

Evidence for multiple ecological roles of Leptographium abietinum, a symbiotic fungus associated with the North American spruce beetle – Thomas S Davis – Fungal Ecology

Plant, root, and soil microbiome

Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially-processed plant-derived carbon – Evan P Starr – Microbiome

Swift Acid Rain Sensing by Synergistic Rhizospheric Bioelectrochemical Responses – Tian Li – ACS Sensors

Crop Rotation and Straw Application Impact Microbial Communities in Italian and Philippine Soils and the Rhizosphere of Zea mays – Saarah A Maarastawi – Frontiers in Microbiology

Plant growth promoting bacteria associated with corm of Crocus sativus during three growth stages – Ranjit Kour – Letters in Applied Microbiology

Fungal Diversity of Rhizosphere Soil from 11 Varieties of Grapevines at Maturity Stage from Two Vineyards in China – Ping Zhao – Journal of Biobased Materials and Bioenergy

Disruption of microbial community composition and identification of plant growth promoting microorganisms after exposure of soil to rapeseed-derived glucosinolates – Meike Siebers – PLoS One

The value of wet leaves – Todd E. Dawson – New Phytologist

Water and extremophile microbiome 

Biofilm and planktonic bacterial communities in a drinking water distribution system supplied with untreated groundwater – Jianfei Chen – Archives of Microbiology

Marine Environmental Epigenetics – Jose M. Eirin-Lopez – Annual Reviews

Disentangling the complexity of permafrost soil by using high resolution profiling of microbial community composition, key functions and respiration ratesDisentangling the complexity of permafrost soil by using high resolution profiling of microbial community composition, key functions and respiration rates – Oliver Müller – Environmental Microbiology

Effect of different carbon sources on denitrification performance, microbial community structure and denitrification genes – Zhongshuo Xu – Science of The Total Environment

Built environment 

Characterization and Dynamic Shift of Microbial Communities during Start-Up, Overloading and Steady-State in an Anaerobic Membrane Bioreactor –  Nsanzumukiza Martin Vincent – MDPI

Food microbiology

Inactivation of Escherichia coli O157:H7 and Salmonella and Native Microbiota on Fresh Strawberries by Antimicrobial Washing and Coating – Mingming Guo – Journal of Food Protection

Microbial quality of ice cream sold by retail outlets in Erzurum. –  S Çubukçı – CAB Direct

 

Techniques

Preprint: NanoAmpli-Seq: A workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform – Szymon T Calus – bioRxiv

Preprint: Genetic insight into zinc and antimicrobial toxicity uncovers a glycerol phosphate modification on streptococcal rhamnose polysaccharides – Rebecca J. Edgar – bioRxiv

Preprint: Nano-particles from Chaetomium against Rice Blast – Jiao Jiao Song – bioRxiv

Seamless assembly of recombinant adenoviral genomes from high-copy plasmids – Jessica J. Miciak – PLoS One

Twenty-seven years of screening for Shiga toxin-producing Escherichia coli in a university hospital. Brussels, Belgium, 1987-2014 – Klara De Rauw – PLoS One

Microbes in the news

Bacteria Fight Competitors by Turning them Against Each Other – Technology Networks

Non-microbiology Picks

Personalized medicine should not be restricted to the wealthy – Nature

Elucidating the genetic basis of social interaction and isolation – Nature Communications

Evaluation woes: we’re on it, responds DORA – Nature

Italy is squeezing out wet biology research – Nature

Europe’s biggest research fund cracks down on ‘ethics dumping’ – Nature

 

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

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 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 22, 2018

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Have a happy weekend! Today in Microbiome Digest: reviews on microbiome immunity and type 1 diabetes,  metatranscriptome analysis of vaginal microbiome, Differences in gut microbiota associated with age, sex, and stool consistency, microbes in the news, and more…

Events and jobs

Scientist – Genomics and Microbiome – Madison, WI

Bioinformatics Scientific Programmer – Quadram Institute Bioscience

General microbiome

Review: Communication Between the Microbiota and Mammalian Immunity – Kyla S. Ost – Annual Review of Microbiology

Host genotype-specific microbiota do not influence the susceptibility of D. magna to a bacterial pathogen – Marilou P. Sison-Mangus – Scientific Reports

Pregnancy and early life

Book chapter: Implantation Failure 1: Intrauterine Circumstances and Embryo–Endometrium Synchrony at Implantation – Keiji Kuroda – Treatment Strategy for Unexplained Infertility and Recurrent Miscarriage

Special Issue: Microbiome in normal and pathological pregnancies: A literature overview – Carla R. Taddei – American Journal of Reproductive Immunology

Multi-site human microbiome

Bacterial invasion of dentinal tubules from the external root surface with and without an intact cemental layer- a confocal laser scanning microscopic study – Jovita D’souza – Advances in Tissue Engineering and Regenerative Medicine

Human respiratory microbiome

Review: Drug Resistance and Gene Transfer Mechanisms in Respiratory/Oral Bacteria – Jiang S – Journal of Dental Research

Ecology and diversity in upper respiratory tract microbial population structures from a cross-sectional community swabbing study –  Abigail L. Coughtrie – Journal of Medical Microbiology

Human skin microbiome

Skin Microbiota in Obese Women at Risk for Surgical Site Infection After Cesarean Delivery – Kara M. Rood – Scientific Reports

Human vaginal microbiome

Review: Pharmacology of Antiretrovirals in the Female Genital Track for HIV Prevention – Melanie R. Nicol – The Journal of Clinical Pharmacology

Metatranscriptome Analysis of the Vaginal Microbiota Reveals Potential Mechanisms for Protection against Metronidazole in Bacterial Vaginosis – Zhi-Luo Deng – mSphere 

Human gut microbiome

Review: Gut microbiome in type 1 diabetes: A comprehensive review – Zheng P – Diabetes/Metabolism Research and Reviews

A Small Molecule-Screening Pipeline to Evaluate the Therapeutic Potential of 2-Aminoimidazole Molecules Against Clostridium difficile – Thanissery R – Frontiers in Microbiology

Differences in gut microbiota associated with age, sex, and stool consistency in healthy Japanese subjects – Tomohisa Takagi – Journal of Gastroenterology

Dietary Supplementation with a Magnesium-Rich Marine Mineral Blend Enhances the Diversity of Gastrointestinal Microbiota – Erin K. Crowley – Marine Drugs

The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms – Brandon Brooks – Microbiome

Review: Potential Role of the Gut Microbiome in ALS: A Systematic Review – Michelle L. Wright – Biological Research for Nursing

Animal experiments

Lack of liver steatosis in germ-free mice following hypercaloric diets – Stephan C. Bischoff – European Journal of Nutrition

 Plant, root, and soil microbiome

Exploring Elicitors of the Beneficial Rhizobacterium Bacillus amyloliquefaciens SQR9 to Induce Plant Systemic Resistance and Their Interactions With Plant Signaling Pathways – Gengwei Wu – Molecular Plant-Microbe Interactions

Correlation and Distribution of Xenobiotics Genes and Metabolic Activities with Level of Total Petroleum Hydrocarbon in Soil, Sediment and Estuary Water in the Niger Delta Region of Nigeria – U. O. Edet – Asian Journal of Biotechnology and Genetic Engineering

Review: Status and future of disease protection and grape berry quality alteration by microorganisms in viticulture – Misa Otoguro – Letters in Applied Microbiology

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

Water and extremophile microbiome

Mini-Review: Future direction in marine bacterial agarases for industrial applications -Saeid Tamadoni Jahromi – Applied Microbiology and Biotechnology

Prokaryotic assemblages in the maritime Antarctic Lake Limnopolar (Byers Peninsula, South Shetland Islands) – M. Papale – Extremophiles

Taxonomy, phylogeny and ecology of cultivable fungi present in seawater gradients across the Northern Antarctica Peninsula – Vívian N. Gonçalves – Extremophiles 

A strong link between marine microbial community composition and function challenges the idea of functional redundancy – Pierre E. Galand – The ISME Journal

Probiotics / prebiotics

Gut Microbiota, Probiotics, and Sport: From Clinical Evidence to Agonistic Performance – Marco Pane – Journal of Clinical Gastroenterology

 Microbes in the news

‘Green’-feed: Industrial microbes could feed cattle, pigs, chicken

SMU researchers hope microbes will lead them to strike oil offshore

Scientists Reveal How Gut Microbes ‘Recover’ After Antibiotic Treatment

Celebrate your gut microbiota on the first World Microbiome day!

 Microbes on the market (news about biotech companies)

Human Microbiome Market – Global Industry Analysis, Size, Share, Growth, Trends, and Forecast 2018 – 2026

MaaT Pharma and Lutech Sign Licensing Agreement on Microbiome Therapy for Graft-vs-Host Disease

 

Ashok’s non-microbiology picks

The Rheumatoid Arthritis-Associated Citrullinome – Ronak Tilvawala – Cell Chemical Biology

Inflammation-Induced, STING-Dependent Autophagy Restricts Zika Virus Infection in the Drosophila Brain – Yuan Liu – Cell Host & Microbe

Distinct progenitor lineages contribute to the heterogeneity of plasmacytoid dendritic cells – Patrick Fernandes Rodrigues – Nature Immunology

A synaptic threshold mechanism for computing escape decisions – Dominic A. Evans – Nature

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 18, 2018

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Have a good Monday! Today in Microbiome Digest: reviews about the relationship between microbiome and brain function, vaccine response and dermatology. Studies about psoriasis and the gut microbiology, the effect of osmotic changes on the gut microbiota, protocols for oral microbiota profiling in lab classes, the role of indole in gut inflammation and more…

Human and General Microbiome

Review: Bile acids and FXR in functional gastrointestinal disorders – Paula Mosińska – Digestive and Liver Disease

Review: The Microbiome in Psychology and Cognitive Neuroscience – Amar Sarkar – Trends in Cognitive Sciences

Review: The influence of the intestinal microbiome on vaccine responses – Petra Zimmermann – Vaccine

Review: Close Encounters of Three Kinds: Bacteriophages, Commensal Bacteria, and Host Immunity – Eric C. Keen – Trends in Microbiology

The microbiome in dermatology – Shenara Musthaq – Clinics in Dermatology

Is psoriasis a bowel disease? Successful treatment with bile acids and bioflavonoids suggests it is – P. Haines Ely – Clinics in Dermatology

Microbial markers in colorectal cancer detection and/or prognosis – Romain Villéger – World Journal of Gastroenterology

Neurotransmitter modulation by the gut microbiota – Philip Strandwitz – Brain Research

Intestinal microbiota assessment in cirrhotic patients from a Mexican mestizo population – C. Pérez-Monter – Revista de Gastroenterología de México (Article in Spanish)

Profiling the Urinary Microbiota in Male Patients With Bladder Cancer in China – Peng Wu – Frontiers in Cellular and Infection Microbiology

Analysis of human C24 bile acids metabolome in serum and urine based on enzyme digestion of conjugated bile acids and LC-MS determination of unconjugated bile acids – Pingping Zhu – Analytical and Bioanalytical Chemistry

Tobacco-smoking-related prevalence of methanogens in the oral fluid microbiota – Ghiles Grine – Scientific Reports

Effect of rectal douching/enema on rectal gonorrhoea and chlamydia among a cohort of men who have sex with men on HIV pre-exposure prophylaxis – Adiba Hassan – Sexually Transmitted Infections

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

The urinary microbiome in women with mixed urinary incontinence compared to similarly aged controls – Yuko M. Komesu – International Urogynecology Journal

The influence of in vitro pectin fermentation on the human fecal microbiome – So-Jung Bang – AMB Express

Host genetics and microbiome associations through the lens of genome wide association studies – Omer Weissbrod – Current Opinion in Microbiology

Cutibacterium acnes and the shoulder microbiome – Boyang Qiu – Journal of Shoulder and Elbow Surgery

 

Animal Microbiome / Animal Experiments

Transient Osmotic Perturbation Causes Long-Term Alteration to the Gut Microbiota – Carolina Tropini – Cell

Probiotics L. acidophilus and B. clausii Modulate Gut Microbiota in Th1- and Th2-Biased Mice to Ameliorate Salmonella Typhimurium-Induced Diarrhea – Biswaranjan Pradhan – Probiotics and Antimicrobial Proteins

Altered microRNA regulation of short chain fatty acid receptors in the hypertensive kidney is normalized with hydrogen sulfide supplementation – Gregory J. Weber – Pharmacological Research

The effect of antibiotics on social aversion following early life inflammation – Amanda C. Kentner – Physiology & Behavior

Analysis of the Gut Microbial Diversity of Dairy Cows During Peak Lactation by PacBio Single-Molecule Real-Time (SMRT) Sequencing – Weicheng Li – Current Microbiology

Diet Modifies Colonic Microbiota and CD4+ T Cell Repertoire to Induce Flares of Colitis in Mice With Myeloid-cell Expression of Interleukin 23 – Lili Chen – Gastroenterology

Chronic exposure to fungicide propamocarb induces bile acid metabolic disorder and increases trimethylamine in C57BL/6J mice – Sisheng Wu – Science of The Total Environment

Distribution of Salmonella Enteritidis in internal organs and variation of cecum microbiota in chicken after oral challenge – Jinxin Zeng – Microbial Pathogenesis

The comparative genomics of Bifidobacterium callitrichos reflects dietary carbohydrate utilization within the common marmoset gut – Korin Albert – Microbial Genomics

The gut microbiota metabolite indole alleviates liver inflammation in mice – Martin Beaumont – The FASEB Journal

Alpha-Ketoglutarate in Low-Protein Diets for Growing Pigs: Effects on Cecal Microbial Communities and Parameters of Microbial Metabolism – Jiashun Chen – Frontiers in Microbiology

Berberine Regulates Treg/Th17 Balance to Treat Ulcerative Colitis Through Modulating the Gut Microbiota in the Colon

Screening of multimeric β-xylosidases from the gut microbiome of a higher termite, Globitermes brachycerastes – Huantian Cui – Frontiers in Pharmacology

Impact of Gut Microbiota and Diet on the Development of Atherosclerosis in Apoe-/- Mice – Annika Lindskog Jonsson – Arteriosclerosis, Thrombosis, and Vascular Biology

Saturated long-chain fatty acid-producing bacteria contribute to enhanced colonic motility in rats – Ling Zhao – Microbiome

News in Brief: Antibiotics Protect Against Liver Tumors in Mice in Cancer Discovery

 

Water Microbiome

Methanogenic community shifts during the transition from sewage mono-digestion to co-digestion of grass biomass – Justus Hardegen – Bioresource Technology

 

Protocols and Methodologies

Simple Protocol for Molecular Fingerprinting of Human Oral Microbiota Samples in Lab Classes – Ana C. Henriques – Journal of Microbiology & Biology Education

Sample tracking in microbiome community profiling assays using synthetic 16S rRNA gene spike-in controls – Dieter M. Tourlousse – Scientific Reports

Taxonomy-aware feature engineering for microbiome classification – Mai Oudah – BMC Bioinformatics

 

June 14, 2018

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Microbial inhabitants of chimpanzee beds, the California cat flea microbiome, butterfly-associated bacterial communities.

General microbiome

Bistability in a system of two species interacting through mutualism as well as competition: Chemostat vs. Lotka-Volterra equations – Stefan Vet – PLOS ONE

Multi-site human microbiome

Review: The interaction between iNKT cells and the mucosal microbiota – Fatma Zehra Hapil – Immunology

Human skin microbiome

Cutibacterium acnes (Propionibacterium acnes) and acne vulgaris: a brief look at the latest updates – B Dréno – Journal of the European Academy of Dermatology and Venereology

Human gut microbiome

Review: Gut dysbiosis: a potential link between increased cancer risk in ageing and inflammaging – Arya Biragyn – The Lancet Oncology

The microbiome of translocated bacterial populations in patients with and without inflammatory bowel disease – Christopher John Kiely – Internal Medicine Journal

Animal experiments

Oxaliplatin-induced changes in microbiota, TLR4+ cells and enhanced HMGB1 expression in the murine colon – Vanesa Stojanovska – PLOS ONE

Bifidobacteria attenuate the development of metabolic disorders, with inter- and intra-species differences – Guangsu Zhu – Food & Function

Immunomodulation and effects on microbiota after in ovo administration of chicken cathelicidin-2 – Tryntsje Cuperus – PLOS ONE

Animal microbiome

Apparent Total Tract Macronutrient Digestibility, Serum Chemistry, Urinalysis, and Fecal Characteristics, Metabolites and Microbiota of Adult Dogs Fed Extruded, Mildly Cooked, and Raw Diets – Kiley M Algya – Journal of Animal Science

Assessing Cat Flea Microbiomes in Northern and Southern California by 16S rRNA Next-Generation Sequencing – Elton J R Vasconcelos – Vector-Bronze and Zoonotic Diseases

Pre-print: High similarity in the microbiota of cold-water sponges of the Genus Mycale from two different geographical areas – César A Cárdenas – PeerJ

Synchronized shift of oral, faecal and urinary microbiotas in bats and natural infection dynamics during seasonal reproduction – Muriel Dietrich – Royal Society Open Science

Dietary and developmental shifts in butterfly-associated bacterial communities – Kruttika Phalnikar – Royal Society Open Science

Plant, root, and soil microbiome

Impact of pyrometallurgical slags on sunflower growth, metal accumulation and rhizosphere microbial communities – A C Agnello – Chemosphere

Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures – Daniel R Lammel – Microbiome

Review: A three-act play: pentachlorophenol threats to the cork oak forest soils mycobiome – Adélia Varela – Current Opinion in Microbiology

Soil homogenization and microedges: perspectives on soil‐based drivers of plant diversity and ecosystem processes – Holly J Stover – Ecosphere

Soils beneath different arctic shrubs have contrasting responses to a natural gradient in temperature – Qiong Zhao – Ecosphere

Effects of straw return on bacterial communities in a wheat-maize rotation system in the North China Plain – Dali Yu – PLOS ONE

Pre-print: Convergent gain and loss of genomic islands drives lifestyle changes in plant-associated bacteria – Ryan A Melnyk – bioRxiv

Water and extremophile microbiome

Vertical and horizontal biogeographic patterns and major factors affecting bacterial communities in the open South China Sea – Yi Li – Scientific Reports

Built environment

Ecology of sleeping: the microbial and arthropod associates of chimpanzee beds – Megan S Thoemmes – Royal Society Open Science

Bacteria art

Creative Culture: Bacterial Art Project Combines Art and Science – Candice Dyer – Brenau Window Online

Science, career, and publishing

Bioinformatics core competencies for undergraduate life sciences education – Melissa A Wilson Sayres – PLOS ONE

Pre-print: Outcomes of early NIH-funded investigators: Experience of the National Institute of Allergy and Infectious Diseases – Patricia A Haggerty – bioRxiv

June 13, 2018

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Events and jobs

Computational scientists (from post-master to postdoc fellowships) in metagenomics and microbial genomics : Trento, Italy – The Laboratory of Computational Metagenomics

General microbiome

Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative – Jun Wang, Microbiome Announcement

Microbial ecology

Everything is not everywhere: a tale on the biogeography of cyanobacteria – Karine Felix Ribeiro, Hydrobiologia

A Meta‐Analysis of Temperature Sensitivity as a Microbial Trait – Charlotte J. Alster, Global Change Biology

Microbial island biogeography: isolation shapes the life history characteristics but not diversity of root-symbiotic fungal communities – John Davison, ISME

Bacillus thuringiensis produces the lipopeptide thumolycin to antagonize microbes and nematodes – Dehong Zheng, Microbiological Research

Qualitative analysis of biosurfactants from Bacillus species exhibiting antifungal activity – Ambrin Sarwar, Plos One

Antarctic cryptoendolithic fungal communities are highly adapted and dominated by Lecanoromycetes and Dothideomycetes – Claudia Coleine, Frontiers in Microbiology

Pregnancy and early life

The Microbiome and Metabolome of Preterm Infant Stool Are Personalized and Not Driven by Health Outcomes, Including Necrotizing Enterocolitis and Late-Onset Sepsis – Stephen Wandro, mSphere

The role of breast milk in the colonization of neonatal gut and skin with coagulase-negative staphylococci – Hiie Soeorg, Pediatric Research

Multisite human microbiome

Prion-like Propagation of α-synuclein in the gut-brain axis – Ying Chen, Brain Research Bulletin

Microbiome-Gut-Brain Axis and Toll-Like Receptors in Parkinson’s Disease – Valentina Caputi, International Journal of Molecular Sciences

Current Insights in Microbiome Shifts in Sjogren’s Syndrome and Possible Therapeutic Interventions – Christina Tsigalou, Frontiers in Immunology

Comparison of Infant Gut and Skin Microbiota, Resistome and Virulome between Neonatal Intensive Care Unit (NICU) Environments – Suchitra K. Hourigan, Frontiers in Microbiology

Human skin microbiome

Skin Microbiota in Obese Women at Risk for Surgical Site Infection After Cesarean Delivery – Kara M. Rood, Scientific Reports

Cutibacterium acnes (Propionibacterium acnes) and acne vulgaris: a brief look at the latest updates – B. Dréno, Journal of the European Academy of Dermatology and Venereology

Characterisation of Cutibacterium acnes phylotypes in acne and in vivo exploratory evaluation of Myrtacine® – S. Pécastaings, Journal of the European Academy of Dermatology and Venereology

Human oral microbiome

Analysis of the oral microbiome on the surface of modified dental polymers – Denise  Tornavoi de Castro, Archives of Oral Biology

Genetic Association with Subgingival Bacterial Colonization in Chronic Periodontitis – Franco Cavalla, Genes

Biological and cultural drivers of oral microbiota in Medieval and Post-Medieval London, UK – Andrew G Farrer, bioRxiv

Human gut microbiome

Breath methane concentrations and markers of obesity in patients with functional gastrointestinal disorders – Clive H. Wilder-Smith, United European Gastroenterology Journal

The Intersection Between Colonization Resistance, Antimicrobial Stewardship, and Clostridium difficile – Rossana Rosa, Current Infectious Disease Reports

Celiac Disease and Fecal Microbiota Transplantation: A New Beginning? – Shmuel Golfeyz MD, Correspondence

Gut microbiota metabolites, amino acid metabolites and improvements in insulin sensitivity and glucose metabolism: the POUNDS Lost trial – Yoriko Heianza, Nutrition

Cutting the Gordian Knot of the Microbiota – Kimberly S.Vasquez, Molecular Cell

Host: Microbiome co-metabolic processing of dietary polyphenols – An acute, single blinded, cross-over study with different doses of apple polyphenols in healthy subjects – Kajetan Trost, Food Research International

Clinical trials of kimchi intakes on the regulation of metabolic parameters and colon health in healthy Korean young adults – Hee-Young Kim, Journal of Functional Foods

Animal experiments

Propolis from Different Geographic Origins Suppress Intestinal Inflammation in a Model of DSS‐Induced Colitis is Associated with Decreased Bacteroides spp. in the Gut – Kai Wang, Molecular Nutrition and Food Research

Effect of direct-fed microbials on culturable gut microbiotas in broiler chickens: a meta-analysis of controlled trials – Chhaiden Heak, Asian-Australasian Journal of Animal Sciences

A dietary isothiocyanate-enriched moringa (Moringa oleifera) seed extract improves glucose tolerance in a high-fat-diet mouse model and modulates the gut microbiome – Asha Jaja-Chimedza, Journal of Functional Foods

The enteric microbiota regulates jejunal Paneth cell number and function without impacting intestinal stem cells – Alexi A. Schoenborn, Gut Microbes

Comprehensive longitudinal microbiome analysis of the chicken cecum reveals a shift from competitive to environmental drivers and a window of opportunity for Campylobacter – Umer Zeeshan Ijaz, bioRxiv

Microbial quantity impacts Drosophila nutrition, development, and lifespan – Erin S. Keebaugh, iScience

Absence of Gut Microbiota Reduces Emotional Reactivity in Japanese Quails (Coturnix japonica) – Narjis Kraimi, Frontiers in Physiology

Animal microbiome

Identification of circular single-stranded DNA viruses in faecal samples of Canada lynx (Lynx canadensis), moose (Alces alces) and snowshoe hare (Lepus americanus) inhabiting the Colorado San Juan Mountains – Simona Kraberger, Infection, Genetics and Evolution

Diverse novel resident Wolbachia strains in Culicine mosquitoes from Madagascar – Claire L Jeffries, bioRxiv

Sample treatment optimization for fish stool metabolomics – Takeshi Hano, Journal of Chromatography B

Plant, root, and soil microbiome

Two decades of altered snow cover does not affect soil microbial ability to catabolize carbon compounds in an oceanic alpine heath – E.R. Jasper Wubs, Soil Biology and Biochemistry

Grazing and resource availability control soil nematode body size and abundance‐mass relationship in semi‐arid grassland – W. S. Andriuzzi, Journal of Animal Ecology

Isolation and screening of antibiotic producing actinomycetes from rhizosphere and agricultural soils – Atsede Muleta, African Journal of Biotechnology

Responses of Bougainvillea spectabilis to elevated atmospheric CO2 under galaxolide (HHCB) pollution and the mechanisms of its rhizosphere metabolism – Minzhe Zhang, Journal of Soils and Sediments

Differential effect of the nitrogen form on the leaf gas exchange, amino acid composition, and antioxidant response of sweet pepper at elevated CO2 – María C. Piñero, Plant Growth Regulation

Viral metagenomics analysis and eight novel viral genomes identified from the Dushanzi mud volcanic soil in Xinjiang, China – Dan-Ting Yu, Journal of Soils and Sediments

Efficacy of Bacillus subtilis native strains for biocontrol of Phytophthora crown and root rot of pistachio in Iran – Mohammad Moradi, Tropical Plant Pathology

Modification of plant cell wall chemistry impacts metabolome and microbiome composition in Populus PdKOR1 RNAi plants – Allison M. Veach, Plant and Soil

Continuous application of different fertilizers induces distinct bulk and rhizosphere soil protist communities – Sai Guo, European Journal of Soil Biology

Microbial communities and natural fermentation of corn silages prepared with farm bunker-silo in Southwest China – Hao Guan, Bioresource Technology

Cultivated methanotrophs associated with rhizospheres of traditional rice landraces from Western India belong to Methylocaldum and Methylocystis – Monali C. Rahalkar, 3 Biotech

Metal(loid)-resistant bacteria reduce wheat Cd and As uptake in metal(loid)-contaminated soil – Xiao-Han Wang, Environmental Pollution

Enhanced removal of nitrate in the maize rhizosphere by plant growth-promoting Bacillus megaterium NCT-2, and its colonization pattern in response to nitrate – Shaohua Chu, Chemosphere

Bioactive luteoloside produced by Myroides odoratimimus, solvent-tolerant bacterium form the rhizosphere of Lonicera japonica –  Y. X. Zhao, Natural Product Research

Potential application of selected metal resistant phosphate solubilizing bacteria isolated from the gut of earthworm (Metaphire posthuma) in plant growth promotion – Jayanta  Kumar Biswas, Geoderma

Effects of Pseudomonas chenduensis and biochar on cadmium availability and microbial community in the paddy soil – Lingjuan Li, Science of The Total Environment

Continuous application of different fertilizers induces distinct bulk and rhizosphere soil protist communities – Sai Guo, European Journal of Soil Biology

Analysis on metabolic functions of stored rice microbial communities by BIOLOG ECO microplates – Zhiwen Ge, Frontiers in Microbiology

Effects of discrete bioactive microbial volatiles on plants and fungi – Birgit Piechulla, Plant, Cell, and Environment

Phylogenetic-scale disparities in the soil microbial diversity–ecosystem functioning relationship – Marta Goberna, ISME

Similar soil microbial community structure across different environments after long‐term succession: evidence from volcanoes of different ages – Shangqi Xu, Journal of Basic Microbiology

Water and extremophile microbiome

Comparison among the microbial communities in the lake, lake wetland, and estuary sediments of a plain river network – Wei Huang, Microbiology Open

The distinctive microbial community improves composting efficiency in a full-scale hyperthermophilic composting plant – Zhen Yu, Bioresource Technology

Co-occurrence Networks Among Bacteria and Microbial Eukaryotes of Lake Baikal During a Spring Phytoplankton Bloom – Ivan S. Mikhailov, Microbial Ecology

The Legacy Effects of Winter Climate on Microbial Functioning After Snowmelt in a Subarctic Tundra – Maria Väisänen, Microbial Ecology

Characterization of phototrophic microorganisms and description of new cyanobacteria isolated from the saline-alkaline crater-lake Dziani Dzaha (Mayotte, Indian Ocean) – M. Cellamare, FEMS Microbiology Ecology

Methanogens in the Antarctic Dry Valley Permafrost – Tatiana A. Vishnivetskaya, FEMS Microbiology Ecology

Bacterial Diversity in an Alpine Debris-Free and Debris-Cover Accumulation Zone Glacier Ice, North Sikkim, India – Mingma Thundu Sherpa, Indian Journal of Microbiology

Culturing the ubiquitous freshwater actinobacterial acI lineage by supplying a biochemical ‘helper’ catalase – Suhyun Kim, bioRxiv

Assessing the effect of pretreatments on the structure and functionality of microbial communities for the bioconversion of microalgae to biogas – Olivia Córdova, Frontiers in Microbiology

Great Salt Lake microbiology: a historical perspective – Bonnie K. Baxter, International Microbiology

Life from the ashes: survival of dry bacterial spores after very high temperature exposure – Lynda Beladjal, Extremophiles

Microbial and geochemical controls on waste rock weathering and drainage quality – Sharon Blackmore, Science of The Total Environment

Characterization and high-throughput sequencing of a trichlorophenol-dechlorinating microbial community acclimated from sewage sludge – Jiaxiu Song, Journal of Cleaner Production

Impacts of surface-applied residues on N-cycling soil microbial communities in miscanthus and switchgrass cropping systems – Karen A. Thompson, Applied Soil Ecology

Water is a critical factor in evaluating and assessing microbial colonization and destruction of Angkor sandstone monuments – Xiaobo Liu, International Biodeterioration & Biodegradation

Methanogenic community shifts during the transition from sewage mono-digestion to co-digestion of grass biomass – Justus Hardegen, Bioresource Technology

Bacterial lineages putatively associated with the dissemination of antibiotic resistance genes in a full-scale urban wastewater treatment plant – Carlos Narciso-da-Rocha, Environment International

Impact of organic waste composition on life cycle energy production, global warming and Water use for treatment by anaerobic digestion followed by composting – Sara A. Pace, Resources, Conservation and Recycling

1H NMR metabolomics of microbial metabolites in the four MW agricultural biogas plant reactors: A case study of inhibition mirroring the acute rumen acidosis symptoms – Boštjan Murovec, Journal of Environmental Management

Comparative Metagenomics Provides Insight into the Ecosystem Functioning of the Shark Bay Stromatolites, Western Australia – Joany Babilonia, Frontiers in Microbiology

Assessing the abundance of fungal populations in a full-scale membrane bioreactor (MBR) treating urban wastewater by using quantitative PCR (qPCR) – P. Maza-Márquez, Journal of Environmental Management

Food microbiology

Occurrence of lactic acid bacteria and yeasts at species and strain level during spontaneous fermentation of mawè, a cereal dough produced in West Africa – Marcel Houngbédji, Food Microbiology

Probiotics / prebiotics

Probiotics in IBD: Combining in vitro and in vivomodels for selecting strains with both anti-inflammatory potential as well as a capacity to restore the gut epithelial barrier – Mazen Zaylaa, Journal of Functional Foods

Can prebiotics assist in the management of cognition and weight gain in schizophrenia? – Amy Chia-Ching Kao, Psychoneuroendocrinology

Probiotic potentials of Lactobacillus plantarum isolated from fermented durian (Tempoyak), a Malaysian traditional condiment – Asmariah Ahmad, Food Science and Nutrition

Bioinformatics

Identifying Heritable Communities of Microbiome by Root-Unifrac and Wishart Distribution – Yunfan Tang, bioRxiv

PARTIE: a partition engine to separate metagenomic and amplicon projects in the Sequence Read Archive – Pedro J. Torres, Bioinformatics

Techniques

Dead or Alive? Molecular life-dead distinction in human stool samples reveals significantly different composition of the microbial community – Alexandra Perras, bioRxiv

Critical Assessment of Methods to Quantify Biofilm Growth and Evaluate Antibiofilm Activity of Host Defence Peptides – Evan F. Haney, Biomolecules