Category Archives: Human oral

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

September 29, 2017

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General microbiome

Metabolic and process engineering for biodesulfurization in Gram-negative bacteria – I. Martínez, Journal of Biotechnology

Biofilms: Survival and defense strategy for pathogens – Ashutosh Kumar, International Journal of Medical Microbiology

Effect of Substrate Conversion on Performance of Microbial Fuel Cells and Anodic Microbial Communities – Zhao Yang-Guo, Environmental Engineering Science

Comparison of the impacts of zinc ions and zinc nanoparticles on nitrifying microbial community – Qiang Wu, Journal of Hazardous Materials

Models of microbiome evolution incorporating host and microbial selection – Qinglong Zeng, Microbiome

Pregnancy and early life

Impact of delivery mode on the colostrum microbiota composition – Marco Toscano, BMC Microbiology

Multi-site human microbiome

Human Microbiome in Brazil – Luciana Campos Paulino, The Brazilian Microbiome

Forensic genetics and genomics: Much more than just a human affair – Miguel Arenas, PLoS Genetics

South Asian Health: Inflammation, Infection, Exposure, and the Human Microbiome – Jennifer Leng, Journal of Immigrant and Minority Health

Natural Products as Platforms To Overcome Antibiotic Resistance – Sean E. Rossiter, Chemical Reviews

Intestinal Dysbiosis and Rheumatoid Arthritis: A Link between Gut Microbiota and the Pathogenesis of Rheumatoid Arthritis – Gabriel Horta-Baas, Journal of Immunology Research

Human respiratory microbiome

Individual Patterns of Complexity in Cystic Fibrosis Lung Microbiota, Including Predator Bacteria, over a 1-Year Period – Juan de Dios Caballero, mBio

Sputum microbiota in severe asthma patients: Relationship to eosinophilic inflammation – Naijian Li, Respiratory Medicine

Human skin microbiome

Culture characterization of the skin microbiome in type 2 diabetes mellitus: a focus on the role of innate immunity – Akshay Thimmappaiah Jagadeesh, Diabetes Research and Clinical Practice

Human vaginal microbiome

Lactobacillus iners-dominated vaginal microbiota is associated with increased susceptibility to Chlamydia trachomatis infection in Dutch women: a case–control study – Robin van Houdt, Epidemiology

Human gut microbiome

Bacterial chat: intestinal metabolites and signals in host -microbiota -pathogen interactions – Bruna C. Lustri, Infection and Immunity

Gut inflammation and dysbiosis in human motor neuron disease – Julie Rowin, Physiological Reports

Molecular basis of gut microbiome-associated colorectal cancer: A synthetic perspective – Alan R. Healy, Journal of American Chemical Society

Metagenomic Paleomicrobiology Characterizes Fecal Microbiomes and Viromes of Pre-Columbian Cultures from Vieques, Puerto Rico – Jessica I. Rivera-Perez, ProQuest

A randomised trial of the effect of omega-3 polyunsaturated fatty acid supplements on the human intestinal microbiota – Henry Watson, BMJ Journals

Functional Changes in the Gut Microbiome Contribute to Transforming Growth Factor β-Deficient Colon Cancer – Scott G. Daniel, mSystems

The Induction of Oxalate Metabolism In Vivo Is More Effective with Functional Microbial Communities than with Functional Microbial Species – Aaron W. Miller, mSystems

Thiamine Acquisition Strategies Impact Metabolism and Competition in the Gut Microbe Bacteroides thetaiotaomicron – Zachary A. Costliow, mSystems

Human oral microbiome

Host Genetic and Environemental Associations and the Human Salivary Microbiome – Brittany Ann Demmitt, ProQuest

Animal microbiome

Pathogenesis of oral FIV infection – Craig Miller, PLoS ONE

Photosynthetic epibionts and endobionts of Pacific oyster shells from oyster reefs in rocky versus mudflat shores – Laurent Barillé, PLoS ONE

Free-living and captive turtles and tortoises as carriers of new Chlamydia spp. – Agata Mitura, PLoS ONE

Microbiomes Associated with Animals: Implications for Livestock and Animal Production – Hilario Cuquetto Mantovani, The Brazilian Microbiome

Maintenance of distal intestinal structure in the face of prolonged fasting: A comparative examination of species from five vertebrate classes – Marshall D. McCue, The Anatomical Record

Plant, root, and soil microbiome

Assessment of derelict soil quality: Abiotic, biotic and functional approaches – Quentin Vincent, Science of The Total Environment

Endophytic fungal communities of Polygonum acuminatum and Aeschynomene fluminensis are influenced by soil mercury contamination – William Pietro-Souza, PLoS ONE

Shifts in the bacterial community composition along deep soil profiles in monospecific and mixed stands of Eucalyptus grandis and Acacia mangium – Arthur Prudêncio de Araujo Pereira, PLoS ONE

Temporal dynamics in microbial soil communities at anthrax carcass sites – Karoline Valseth, BMC Microbiology

Pyrosequencing reveals soil enzyme activities and bacterial communities impacted by graphene and its oxides – Yan Rong, Journal of Agriculture and Food Chemistry

Alterations in soil fungal community composition and network assemblage structure by different long-term fertilization regimes are correlated to the soil ionome – Chao Xue, Biology and Fertility of Soils

The Brazilian Soil Microbiome – Fernando Dini Andreote, The Brazilian Microbiome

Lechevalieria rhizosphaerae sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.) and emended description of the genus Lechevalieria – Junwei Zhao, International Journal of Systematic and Evolutionary Microbiology

Carbon nanomaterials alter plant physiology and soil bacterial community composition in a rice-soil-bacterial ecosystem – Yi Hao, Environmental Pollution

Potential sources of microbial colonizers in an initial soil ecosystem after retreat of an alpine glacier – Thomas Rime, ISME

Jaminaea pallidilutea sp. nov. (Microstromatales), a basidiomycetous yeast isolated from plant material of mangrove forests in Iran – Shaghayegh Nasr, International Journal of Systematic and Evolutionary Microbiology

Klebsiella sp. confers enhanced tolerance to salinity and plant growth promotion in oat seedlings (Avena sativa) – Swapnil Sapre, Microbiological Research

Bacterial traits and quality contribute to the diet choice and survival of bacterial-feeding nematodes – Ting Liu, Soil Biology and Biochemistry

A novel Burkholderia ambifaria strain able to degrade the mycotoxin fusaric acid and to inhibit Fusarium spp. growth – Ester Simonetti, Microbiological Research

Impact of herbicide application on Beneficial soil microbial community, Nodulation and Yield parameters of chickpea (Cicer arietinum L.) – Raghavendra, K. S, Bulletin of Environment, Pharmacology and Life Sciences

Isolation And Characterization of Phosphate Solubilizing Microorganisms From Maize Rhizosperic Soils – S. Vinod Babu, Bulletin of Environment, Pharmacology and Life Sciences

Aerobic deterioration of corn stalk silage and its effect on methane production and microbial community dynamics in anaerobic digestion – Huan Zhang, Bioresource Technology

Plant Microbiome: Composition and Functions in Plant Compartments – Maike Rossmann, The Brazilian Microbiome

Changing soil legacies to direct restoration of plant communities – E Pernilla Brinkman, AoB Plants

Water and extremophile microbiome

Change in Emiliania huxleyi Virus Assemblage Diversity but Not in Host Genetic Composition during an Ocean Acidification Mesocosm Experiment – Andrea Highfield, Viruses

Shifts in diversity and function of lake bacterial communities upon glacier retreat – Hannes Peter, ISME

Expression and characterization of a new heat-stable endo-type alginate lyase from deep-sea bacterium Flammeovirga sp. NJ-04 – Benwei Zhu, Extremophiles

Wastewater treatment plant effluent introduces recoverable shifts in microbial community composition in receiving streams – Jacob R. Price, Science of The Total Environment

Insight into the microbial community and its succession of a coupling anaerobic-aerobic biofilm on semi-suspended bio-carriers – Bing Tang, Bioresource Technology

Acclimation to extremely high ammonia levels in continuous biomethanation process and the associated microbial community dynamics – Hailin Tian, Bioresource Technology

Effect of hydraulic retention time on microbial community in biochemical passive reactors during treatment of acid mine drainage – Yaneth Vasquez, Bioresource Technology

Microbial megacities fueled by methane oxidation in a mineral spring cave – Clemens Karwautz, ISME

Built environment

Microbes and associated soluble and volatile chemicals on periodically wet household surfaces – Rachel I. Adams, Microbiome

Food microbiology

Traditional Norwegian Kveik Yeasts: Underexplored Domesticated Saccharomyces cerevisiae Yeasts – Richard Preiss, bioRxiv

Probiotics / prebiotics

Prebiotic Oligosaccharides: Special Focus on Fructooligosaccharides, Its Biosynthesis and Bioactivity – Sudhir P. Singh, Applied Biochemistry and Biotechnology

Single-strain vs multi-strain probiotic supplementation strategy against rheumatoid arthritis – Giancarlo Ceccarelli, Arthritis and Rheumatology

The Genomic Basis of Lactobacilli as Health-Promoting Organisms –  Elisa Salvetti, Microbiology Spectrum

Phages and viruses

Phage mobility is a core determinant of phage-bacteria coexistence in biofilms – Matthew Simmons, bioRxiv

Bioinformatics

Bioinformatics for Microbiome Research: Concepts, Strategies, and Advances – Leandro Nascimento Lemos, The Brazilian Microbiome

Techniques

A universal, genome-wide guide finder for CRISPR/Cas9 targeting in microbial genomes – Michelle Spoto, bioRxiv

Direct PCR offers a fast and reliable alternative to conventional DNA isolation methods for animal gut microbiomes – Elin Videvall, bioRxiv

Microbes in the news

Artwork brings ‘echoes of DNA’ to UB’s new medical school building – ELLEN GOLDBAUM, UBNow

JooMo launches new body wash with skin bacteria tech – Lucy Whitehouse, Cosmetics Design Europe

September 27, 2017

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Human oral microbiome

Complex Intratissue Microbiota Forms Biofilms in Periodontal Lesions – Baek K – Journal of Dental Research

Human vaginal microbiome

Lactobacillus iners-dominated vaginal microbiota is associated with increased susceptibility to Chlamydia trachomatis infection in Dutch women: a case–control study – Robin van Houdt – Sexually Transmitted Infections

Human gut microbiome

[Review] Modulation of Type 1 Diabetes Risk by the Intestinal Microbiome – Knip M – Current Diabetes Reports

[Review] The Relationship Between the Human Genome and Microbiome Comes into View – Julia K. Goodrich – Annual Review of Genetics

Animal microbiome

[pre-print] The virome of Drosophila suzukii, an invasive pest of soft fruit – Nathan C. Medd – bioRxiv

Characterisation of North American Brucella isolates from marine mammals – Adrian M. Whatmore – PLOS ONE

Denitrification potential of the eastern oyster microbiome using a 16S rRNA gene based metabolic inference approach – Ann Arfken – PLOS ONE

Effects of Eimeria tenella infection on chicken caecal microbiome diversity, exploring variation associated with severity of pathology – Sarah E. Macdonald – PLOS ONE

Microbial characterization of bee pollen from the Vesuvius area collected by using three different traps – Gianluigi Mauriello – PLOS ONE

Plant, root, and soil microbiome

Multiscale Investigation on Biofilm Distribution and its Impact on Macroscopic Biogeochemical Reaction Rates – Zhifeng Yan – Water Resources Research

Comparative metagenomics approaches to characterize the soil fungal communities of western coastal region, Saudi Arabia – Tarek A. A. Moussa – PLOS ONE

Bacterial and diazotrophic diversities of endophytes in Dendrobium catenatum determined through barcoded pyrosequencing – Ou Li – PLOS ONE

A secreted antibacterial neuropeptide shapes the microbiome of Hydra – René Augustin – Nature Communications

Probiotics / prebiotics

Methanobrevibacter attenuation via probiotic intervention reduces flatulence in adult human: A non-randomised paired-design clinical trial of efficacy – Minseok Seo – PLOS ONE

Bioinformatics

Predicting metabolic adaptation from networks of mutational paths – Christos Josephides & Peter S. Swain – Nature Communications

Microbes in the news 

Florida Seawater Bacteria Death Toll Rises – Patch

Researchers Find New Microbial Communities in Human Body

Microbes on the market

Paris-based Eligo Bioscience secures $20 million to bring Precision Medicine to the Microbiome – EU-Startups

Science, publishing, and career

New open-access journal Metabarcoding & Metagenomics joins the lines of publisher Pensoft – EurekAlert!

Ed’s non-microbiology picks

Infants make more attempts to achieve a goal when they see adults persist – Julia A. Leonard – Science

University of Tokyo pair invent loop-based quantum computing technique

Cancer immunotherapy with recombinant poliovirus induces IFN-dominant activation of dendritic cells and tumor antigen–specific CTLs – Michael C. Brown – Science Translational Medicine

Stereodivergent synthesis with a programmable molecular machine – Salma Kassem, – Nature

Trispecific broadly neutralizing HIV antibodies mediate potent SHIV protection in macaques – Ling Xu – Science

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 25, 2017

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General microbiome

Comprehensive analysis of central carbon metabolism reveals multiple connections between nutrients, biosynthetic capacity, and cell morphology in Escherichia coli – CS Westfall – bioRxiv

 

 

Human oral microbiome

Periodontal Pathogen Colonization in Young Children by PCR Quantification – A Longitudinal Survey. – K Takahashi – The Journal of Clinical Pediatric Dentistry

 

 

Human nearly-sterile sites 

The Gut Microbial Metabolite Trimethylamine-N-Oxide Is Present in Human Cerebrospinal Fluid. – D Del Rio – Nutrients

 

Human gut microbiome

Obesity increases the risk of small intestinal bacterial overgrowth (SIBO). – BC Roland – Neurogastroenterology & Motility

Consumption of Two Healthy Dietary Patterns Restored Microbiota Dysbiosis in Obese Patients With Metabolic Dysfunction. –  C Haro – Molecular nutrition & Food Research

The Gut Microbiota and Pediatric Multiple Sclerosis: Recent Findings. – H Tremlett – Neurotherapeutics

Review: Role of the intestinal microbiota in the immunomodulation of influenza virus infection. – CJ Chen – Microbes and Infection

Effect of vitamin A supplementation on gut microbiota in children with autism spectrum disorders – a pilot study. – J Liu – BMC Microbiology

Modulation of the gut microbiota: a focus on treatments for irritable bowel syndrome. – LA Harris – Postgraduate Medicine

Gut Microbiome-based Therapeutics in Liver Cirrhosis: Basic Consideration for the Next Step. – H Fukui – Journal of Clinical and Translational Hepatology

 

Animal experiments 

Effects of dietary threonine supplementation on intestinal barrier function and gut microbiota of laying hens. – XY Dong – Poultry Science

Lack of NLRP3-inflammasome leads to gut-liver axis derangement, gut dysbiosis and a worsened phenotype in a mouse model of NAFLD. – P Irene – Scientific Reports

RNA-Seq Profiling of Intestinal Expression of Xenobiotic Processing Genes in Germ-Free Mice. – ZD Fu – Drug Metabolism and Disposition

Differential effects of rice bran cultivars to limit Salmonella Typhimurium in chicken cecal in vitro incubations and impact on the cecal microbiome and metabolome. – PM Rubinelli – PLoS One

Houttuynia cordata Facilitates Metformin on Ameliorating Insulin Resistance Associated with Gut Microbiota Alteration in OLETF Rats. – JH Wang – Genes (Basel)

Lack of Effect of Murine Astrovirus Infection on Dextran Sulfate-induced Colitis in NLRP3-deficient Mice. – SR Compton – Comparative Medicine

 

Animal microbiome 

A distinctive and host-restricted gut microbiota in populations of a cactophilic Drosophila species. – VG Martinson – Applied and Environmental Microbiology

Gastrointestinal microbial population of turkey (Meleagris gallopavo) affected by hemorrhagic enteritis virus. – S D’Andreano – Poultry Science

 

Plant, root, and soil microbiome

Colonization of Paracoccus sp. QCT6 and Enhancement of Metribuzin Degradation in Maize Rhizosphere Soil. – X Huang – Current Microbiology

Verrucosispora rhizosphaerae sp. nov., isolated from mangrove rhizosphere soil. – QY Xie – Antonie van Leeuwenhoek

Oomycete Communities Associated with Reed Die-Back Syndrome. – M Cerri – Frontiers in Plant Science

 

Water and extremophile microbiome 

Depth distribution and assembly of sulfate-reducing microbial communities in marine sediments of Aarhus Bay. – LM Jochum – Applied and Environmental Microbiology

Bottled aqua incognita: microbiota assembly and dissolved organic matter diversity in natural mineral waters. – CC Lesaulnier – Microbiome

 

Built environment 

Metagenomic characterization of ambulances across the USA. – NB O’ Hara – Microbiome

 

Food microbiology

Comparative analysis of the microbial communities in raw milk produced in different regions of Korea. – IS Kim – Asian-Australasian Journal of Animal Sciences

 

 

Techniques

DNA microarray assay and real-time PCR as useful tools for studying the respiratory tract Mycoplasma populations in young dairy calves. – M Bottinelli – Journal of Medical Microbiology

 

Microbes in the news

London Underground covered in vomit and diarrhoea-inducing bacteria found in human POO – Daily Star

BioArt and Bacteria Exhibition is Coming to Oxford – Labiotech.eu

Drug-resistant bacteria emerge from drug companies’ untreated effluents – The Hindu

Vivid green bacteria bloom in the river running through Toledo – Michigan Radio

Kingwood woman dies from flesh-eating bacteria after cutting elbow in flooded home, officials say  – Click2Houston

Microbiome-Derived Immune Modulators (Pediatric) – Puretech Health

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 21, 2017

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Additional data and new analyses from the NIH Human Microbiome Project, understanding lambda phage integration in its effects on the host, a yeast fermentation method for use in wine making.

Pregnancy and early life

Pre-print: Genetic diversity and mother-child overlap of the gut associated microbiota determined by reduced genome sequencing – Anuradha Ravi – bioRxiv

Multi-site human microbiome

Strains, functions and dynamics in the expanded Human Microbiome Project – Jason Lloyd-Price – Nature

Phages and viruses

Combining Comprehensive Analysis of Off-Site Lambda Phage Integration with a CRISPR-Based Means of Characterizing Downstream Physiology – Yu Tanouchi – mBio

Techniques

The 16S rRNA gene-based PCR method used for the detection of segmented filamentous bacteria in the intestinal microbiota generates false-positive results – Forough L Nowrouzian – Acta Pathologica, Microbiologica, et Immunologica Scandinavica

Pre-print: Wine yeast phenomics: a standardized fermentation method for assessing quantitative traits of Saccharomyces cerevisiae strains in enological conditions – Emilien Peltier – bioRxiv

More microbes

Pre-print: Comprehensive analysis of central carbon metabolism reveals multiple connections between nutrients, biosynthetic capacity, and cell morphology in Escherichia coli – Corey S Westfall – bioRxiv

Microbes in the news

What’s the latest on gut microbiota? Concordia microbiology undergrads publish their findings – Phys.Org

Microbes on the market

Ixcela Launches Over-the-Counter Gut Health Test and Sophisticated Internal Wellness Program – Business Wire

Avadim Technologies Inc. Announces Partnership With Cardinal Health, Inc. – Market Wired

September 20, 2017

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General microbiome

The human bitter taste receptor T2R38 is broadly tuned for bacterial compounds –  C Verbeurgt – PLoS One

Differential signal sensitivities can contribute to the stability of multispecies bacterial communities. – J Juhász – Biology Direct

Applying allometric theory to fungi – CA Aguilar-Trigueros – The ISME Journal

The Editorial on the Research Topic The Impact of Microorganisms on Consumption of Atmospheric Trace Gases – S Kolb – Frontiers in Microbiology

 

Human oral microbiome

Variations in oral microbiota associated with oral cancer. – H Zhao – Scientific Reports

Metabolic crosstalk regulates Porphyromonas gingivalis colonization and virulence during oral polymicrobial infection. – M Kuboniwa – Nature Microbiology

 

 

Human gut microbiome

Normalization of the microbiota in patients after treatment for colonic lesions – MA Sze – bioRxiv

Review: Modulation of the gut microbiome: a systematic review of the effect of bariatric surgery. – Y Guo – European Journal of Endocrinology

Urinary intermediates of tryptophan as indicators of the gut microbial metabolism. – T Pavlova – Analytica Chimica Acta

Recent urbanization in China is correlated with a Westernized microbiome encoding increased virulence and antibiotic resistance genes. – K Winglee – Microbiome

Continued Alcohol Misuse in Human Cirrhosis is Associated with An Impaired Gut-Liver Axis. – JS Bajaj – Alcoholism, Clinical and Experimental Research

Fructooligosaccharide (FOS) and Galactooligosaccharide (GOS) Increase Bifidobacterium but Reduce Butyrate Producing Bacteria with Adverse Glycemic Metabolism in healthy young population. – F Liu – Scientific Reports

 

Animal experiments 

Experimental colitis delays and reduces the severity of collagen-induced arthritis in mice – J Hablot – PLoS One

Identification of a mouse Lactobacillus johnsonii strain with deconjugase activity against the FXR antagonist T-β-MCA – M DiMarzio – PLoS One

The effect of age on the intestinal mucus thickness, microbiota composition and immunity in relation to sex in mice – M Elderman – PLoS One

Review:Role of the gastrointestinal microbiota in small animal health and disease. – A Redfern – The Veterinary Record

Gut Microbiota and IL-17A: Physiological and Pathological Responses. – B Douzandeh-Mobarrez – Probiotics and Antimicrobial Proteins

 

Animal microbiome 

The microbiota of water buffalo milk during mastitis – C Catozzi – PLoS One

What determines sclerobiont colonization on marine mollusk shells? – VO Agostini – PLoS One

Season, but not symbiont state, drives microbiome structure in the temperate coral Astrangia poculata. – KH Sharp – Microbiome

Metagenomic analysis of bacterial community structure and diversity of lignocellulolytic bacteria in Vietnamese native goat rumen. – HT Do – Asian-Australasian Journal of Animal Sciences

Comparative analysis of midgut bacterial communities in three aedine mosquito species from dengue-endemic and non-endemic areas of Rajasthan, India. – SS Charan – Medical and Veterinary Entomology

Microbiome of Pacific Whiteleg shrimp reveals differential bacterial community composition between Wild, Aquacultured and AHPND/EMS outbreak conditions. – F Cornejo-Granados – Scientific Reports

 

Plant, root, and soil microbiome

Evolution with a seed bank: the population genetic consequences of microbial dormancy – WR Shoemaker – bioRxiv

Longispora urticae sp. nov., isolated from rhizosphere soil of Urtica urens L., and emended descriptions of the species Longispora albida and Longisporafulva. – C Piao – International Journal of Systematic and Evolutionary Microbiology

Actinomycetes benefaction role in soil and plant health. – AA Bhatti – Microbial Pathogenesis

Environmental parameters altered by climate change affect the activity of soil microorganisms involved in bioremediation – I Alkorta – FEMS Microbiology Letters

Micropredator niche differentiation between bulk soil and rhizosphere of an agricultural soil depends on bacterial prey. – L Zhang – FEMS Microbiology Ecology

Soil microbial communities drive the resistance of ecosystem multifunctionality to global change in drylands across the globe. – M Delgado-Baquerizo  – Ecology Letters

Paenibacillus arcticus sp. nov., isolated from Arctic soil. – IT Cha – International Journal of Systematic and Evolutionary Microbiology

Mineral phosphorus fertilization modulates interactions between maize, rhizosphere yeasts and arbuscular mycorrhizal fungi – M Sarabia – Rhizosphere

Zinc Solubilizing Bacillus cereus and related species Modulates Growth, Yield and Zinc Biofortification of Soybean and Wheat Seeds Cultivated in Central India – R Khande – Rhizosphere

Utilisation of mucilage C by microbial communities under drought – MA Ahmed – Biology and Fertility of Soils

 

Built environment

Walker occupancy has an impact on changing airborne bacterial communities in an underground pedestrian space, as small-dust particles increased with raising both temperature and humidity – T Okubo – PLoS One

 

Food microbiology

Diversity and dynamics stability of bacterial community in traditional solid-state fermentation of Qishan vinegar – X Gan – Annals of Microbiology

 

Phages and viruses

Isolation and identification of enteroviruses from sewage and sewage-contaminated water samples from Ibadan, Nigeria, 2012-2013. – JA Adeniji – bioRxiv

The virome of Drosophila suzukii, an invasive pest of soft fruit – NC Medd – bioRxiv

Immune Loss as a Driver of Coexistence During Host-Phage Coevolution – JL Weissman – bioRxiv

 

Bioinformatics

Bioinformatics in the Netherlands: the value of a nationwide community  – CWG  van Gelder – Briefings in Bioinformatics

 

Techniques

Longitudinal multiparameter single-cell analysis of macaques immunized with pneumococcal protein-conjugated or unconjugated polysaccharide vaccines reveals distinct antigen specific memory B cell repertoires – B Lia – PLoS One

Methods matter: Influential purification and analysis parameters for intracellular parasite metabolomics – MA Carey – bioRxiv

COREMIC: a web-tool to search for a root-zone associated CORE MICrobiome – RR Rodrigues – bioRxiv

Quorum sensing improves current output with Acidithiobacillus ferrooxidans. – N Chabert – Microbial Biotechnology

Transcriptome analysis of Pseudostellaria heterophylla in response to the infection of pathogenic Fusarium oxysporum. – X Qin – BMC Plant Biology

Regulatory networks underlying mycorrhizal development delineated by genome-wide expression profiling and functional analysis of the transcription factor repertoire of the plant symbiotic fungus Laccaria bicolor. – Y Daquerre – BMC Genomics

 

Microbes in the news

Rocks, not bacteria, triggered Earth’s oxidation – Cosmos

The Table At Your Favorite Restaurant May Be Way Grosser Than You ThoughtThe Table At Your Favorite Restaurant May Be Way Grosser Than You Thought – Men’s Health

Researchers unlock potential pathway to treat flesh-eating bacteria – Phys.org

Revealed: The nasty infections you can pick up at the gym – and how to avoid deadly bacteria lingering on your workout gear  – Daily Mail Online

Flagship seeks $500M for sixth fund; unveils another microbiome firm – Fierce Biotech

CAN SPRAYING BACTERIA IN YOUR FACE ACTUALLY HAVE HEALTH BENEFITS? – CDA Press

Space-Grown Bacteria Could Pose Major Problems for Astronauts – Health Line

See jerkface bacteria hiding in tumors and gobbling chemotherapy drugs – Ars Technica

How BIOHM’s At Home Candida Test Is Giving Consumers Peace of Mind – Forbes

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