Category Archives: Microbial Ecology

October 24, 2018

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Today’s digest is full of REALLY cool science and features including a 3D image of the human lung microbiome and metabolome, how gut microbiome of wild mice promotes fitness, and an interesting perspective piece on how environmental filtering applies to microbiomes.

General microbiome

Environmental Filtering Is a Relic. A Response to Cadotte and Tucker.

Aguilar-Trigueros CA- Trends in Ecology and Evolution

Gut microbiome

The Leaky Gut and Altered Microbiome in Chronic Kidney Disease.

Lau WL- Journal of Renal Nutrition

Linking the Gut Microbial Ecosystem with the Environment: Does Gut Health Depend on Where We Live?

Tasnim N- Frontiers in Microbiology

Skin microbiome

High-Altitude Living Shapes the Skin Microbiome in Humans and Pigs.

Zeng B- Frontiers in Microbiology

Lung microbiome

Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung

Garg N- Cell Host and Microbe

Animal microbiome

Wild Mouse Gut Microbiota Promotes Host Fitness and Improves Disease Resistance

Rosshart SP- Cell

Plant and soil microbiome

Soil bacterial community mediates the effect of plant material on methanogenic decomposition of soil organic matter

Yuan Q- Soil Biology and Biochemistry

Bacterial communities in soil become sensitive to drought under intensive grazing

Jurburg SD- Science of the Total Environment

Prokaryotic Community Distribution along an Ecological Gradient of Salinity in Surface and Subsurface Saline Soils.

Xie K- Scientific reports

Marine and inland water microbiome

Transcriptional activities of the microbial consortium living with the marine nitrogen-fixing cyanobacterium Trichodesmium reveal potential roles in community-level nitrogen cycling

Lee MD-Applied and Environmental Microbiology

Dynamic microbial populations along the Cuyahoga River.

Cannon MV-  PloS one

Preprint

High degree of virulence gene diversity in Streptococcus pyogenes isolated in Central Italy

Bencardino D- BioRxiv

Microbiome News

I Wish I’d Known This Before I Gave Birth

-mindbodygreen.com

October 19, 2017

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Today, we have a short Digest but with interesting remarks: Alzheimer’s disease associated microbiome, the bacterial tree of Life and more.

 

Human Microbiome

Gut microbiome alterations in Alzheimer’s disease – Nicholas M. Vogt – Scientific Reports

Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease – Veronika B. Dubinkina – Microbiome (BMC)

Male-specific Association Between Fat Free Mass Index and Faecal Microbiota in 2 to 3 Year Old Australian Children – Paula Smith-Brown – Journal of Pediatric Gastroenterology & Nutrition

 

General Microbiome

Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing – Noelle R. Noyes – Microbiome (BMC)

Sulfites inhibit the growth of four species of beneficial gut bacteria at concentrations regarded as safe for food – Sally V. Irwin – PLoS ONE

Research Highlights: Host-microbe interactions: Aiming at GPCRs – Mirella Bucci – Nature Chemical Biology

 

Animal Microbiome

Recombinant Incretin-Secreting Microbe Improves Metabolic Dysfunction in High-Fat Diet Fed Rodents – Paul M. Ryan – Scientific Reports

Microbiota Diversification and Crash Induced by Dietary Oxalate in the Mammalian Herbivore Neotoma albigula – Aaron W. Miller – mSphere

Commentary: Microbes REV up Host Metabolism around the Clock – Geoffrey N. Pronovost – Immunity

Impact of age-related mitochondrial dysfunction and exercise on intestinal microbiota composition – David Houghton – The Journals of Gerontology Series A

Comparative Analysis of Gut Microbiota of Culex restuans (Diptera: Culicidae) Females From Different Parents – Ephantus J Muturi – Journal of Medical Entomology

 

Beneficial Microbes and Molecules

Maternal milk feedings reduce sepsis, necrotizing enterocolitis and improve outcomes of premature infants – J Cortez – Journal of Perinatology

Therapeutic potential of Bifidobacterium breve strain A1 for preventing cognitive impairment in Alzheimer’s disease – Yodai Kobayash – Scientific Reports

Recombinant Incretin-Secreting Microbe Improves Metabolic Dysfunction in High-Fat Diet Fed Rodents – Paul M. Ryan – Scientific Reports

 

Environmental Microbiome

The plant circadian clock influences rhizosphere community structure and function – Charley J Hubbard – The ISME Journal

 

Evolution

Towards a balanced view of the bacterial tree of life – Frederik Schulz – Microbiome (BMC)

 

Extremophiles

Primary and heterotrophic productivity relate to multi-kingdom diversity in a hypersaline mat – Hans C. Bernstein – FEMS Microbiology Ecology

 

Non-Microbiology picks

Sci-Hub provides access to nearly all scholarly literature – Daniel S Himmelstein – PeerJ Preprints

Nature index: On the biotech block – Alexandra Ossola – Nature

 

October 18, 2017

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Today, several reviews, including a trio of reviews about connections between HIV and microbiome.

Gut microbiome

Gut bacterial communities of diarrheic patients with indications of Clostridioides difficile infection – Dominik Schneider – Scientific Data (NPG)

News and Views: Gastric cancer: The gastric microbiota — bacterial diversity and implications – Manish A. Shah – Nature Reviews Gastroenterology & Hepatology

Review: The hygiene hypothesis in autoimmunity: the role of pathogens and commensals – Jean-François Bach – Nature Reviews Immunology

The Bacteroidales produce an N-acylated derivative of glycine with both cholesterol-solubilising and hemolytic activity – Alli Lynch – Scientific Reports

Gastric acid suppression promotes alcoholic liver disease by inducing overgrowth of intestinal Enterococcus – Cristina Llorente – Nature Communications

High-Fat Diet Changes Fungal Microbiomes and Interkingdom Relationships in the Murine Gut – Timothy Heisel – mSphere

Review: Gut Microbiota and Nonalcoholic Fatty Liver Disease: Insights on Mechanisms and Therapy – Junli Ma – Nutrients (MDPI)

Review article: The gut microbiome in inflammatory bowel disease-avenues for microbial management – J. McIlroy – Alimentary Pharmacology & Therapeutics

Commentary: Regulation of glucagon-like peptide-1 sensitivity by gut microbiota dysbiosis – Shunsuke Yamane – Journal Of Diabetes Investigation

Low-grade small intestinal bacterial overgrowth is common in patients with non-alcoholic steatohepatitis on quantitative jejunal aspirate culture – UC Ghoshal – Indian Journal of Gastroenterology

 

Reproductive tract microbiome

The microbiota continuum along the female reproductive tract and its relation to uterine-related diseases – Chen Chen – Nature Communication

 

Microbiome in general

The microbiome beyond the horizon of ecological and evolutionary theory – Britt Koskella – Nature Ecology & Evolution

Trios—promising in silico biomarkers for differentiating the effect of disease on the human microbiome network – Zhanshan (Sam) Ma – Scientific Reports

 

Beneficial microbes and molecules

Prebiotic and Synbiotic Modifications of Beta Oxidation and Lipogenic Gene Expression after Experimental Hypercholesterolemia in Rat Liver – Claudia C. Alves – Frontiers in Microbiology

Vildagliptin increases butyrate-producing bacteria in the gut of diabetic rats – Qian Zhang – PLoS ONE

Caprylic and Polygalacturonic Acid Combinations for Eradication of Microbial Organisms Embedded in Biofilm – Joel Rosenblatt – Frontiers in Microbiology

PostScript: Faecal microbiota transplantation donor stools need screening for poliovirus – Peter Gerald Speck – Gut (BMJ)

 

Environmental research

Bacterial and fungal communities respond differently to varying tillage depth in agricultural soils – Craig Anderson – PeerJ

Microbial community diversity patterns are related to physical and chemical differences among temperate lakes near Beaver Island, MI – Miranda H. Hengy – PeerJ

Diversity and Structure of Diazotrophic Communities in Mangrove Rhizosphere, Revealed by High-Throughput Sequencing – Yanying Zhang – Frontiers in Microbiology

 

HIV and microbiome

Review: HIV and aging: role of the microbiome – Seema N. Desai – Current Opinion in HIV & AIDS

Review: The functional consequences of the microbiome in HIV: insights from metabolomic studies – Sergio Serrano-Villar – Current Opinion in HIV & AIDS

Review: Cross-reactivity of HIV vaccine responses and the microbiome – Wilton B Williams – Current Opinion in HIV & AIDS

 

Respiratory tract microbiome

Lung Microbiota is Related to Smoking Status and to Development of ARDS in Critically Ill Trauma Patients – Ariane R Panzer – American Journal of Respiratory and Critical Care Medicine

 

More microbes

Adjacent-possible ecological niche: growth of Lactobacillus species co-cultured with Escherichia coli in a synthetic minimal medium – Kouhei Mizuno – Scientific Reports

 

October 15, 2017

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General microbiome

Metagenome Analyses of Multispecies Microbial Biofilms: First Steps Toward Understanding Diverse Microbial Systems on Surfaces – Christel Schmeisser, Functional Metagenomics: Tools and Applications

Prediction analysis for microbiome sequencing data – Tao Wang, arxiv

Metagenomic Cosmid Libraries Suitable for Functional Screening in Proteobacteria – Jiujun Cheng, Functional Metagenomics: Tools and Applications

Moulds associated with contaminated ocular and injectable drugs: FDA recalls, epidemiology considerations, drug shortages, and aseptic processing – Donald G. Ahearn, Medical Mycology

Human skin microbiome

High-Altitude Living Shapes the Skin Microbiome in Humans and Pigs – Bo Zeng, Frontiers in Microbiology

Human vaginal microbiome

Role of Molecular Biology in Diagnosis and Characterization of Vulvo-Vaginitis in Clinical Practice – Donders G.G.G., Gynecologic and Obstetric Investigation

Human gut microbiome

A Review of the Oesophageal Microbiome in Health and Disease – Dervla Kelly, Methods in Microbiology

Prediction of functional profiles of gut microbiota from 16S rRNA metagenomic data provides a more robust evaluation of gut dysbiosis occurring in Japanese type 2 diabetic patients – Ryo Inoue, Journal of Clinical Biochemistry and Nutrition

Human oral microbiome

The Effect of Supragingival Biofilm Re-development on the Subgingival Microbiota in Chronic Periodontitis – Fátima Aparecida Rocha Resende Hartenbach, Archives of Oral Biology

Animal experiments

Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice – Jessica L. Mark Welch, PNAS

Comparative study of probiotic effects of Lactobacillusand Bifidobacteria strains on cholesterol levels, liver morphology and the gut microbiota in obese mice – Rostyslav V. Bubnov, The EPMA Journal

Study on improving anaerobic co-digestion of cow manure and corn straw by fruit and vegetable waste: methane production and microbial community in CSTR process – Xuemei Wang, Bioresource Technology

Animal microbiome

Perinatal Bisphenol A Exposure Induces Chronic Inflammation in Rabbit Offspring via Modulation of Gut Bacteria and Their Metabolites – Lavanya Reddivari, mSystems

Hymenobacter cavernae sp. nov., isolated from a karst cave – Hai-Zhen Zhu, International Journal of Systematic and Evolutionary Microbiology

Plant, root, and soil microbiome

Ciceribacter thiooxidans sp. nov., a novel nitrate-reducing thiosulfate-oxidizing bacterium isolated from sulfide-rich anoxic sediment – Tongchu Deng, International Journal of Systematic and Evolutionary Microbiology

Deinococcus taklimakanensis sp. nov., isolated from desert soil –  Zuobing Liu, International Journal of Systematic and Evolutionary Microbiology

Improvement of the catalytic characteristics of a salt-tolerant GH10 xylanase from Streptomyce rochei L10904 – Qin Li, International Journal of Biological Macromolecules

Trees harness the power of microbes to survive climate change – Jennifer A. Lau, PNAS

Exploring the earthworm gut as model for soil microbial ecology – Fatima Hussain, MBL

Soil proteomics for exploitation of microbial diversity in Fusarium wilt infected and healthy rhizosphere soils of tomato – R. Manikandan, Physiological and Molecular Plant Pathology

The intimate talk between plants and microorganisms at the leaf surface – Wendy Aragón, Journal of Experimental Botany

Metagenomics of Plant Microbiomes – G. Brader, Functional Metagenomics: Tools and Applications

Effects of different soil remediation methods on inhibition of lead absorption and growth and quality of Dianthus superbus L. – Xiaoyu Yang, Environmental Science and Pollution Research

Interactions of Root-Feeding Insects with Fungal and Oomycete Plant Pathogens – Telsa Willsey, Frontiers in Plant Science

Soil proteomics for exploitation of microbial diversity in Fusarium wilt infected and healthy rhizosphere soils of tomato – R. Manikandan, Physiological and Molecular Plant Pathology

Switchgrass Yield, Nutrient Uptake, And Rhizosphere Microbial Community Composition As Affected By Cultivar And Soil Fertility – Anne Sawyer, University of Minnesota Digital Conservancy

Ecoenzymatic stoichiometry and microbial nutrient limitation in rhizosphere soil in the arid area of the northern Loess Plateau, China – Yongxing Cui, Soil Biology and Biochemistry

Soil microbiota respond to green manure in organic vineyards – Claudia M. O. Longa, Journal of Applied Microbiology

Water and extremophile microbiome

Anoxynatronum buryatiense sp. nov., an anaerobic alkaliphilic bacterium from a low mineralization soda lake in Buryatia, Russia – Yana Ryzhmanova, International Journal of Systematic and Evolutionary Microbiology

100 kGy gamma-affected microbial communities within the ancient Arctic permafrost under simulated Martian conditions – Vladimir S. Cheptsov, Extremophiles

Effect of environmental parameters on biodiversity of the fungal component in lithic Antarctic communities – Laura Selbmann, Extremophiles

Biomineralisation of carbonate and sulphate by the halophilic bacterium Halomonas maura at different manganese concentrations – Almudena Rivadeneyra, Extremophiles

Biosurfactant production by haloalkaliphilic Bacillusstrains isolated from Red Sea, Egypt – Khouloud M.Barakat, The Egyptian Journal of Aquatic Research

Mass Spectrometry for the Study of Microbial Communities in Environmental Waters – Inês C. Santos, Advances in Chemical Pollution, Environmental Management and Protection

Responses of microbial community to pH stress in bioleaching of low grade copper sulfide – Yuguang Wang, Bioresource Technology

Mass Spectrometry for the Study of Microbial Communities in Environmental Waters – Inês C. Santos, Advances in Chemical Pollution, Environmental Management and Protection

Waste microbes

Microbial characteristics analysis and kinetic studies on substrate composition to methane after microbial and nutritional regulation of fruit and vegetable wastes anaerobic digestion – Chunhui Zhao, Bioresource Technology

Antibiotic resistance genes and associated microbial community conditions in aging landfill systems – Dong Wu, Environmental Science and Technology

Bioinformatics

Bioinformatics in Microbiome Analysis – Yuhan Hao, Methods in Microbiology

Techniques

Enhancing Metagenomic Approaches Through Synthetic Biology – Luana de Fátima Alves, Functional Metagenomics: Tools and Applications

Enhancing Functional Metagenomics of Complex Microbial Communities Using Stable Isotopes – Marcela Hernández, Functional Metagenomics: Tools and Applications

The P/N (Positive-to-Negative Links) Ratio in Complex Networks—A Promising In Silico Biomarker for Detecting Changes Occurring in the Human Microbiome – Zhanshan (Sam) Ma, Microbial Ecology

Challenges and Opportunities in Discovery of Secondary Metabolites Using a Functional Metagenomic Approach – Alinne L. R. Santana-Pereira, Functional Metagenomics: Tools and Applications

Emerging whole-cell modeling principles and methods – Arthur P. Goldberg, arxiv

Expression Platforms for Functional Metagenomics: Emerging Technology Options Beyond Escherichia coli – Anna Lewin, Functional Metagenomics: Tools and Applications

Microbes in the news

AST: The Linchpin of Antimicrobial Stewardship – James Lewis, ModernMedicine Network

The Black Death Rages In Madagascar –  Julianna LeMieux, American Council on Science and Health

Report: 17 New Species Of Bacteria Found Every Day In World’s Rainforest Cafés – The Onion (Satire)

October 4, 2017

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Today’s digest features excellent reviews on recent advances in cryo-electron microscopy technology for understanding bacterial ribosome assembly,  and impact of gut microbiome on therapeutics. Happy reading!

General microbiome

Towards standards for human fecal sample processing in metagenomic studies – Paul I Costea – Nature Biotechnology

Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium – Rashmi Sinha – Nature Biotechnology

Editorial : Microbiome yarns: microbiome basis of memory – Kenneth Timmis – Microbial Biotechnology

Review : Cross Talk: The Microbiota and Neurodevelopmental Disorders – John R. Kelly – Frontiers in Neuroscience

Review : Gut Microbiota, Immune System, and Bone – P. D’Amelio – Calcified Tissue International

Pregnancy and early life

Meconium microbiome as a new source of information about long-term health and disease: questions and answers – P. Wilczyńska – The Journal of Maternal-Fetal & Neonatal Medicine

Evolution in fecal bacterial/viral composition in infants of two central African countries (Gabon and Republic of the Congo) during their first month of life – Lionel Brazier – Plos one

A longitudinal study of the infant nasopharyngeal microbiota: The effects of age, illness and antibiotic use in a cohort of South East Asian children – Susannah J. Salter – Plos one

Human gut microbiome

Review : Microbiota in digestive cancers: our new partner? – Anthony Lopez – Carcinogenesis

*Review : Impacts of the Human Gut Microbiome on Therapeutics – Yoshiki Vázquez-Baeza – Annual Reviews

Associations between acute gastrointestinal GvHD and the baseline gut microbiota of allogeneic hematopoietic stem cell transplant recipients and donors – C Liu – Leukemia

Natural polyreactive IgA antibodies coat the intestinal microbiota – Jeffrey J. Bunker – Science

Time of day and eating behaviors are associated with the composition and function of the human gastrointestinal microbiota – Jennifer L Kaczmarek – The American Journal of Clinical Nutrition

The Effects of an Environmentally Relevant Level of Arsenic on the Gut Microbiome and its Functional Metagenome – Liang Chi – Toxicological Sciences

Animal experiments

Probiotics modulate gut microbiota and improve insulin sensitivity in DIO mice – Renata A.Bagarolli – The Journal of Nutritional Biochemistry

Decaffeinated green and black tea polyphenols decrease weight gain and alter microbiome populations and function in diet-induced obese mice – Susanne M. Henning – European Journal of Nutritional

Microbiota-related Changes in Bile Acid & Tryptophan Metabolism are Associated with Gastrointestinal Dysfunction in a Mouse Model of Autism – Anna V. Golubeva – EBioMedicine

Repeated Oral Exposure to Nε-Carboxymethyllysine, a Maillard Reaction Product, Alleviates Gut Microbiota Dysbiosis in Colitic Mice – Nesreen ALJahdali – Digestive Disease Sciences

Comparison of the Luminal and Mucosa-Associated Microbiota in the Colon of Pigs with and without Swine Dysentery – Eric R. Burrough – Frontiers in Veterinary Science

Animal microbiome

Untangling the cecal microbiota of feral chickens by culturomic and metagenomic analyses – Chiara Ferrario – Environmental Microbiology

Bacterial community associated with worker honeybees (Apis mellifera) affected by European foulbrood – Tomas Erban – PeerJ

Comparative characterization of bacterial communities in geese fed all-grass or high-grain diets – Qi Xu – Plos One

Plant, root, and soil microbiome

Implication of graphene oxide in Cd-contaminated soil: A case study of bacterial communities – TingXiong – Journal of Environmental Management

Elucidating the microbial community associated with the protein preference of sludge degrading worms – Steef de Valk – Environmental Technology

Bacterial microbiomes of individual ectomycorrhizal Pinus sylvestris roots are shaped by soil horizon and differentially sensitive to nitrogen addition – Srisailam Marupakula – Environmental Microbiology

A comparative study of composting the solid fraction of dairy manure with or without bulking material: performance and microbial community dynamics – Xiao-ZhongZhong -Bioresource Technology

Water and extremophile microbiome

Individual-level trait diversity predicts phytoplankton community properties better than species richness or evenness – Simone Fontana – The ISME Journal

Bacterial community dynamics within an aerobic granular sludge reactor treating wastewater loaded with pharmaceuticals – Catarina L.Amorim – Ecotoxicology and Environmental Safety

Food Microbiology

Chlorogenic acid versus amaranth’s caffeoylisocitric acid – Gut microbial degradation of caffeic acid derivatives – Maren Vollmer – Food Research International

Probiotics / prebiotics

Specific signatures of the gut microbiota and increased levels of butyrate in children treated with fermented cow’s milk containing heat-killed Lactobacillus paracasei CBA L74 – Roberto Berni Canani – Applied and Environmental Microbiology

Beneficial effects of a probiotic blend on gastrointestinal side effects induced by leflunomide and amlodipine in a rat model – S.C. Song – Beneficial Microbes

Phages and viruses

Characterization of the human DNA gut virome across populations with different subsistence strategies and geographical origin – Simone Rampelli – Environmental Microbiology

Metabolomics

Identification of phenolic metabolites in human urine after the intake of a functional food made from grape extract by a high resolution LTQ-Orbitrap-MS approach – Gemma Sasot – Food Research International
http://www.sciencedirect.com/science/article/pii/S0963996917300297?via%3Dihub

Bioinformatics

A broken promise: microbiome differential abundance methods do not control the false discovery rate – Stijn Hawinkel – Briefings in Bioinformatics
https://academic.oup.com/bib/article/doi/10.1093/bib/bbx104/4091293/A-broken-promise-microbiome-differential-abundance

Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes – Nathan D. Olson – Briefings in Bioinformatics

Ananke: temporal clustering reveals ecological dynamics of microbial communities – Michael W. Hall – PeerJ

Detection of Increased Plasma Interleukin-6 Levels and Prevalence of Prevotella copri and Bacteroides vulgatus in the Feces of Type 2 Diabetes Patients – Aline Zazeri Leite – Frontiers in Immunology

k-SLAM: accurate and ultra-fast taxonomic classification and gene identification for large metagenomic data sets – David Ainsworth – Nucleic Acids Research

Techniques

* The impact of recent improvements in cryo-electron microscopy technology on the understanding of bacterial ribosome assembly – Aida Razi – Nucleic acids Research

Anitha’s non-microbiology picks

A cold, clear view of life wins chemistry Nobel

Nobel physics prize awards discovery in gravitational waves

Medicine Nobel Prize Goes to Circadian Rhythm Researchers

New portable blood analyzer could improve anemia detection worldwide

Computational study sheds doubt on latest theory of birds’ mysterious magnetic compass

 

October 3, 2017

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Review on bioinformatics software for virus sequence analysis, the wild baboon microbiome, potential health risks of spontaneous food fermentation.

Human oral microbiome

Pre-print: Novel genes required for the fitness of Streptococcus pyogenes in human saliva – Luchang Zhu – bioRxiv

Human gut microbiome

Antibiotic use and new-onset inflammatory bowel disease in Olmsted County, Minnesota: a population-based case-control study – Satimai Aniwan – Journal of Crohn’s and Colitis

The Gut Microbiota of Healthy Aged Chinese Is Similar to That of the Healthy Young – Gaorui Bian – mSphere

Animal experiments

Young Pigs Consuming Lysozyme Transgenic Goat Milk Are Protected from Clinical Symptoms of Enterotoxigenic Escherichia coli Infection – Lydia C Garas – The Journal of Nutrition

Whole-Grain Starch and Fiber Composition Modifies Ileal Flow of Nutrients and Nutrient Availability in the Hindgut, Shifting Fecal Microbial Profiles in Pigs – Janelle M Fouhse – The Journal of Nutrition

Lotus Seed Resistant Starch Regulates Gut Microbiota and Increases SCFAs Production and Mineral Absorption in Mice – Hongliang Zeng – Journal of Agricultural and Food Chemistry

Animal microbiome

Microbiota Diversity Within and Between the Tissues of Two Wild Interbreeding Species – Emmanuel Guivier – Microbial Ecology

Group Living and Male Dispersal Predict the Core Gut Microbiome in Wild Baboons – Laura E Grieneisen – Integrative and Comparative Biology

Plant, root, and soil microbiome

Pre-print: Rice paddy Nitrospirae encode and express genes related to sulfate respiration: proposal of the new genus Candidatus Sulfobium – Sarah Zecchin – bioRxiv

Effects of Grazing and Fire Frequency on Floristic Quality and its Relationship to Indicators of Soil Quality in Tallgrass Prairie – George C Manning – Environmental Management

Pre-print: Hunters or gardeners? Linking community structure and function of trap-associated microbes to the nutrient acquisition strategy of a carnivorous plant – Dagmara Sirová – bioRxiv

Multitrophic interactions in the rhizosphere of a temperate forest tree affect plant carbon flow into the belowground food web – H R Maboreke – Soil Biology and Biochemistry

Water and extremophile microbiome

Rhabdanaerobium thermarum gen. nov., sp. nov., a novel anaerobic bacterium isolated from a hot spring – Lan Liu – International Journal of Systematic and Evolutionary Microbiology

Food microbiology

Review: Spontaneous Food Fermentations and Potential Risks for Human Health – Vittorio Capozzi – Fermentation

Phages and viruses

Review: Software Dedicated to Virus Sequence Analysis “Bioinformatics Goes Viral” – Martin Hölzer – Advances in Virus Research

Bioinformatics

Nephele: A cloud platform for simplified, standardized, and reproducible microbiome data analysis – Nick Weber – Bioinformatics

More microbes

Pre-print: A LaeA- and BrlA-dependent cellular network governs tissue-specific secondary metabolism in the human pathogen Aspergillus fumigatus – Abigail L Lind – bioRxiv

Pre-print: Dual RNAseq shows the human mucosal immunity protein, MUC13, is a hallmark of Plasmodium exoerythrocytic infection – Gregory M LaMonte – bioRxiv

October 2, 2017

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This Monday we have quite short digest with interesting review from K. Rosenthal about microbial single cell analysis,  T. K. Hattenrath-Lehmann tells us about microbes associated with harmful algal blooms while G. Chen demonstrates mutualistic interaction between bacteria in anaerobic mixed culture. Enjoy your reading.

Events and jobs

Tenure Track Faculty Position in Microbial Systems/Synthetic Biology, Chestnut Hill, Massachusetts

General microbiome

Review: Beyond the bulk: disclosing the life of single microbial cells  – Katrin Rosenthal – FEMS Microbiology Reviews

Metagenomic assessment of the interplay between the environment and the genetic diversification of Acinetobacter – Marc Garcia-Garcera – Environmental Microbiology

Mutualistic interaction between dichloromethane- and chloromethane-degrading bacteria in an anaerobic mixed culture – Gao Chen – Environmental Microbiology

Human skin microbiome

Antisepsis of the skin before spinal surgery with povidone iodine-alcohol followed by chlorhexidine gluconate-alcohol versus povidone iodine-alcohol applied twice for the prevention of contamination of the wound by bacteria – S. Patrick – The Bone & Joint Journal

Human nearly-sterile sites 

Microbiota regulates bone marrow mesenchymal stem cell lineage differentiation and immunomodulation – E Xiao – Stem Cell Research & Therapy

Human gut microbiome

Sulphate-reducing bacteria from ulcerative colitis patients induce apoptosis of gastrointestinal epithelial cells – Cláudia Mara Lara Melo Coutinho –  Microbial Pathogenesis

Animal experiments

Changes in the microbiota cause genetically modified Anopheles to spread in a population – Andrew Pike – Science

Plant, root, and soil microbiome

Impact of spatial organization on a novel auxotrophic interaction among soil microbes – Xue Jiang – bioRxiv

Novel archaeal thermostable cellulases from an oil reservoir metagenome – Anna Lewin – AMB Express

Periodically spilled-oil input as a trigger to stimulate the development of hydrocarbon-degrading consortia in a beach ecosystem – Kai Zhang – Scientific Reports

Water and extremophile microbiome 

Identification of unique microbiomes associated with harmful algal blooms caused by Alexandrium fundyense and Dinophysis acuminata -Theresa K.Hattenrath-Lehmann – Harmful Algae

Metagenomic insights into zooplankton-associated bacterial communities – Daniele De Corte – Environmental Microbiology

Strong impact of anthropogenic contamination on the co-occurrence patterns of a riverine microbial community – Anyi Hu – Environmental Microbiology

Microbial Diversity in a Hypersaline Sulfate Lake: A Terrestrial Analog of Ancient Mars – Alexandra Pontefract – Frontiers in Microbiology

Bioinformatics

SAMSA2: A standalone metatranscriptome analysis pipeline – Samuel T. Westreich – bioRxiv

Microbes in the news 

Oral sex spreading unstoppable bacteria

 

September 26, 2017

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Today’s digest is a delight for dog lovers – an interesting look at the nasal microbiome of dogs and two interesting studies on freshwater phages. Lastly, researchers in South Korea establish a human stool bank.

Human Gut Microbiome

REVIEW: A review of the relationship between the gut microbiota and amino acid metabolism

Lin R.Amino Acids

Advanced glycation end products dietary restriction effects on bacterial gut microbiota in peritoneal dialysis patients; a randomized open label controlled trial

Yacoub R. PloS one

Oral Microbiome

Exploring the salivary microbiome of children stratified by the oral hygiene index

Mashima I. PLoS ONE

Animal experiments and microbiome

Ground Juniperus pinchotii and urea in supplements fed to Rambouillet ewe lambs Part 2: Ewe lamb rumen microbial communities

Ishaq SL. Journal of Animal Science

Characterization of the nasal and oral microbiota of detection dogs

Isaiah A. PLoS one

Marine and Inland Water microbiome 

Biodiversity and species competition regulate the resilience of microbial biofilm community

Feng K. Molecular Ecology

Plant and soil microbiome

The Fructan Syndrome: Evolutionary Aspects and Common Themes Among Plants and Microbes

Versluys M. Plant, Cell & Environment

Agricultural land use determines functional genetic diversity of soil microbial communities

Manoharan L. Soil Biology and Biochemistry

Synergetic suppression of soybean cyst nematodes by chitosan and Hirsutella minnesotensis via the assembly of the soybean rhizosphere microbial communities

Mwaheb MAMA .Biological Control

Patterns and mechanisms of responses by soil microbial communities to nitrogen addition

Zhou Z. Soil Biology and Biochemistry

Links between plant and fungal diversity in habitat fragments of coastal shrubland.

Maltz MR. PloS one

The response of soil bacterial communities to mining subsidence in the west China aeolian sand area

Shi P. Applied Soil Ecology

Comparative metagenomics approaches to characterize the soil fungal communities of western coastal region, Saudi Arabia

Moussa TAA. PLoS one

Disentangling environmental and host sources of fungal endophyte communities in an experimental beachgrass study

David AS. Molecular Ecology

Virome

Metaproteomics of marine viral concentrates reveals key viral populations and abundant periplasmic proteins in the oligotrophic deep chlorophyll maximum of the deep chlorophyll maximum of the South China Sea

Xie ZX. Environmental Microbiology

Genome characteristics and environmental distribution of the first phage that infects the LD28 clade, a freshwater methylotrophic bacterial group

Moon K. Environmental Microbiology

Protocol

Assessment of molecular detection of anaerobic ammonium-oxidizing (anammox) bacteria in different environmental samples using PCR primers based on 16S rRNA …

Han P. Applied Microbiology and Biotechnology

Use of RNALater® Preservation for Virome Sequencing in Outbreak settings

Kohl C.Frontiers in Microbiology

DESMAN: a new tool for de novo extraction of strains from metagenomes

Quince C. Genome Biology

Microbiome News

Korea’s first stool bank gets down to business

-Korean Biomedical Review

September 22, 2017

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Human Microbiome

Microbiome profile of the amniotic fluid as a predictive biomarker of perinatal outcome – Daichi Urushiyama – Scientific Reports

Role of gut microbiota on cardio-metabolic parameters and immunity in coronary artery disease patients with and without type-2 diabetes mellitus – Lidia Sanchez-Alcoholado – Frontiers in Microbiology

Perspective: Linking the gut microbial ecosystem with the environment: does gut health depend on where we live? – Nishat Tasnim – Frontiers in Microbiology

Effect of caloric restriction on gut permeability, inflammation markers, and fecal microbiota in obese women – Beate Ott – Scientific Reports

Perspective: The immunology of the allergy epidemic and the hygiene hypothesis – Bart N Lambrecht – Nature Immunology

Pearls: The microbiome and the hallmarks of cancer – Laura E. Fulbright – PLoS Pathogens

Exploring the salivary microbiome of children stratified by the oral hygiene index – Izumi Mashima – PLoS ONE

 

Built Site Microbiome

Metagenomic characterization of ambulances across the USA – Niamh B. O’Hara – Microbiome (BMC)

 

Food Microbiome

Review: A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies – Yu Cao – Frontiers in Microbiology

Bottled aqua incognita: microbiota assembly and dissolved organic matter diversity in natural mineral waters – Celine C. Lesaulnier – Microbiome (BMC)

 

Pathogen Research

An engineered bispecific DNA-encoded IgG antibody protects against Pseudomonas aeruginosa in a pneumonia challenge model – Ami Patel – Nature Communications

Illusions regarding Helicobacter pylori clinical trials and treatment guidelines – David Y Graham – Gut (BMJ)

 

Beneficial Microbes

Akkermansia muciniphila May Determine the Ameliorating or Aggravating Effects of Chondroitin Sulfate on Osteoarthritis – Qing-Ping Zeng – Frontiers in Microbiology

Minireview: Next-Generation Beneficial Microbes: The Case of Akkermansia muciniphila – Patrice D. Cani – Frontiers in Microbiology

The PGPR Stenotrophomonas maltophilia SBP-9 augments resistance against biotic and abiotic stress in wheat plants – Prabhat N. Jha – Frontiers in Microbiology

 

Beneficial Molecules

pH-dependant antifungal activity of valproic acid against the human fungal pathogen Candida albicans – Julien Chaillot – Frontiers in Microbiology

Dietary teasaponin ameliorates alteration of gut microbiota and cognitive decline in diet-induced obese mice – Sen Wang – Scientific Reports

Mulberry leaf alleviates streptozotocin-induced diabetic rats by attenuating NEFA signaling and modulating intestinal microflora – Yao Sheng – Scientific Reports

 

Microbial Evolution

New Insights into the Diversity of the Genus Faecalibacterium – Leandro Benevides – Frontiers in Microbiology

 

Environmental Microbiology

Insights into microalga and bacteria interactions of selected phycosphere biofilms using metagenomic, transcriptomic and proteomic approaches – Ines Krohn-Molt – Frontiers in Microbiology

 

Bioinformatics, Genomics and Methodologies

Genomic GC-content affects the accuracy of 16S rRNA gene sequencing based microbial profiling due to PCR bias – Martin I. Bahl – Frontiers in Microbiology

Preprint: Optimizing scoring function of dynamic programming of pairwise profile alignment using derivative free neural network – Kazunori D. Yamada – BioRxiv

Improving contig binning of metagenomic data using dS2 oligonucleotide frequency dissimilarity – Ying Wang – BMC Bioinformatics

A Laboratory Methodology for Dual RNA-Sequencing of Bacteria and their Host Cells In Vitro – James W. Marsh – Frontiers in Microbiology

 

Other

Review: A review of the relationship between the gut microbiota and amino acid metabolism – Rui Lin – Amino Acids (Springer)

 

September 15, 2017

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Events and jobs

 
Assistant or Associate Professor – Microbiology/Infectious Disease, Farmington, US

 
General microbiome

 
Review: Human microbiota in aging and infection: A review – Elisavet Stavropoulou  – Critical Reviews in Food Science and Nutrition

 

Phylogeographic, genomic, and meropenem susceptibility analysis of Burkholderia ubonensis – Erin P. Price – PLOS

 
Pregnancy and early life

 
The relation between cesarean birth and child cognitive development – Cain Polidano – Scientific Reports

 

Simultaneously Monitoring Immune Response and Microbial Infections During Pregnancy through Plasma cfRNA Sequencing – Wenying Pan – Clinical Chemistry

 
Human respiratory microbiome

 
Oral microbiomeTooth Be Told, Genetics Influences Oral Microbiome – Emily R. Davenport – Cell Host & Microbe

 
Host Genetic Control of the Oral Microbiome in Health and Disease – Andres Gomez – Cell Host & Microbe

 

Human nearly-sterile sites 

 

Evaluation of the Bacterial Diversity in the Human Tongue Coating Based on Genus-Specific Primers for 16S rRNA Sequencing – Beili Sun – BioMed Research International

 

Review: Microbiota-Derived Uremic Retention Solutes: Perpetrators of Altered Nonrenal Drug Clearance in Kidney Disease – Alexander J. Prokopienko – Expert Review of Clinical Pharmacology

 

Human gut microbiome

 
Microbial metabolites as mimickers of human molecules – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

 
The intestinal microbiota regulates body composition through NFIL3 and the circadian clock – Yuhao Wang – Science

 
The Landscape of Type VI Secretion across Human Gut Microbiomes Reveals Its Role in Community Composition – Adrian J. Verster – Cell Host & Microbe

 
Butyrate-producing bacteria supplemented in vitro to Crohn’s disease patient microbiota increased butyrate production and enhanced intestinal epithelial barrier integrity – Annelies Geirnaert – Scientific Reports

 
Linking Spatial Structure and Community-Level Biotic Interactions through Cooccurrence and Time Series Modeling of the Human Intestinal Microbiota – Eric J. de Muinck –  mSystems
Review: Microbiota and neurodegenerative diseases – Moira Marizzonip – Current Opinion in Neurology

 
Effect of cytomegalovirus and Epstein–Barr virus replication on intestinal mucosal gene expression and microbiome composition of HIV-infected and uninfected individuals – Gianella Sara – AIDS

 
Systematic Review and Meta-analysis: Fecal Microbiota Transplantation for Treatment of Active Ulcerative Colitis – Narula Neeraj – Inflammatory Bowel Diseases

 
Signatures in the gut microbiota of Japanese infants who developed food allergies in early childhood – Masaru Tanaka – FEMS Microbiology Ecology

 
Quantity and source of dietary protein influence metabolite production by gut microbiota and rectal mucosa gene expression: a randomized, parallel, double-blind trial in overweight humans – Martin Beaumont – The American Journal of Clinical Nutrition
Analysis of Mucosa-Associated Microbiota in Colorectal Cancer – Kehan Xu – Medical Science Monitor

 
Animal experiments 

 
Short-term dietary methionine supplementation affects one-carbon metabolism and DNA methylation in the mouse gut and leads to altered microbiome profiles, barrier function, gene expression and histomorphology – Isabelle R. Miousse – Genes & Nutrition

 
Development of Inflammatory Bowel Disease Is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice – Thomas Sharpton – mSystems

 
Development of a Stable Lung Microbiome in Healthy Neonatal Mice – Matea Kostric – Microbial Ecology

 

Animal microbiome

 

Seasonal variation in nutrient utilization shapes gut microbiome structure and function in wild giant pandas – Qi Wu  – Proceedings of the Royal Society of London B

 
Plant, root, and soil microbiome

 
Soil microbial community responses to acid exposure and neutralization treatment – Doyun Shin – Journal of Environmental Management

 
Spatial patterns of hypolithic cyanobacterial diversity in Northern Australia –  Keith Christian – Ecology & Evolution

 

Food microbiology

 

Short-Term Intake of a Fructose-, Fat- and Cholesterol-Rich Diet Causes Hepatic Steatosis in Mice: Effect of Antibiotic Treatment – Annette Brandt – Nutrients

 
Overview of craft brewing specificities and potentially associated microbiota – Lindsey Rodhouse – Critical Reviews in Food Science and Nutrition

 

Probiotics / prebiotics
Isolation of probiotic piliated Lactobacillus rhamnosus strains from human faecal microbiota using SpaAantiserum-based colony immunoblotting – Zhen-quan Yang – Journal of Microbiology and Biotechnology

 

Phages and viruses
CRISPR-based Herd Immunity Limits Phage Epidemics in Bacterial Populations – Pavel Payne – bioRxiv

 
Bioinformatics
A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome – Imane Allali – BMC Microbiology

 
Minimizing mixing intensity to improve the performance of rice straw anaerobic digestion via enhanced development of microbe-substrate aggregates – Moonkyung Kim – Bioresource Technology

 
Long term effects of cerium dioxide nanoparticles on the nitrogen removal, micro-environment and community dynamics of a sequencing batch biofilm reactor – Yi Xu – Bioresource Technology

 

Microbes in the news 
NIPGR scientists identify bacteria that can devour fungi

 
Are Genes to Blame for Cavity-causing Bacteria?

 
Microbes on the market (news about biotech companies)

 
Newly Launched CoreBiome Touts Microbiome ‘Profiling’ Services

 
Inventor converts waste plastics to fertilizer, fuel

 
Science, publishing, and career

 
The hundred most-cited publications in microbiota of diabetes research: A bibliometric analysis – Jiaxing Tian – Medicine