Lots of papers on gut microbiota in today’s digest!

Multi-site human microbiome

The Female Urinary Microbiota/Microbiome: Clinical and Research Implications.

Brubaker L et al – Rambam Maimonides Med J

A case controlled study examining the bladder microbiome in women with Overactive Bladder (OAB) and healthy controls.
Curtiss N et al. – Eur J Obstet Gynecol Reprod Biol

Human respiratory microbiome

Illumina MiSeq 16S amplicon sequence analysis of bovine respiratory disease associated bacteria in lung and mediastinal lymph node tissue.
Johnston D et al. – BMC Vet Res.

Human gut microbiome

The Gut Microbiota and the Hepatologist: Will Our Bugs Prove to be the Missing Link?

Pallen MJ and Quraishi MN – Digestive Diseases

A Specific Gut Microbiota Dysbiosis of Type 2 Diabetic Mice Induces GLP-1 Resistance through an Enteric NO-Dependent and Gut-Brain Axis Mechanism.

Grasset E et al – Cell Metab

Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease.

Loomba R et al  –  Cell Metab

16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome.

Almonacid DE – PLoS One

Autophagy Genes of Host Responds to Disruption of Gut Microbial Community by Antibiotics.

Singh SB – Dig Dis Sci

Interaction between the gut microbiome and mucosal immune system.

Shi N

Saccharomyces boulardii Administration Changes Gut Microbiota and Attenuates D-Galactosamine-Induced Liver Injury.
Yu L et al. – Sci Rep

Faecal microbiota transplantation for ulcerative colitis.
Drug Ther Bull.

Microbiome and colorectal cancer: Unraveling host-microbiota interactions in colitis-associated colorectal cancer development.
Kang M et al. Semin Immunol

Alpha-ketoglutarate (AKG) lowers body weight and affects intestinal innate immunity through influencing intestinal microbiota.
Chen S et al. – Oncotarget

The composition of gut microbiota in infant and its influencing factors
Liu W et al – Zhonghua Yu Fang Yi Xue Za Zhi

Occurrence of antibiotic resistance genes in the Faecal DNA of healthy omnivores, Ovo-Lacto vegetarians and vegans.
Milanović V et al. Mol Nutr Food Res

Seasonal variation in the copepod gut microbiome in the subtropical North Atlantic Ocean.
Shoemaker KM et al. Environ Microbiol

Models of antimicrobial pressure on intestinal bacteria of the treated host populations.
Volkova VV et al. – Epidemiol Infect

The food-gut human axis: the effects of diet on gut microbiota and metabolome.
De Angelis M et al.

The chicken or the egg dilemma: intestinal dysbiosis in multiple sclerosis.
Ochoa-Repáraz J, et al. – Ann Transl Med.

Impact of faecal microbiota transplantation on mouse digestive colonization with two extensively resistant bacteria.
Mahieu R et al – J Infect.

Plant, root, and soil microbiome

Lactic acid bacteria population dynamics during spontaneous fermentation of radish (Raphanus sativus L.) roots in brine.

Pardali E – World J Microbiol Biotechnol
Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Intraspecific Variation in the Skin-Associated Microbiome of a Terrestrial Salamander.

Prado-Irwin SR – Microb Ecol

Analysis of biofilm bacterial communities under different shear stresses using size-fractionated sediment.

Unraveling microbial structure and diversity of activated sludge in a full-scale simultaneous nitrogen and phosphorus removal plant using metagenomic sequencing.
Guo J et al – Enzyme Microb Technol.

The interacting roles of climate, soils, and plant production on soil microbial communities at a continental scale.
Waldrop MP et al. – Ecology

Correspondence of coral holobiont metabolome with symbiotic bacteria, archaea and Symbiodinium communities.
Sogin EM et al. – Environ Microbiol Rep
Fang H et al. Sci Rep.

Influence of root components of celery on pyrene bioaccessibility, soil enzymes and microbial communities in pyrene and pyrene-diesel spiked soils.
Wei J et al. – Sci Total Environ

Bioinformatics

ICoVeR – an interactive visualization tool for verification and refinement of metagenomic bins.
Broeksema B et al. – BMC Bioinformatics

Pregnancy and early life

Development of the cutaneous microbiome in the preterm infant: A prospective longitudinal study
Mohan Pammi et al. PLoS One

Human respiratory microbiome

The presence of bacterial microcolonies on the maxillary sinus ciliary epithelium in healthy young individuals
Monika Morawska-Kochman et al. PLoS One

Human gut microbiome

Review of mechanisms of deoxynivalenol-induced anorexia: The role of gut microbiota
Zhao Peng et al – JOURNAL OF APPLIED TOXICOLOGY

Probiotics are a good choice in remission of inflammatory bowel diseases: A meta analysis and systematic review
Mahboube Ganji-Arjenaki et al – JOURNAL OF CELLULAR PHYSIOLOGY

Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome.
Labus JS et al – Microbiome

The shrinking human gut microbiome.
Moeller AH. – Curr Opin Microbio

Animal experiments

Maternal obese-type gut microbiota differentially impact cognition, anxiety and compulsive behavior in male and female offspring in mice

Jing Chen et al. PLoS One

Dysbiosis of intestinal microbiota and decrease in paneth cell antimicrobial peptide level during acute necrotizing pancreatitis in rats
Annadora J. et al . PLoS One

Animal microbiome

Bacterial microbiome of the nose of healthy dogs and dogs with nasal disease
Barbara Tress, et al . PLoS One
Characterization of the fecal microbiome during neonatal and early pediatric development in puppies
Blake C. Guard et al. PLoS One

Effects of Saccharomyces cerevisiae fermentation products on dairy calves: Ruminal fermentation, gastrointestinal morphology, and microbial community.
Xiao JX et al – J Diary Sci

Studies on bacterial community composition are affected by the time and storage method of the rumen content
Yury Tatiana Granja-Salcedo et al. PLoS One

Competition drives the response of soil microbial diversity to increased grazing by vertebrate herbivores.
Eldridge DJ et al – Ecology

Diversity of culturable bacterial communities in the intestinal tracts of goldfish (Carassius auratus) and their ability to produce N-acyl homoserine lactone.
Sugita H et al – Folia Microbiol

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Crude oil impairs immune function and increases susceptibility to pathogenic bacteria in southern flounder
Keith M. Bayha et al. PLoS One

Pyrosequencing reveals microbial community dynamics in integrated simultaneous desulfurization and denitrification process at different influent nitrate concentrations.
Chen C et al – Chemosphere

Bioinformatics

Abundance profiling of specific gene groups using precomputed gut metagenomes yields novel biological hypotheses
Konstantin Yarygin et al. PLoS One

Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform
Chongqing Wen et al. PLoS One

The MB Digest Team hopes everyone had a good Labour Day holiday (or just a good day depending on where you are). Our Tuesday digest is full of fresh articles, a few news pieces, and lots going on in the Environmental Microbiome sections. Enjoy!

Events and jobs

PhD in soil microbiology
Teagasc Johnstown Castle

General microbiome

Analysis of stability to cheaters in models of antibiotic degrading microbial communities
András Szilágyi et al. – Journal of Theoretical Biology

Revew: Human genome-microbiome interaction: metagenomics frontiers for the aetiopathology of autoimmune diseases
Aycan Gundogdu & Ufuk Nalbantoglu – Microbial Genomics

Review: Fingerprinting microbiomes towards screening for microbial antibiotic resistance
Naifu Jin et al – Integrative Biology

Comparative genomics and metabolomics analyses of the adaptation mechanism in Ketogulonicigenium vulgare-Bacillus thuringiensis consortium
Nan Jia et al – Nature Scientific Reports

Multi-site human microbiome

Review: A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: implications for research on the pioneer infant microbiome
Maria Elisa Perez-Muñoz et al – Microbiome

Review: Interaction between the gut microbiome and mucosal immune system
Na Shi et al – Military Medical Research

Human gut microbiome

Bacterial Diversity of the Gastric Content of Preterm Infants during Their First Month of Life at the Hospital
Moles L. et al. – Frontiers in Nutrition

Opinion: The shrinking human gut microbiome
Moeller AH – Current Opinion in Microbiology

Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome
Labus JS et al. – Microbiome

Gut microbial metabolites limit the frequency of autoimmune T cells and protect against type 1 diabetes
Eliana Mariño et al. – Nature Immunology

Microbial diseases

The Novel ASIC2 Locus is Associated with Severe Gingival Inflammation
Zhang S. et al. – JDR Clinical & Translational Research

In vitro Multi-Species Biofilms of Methicillin-Resistant Staphylococcus aureus and Pseudomonas aeruginosa and Their Host Interaction during In vivo Colonization of an Otitis Media Rat Model
Yadav MK et al. – Frontiers in Cellular and Infectious Microbiology

Reduction in fecal microbiota diversity and short-chain fatty acid producers in Methicillin-resistant Staphylococcus aureus infected individuals as revealed by PacBio single molecule, real-time sequencing technology
J Zhao et al – European Journal of Clinical Microbiology & Infectious Diseases

Perspective: Treatable traits and therapeutic targets: goals for systems biology in infectious disease
Clark D. Russell & J. Kenneth Baillie – Current Opinion in Systems Biology

General Environmental Microbiome

Review: Effects and mechanisms of biochar-microbe interactions in soil improvement and pollution remediation: A review
Zhu X et al – Environmental Pollution

Sulfur flows and biosolids processing: Using Material Flux Analysis (MFA) principles at wastewater treatment plants
Fisher RM et al. – Journal of Environmental Management

Exploration of the relationship between biogas production and microbial community under high salinity conditions
Shaojie Wang et al – Nature Scientific Reports

Review: Phytoremediation of Water Bodies
E. Etim et al. – Current Environmental Engineering

Review: Role of Phytochelators in Land Reclamation: Recent Progress and Perspectives
Resham Sharma et al. – Current Environmental Engineering

Environmental Metabarcoding Reveals Contrasting Belowground and Aboveground Fungal Communities from Poplar at a Hg Phytomanagement Site
Alexis Durand et al. – Microbial Ecology

Monitoring global protein thiol-oxidation and protein S-mycothiolation in Mycobacterium smegmatis under hypochlorite stress
Melanie Hillion et al – Nature Scientific Reports

A comprehensive multi-omics approach uncovers adaptations for growth and survival of Pseudomonas aeruginosa on n-alkanes
Sarah L Grady et al – BMC Genomics

Interpreting Omic Data for Microbially Influenced Corrosion: Lessons from a Case Study Involving a Seawater Injection System
Craig Bartling et al – OnePetro

Land scale biogeography of arsenic biotransformation genes in estuarine wetland
Si-Yu Zhang et al – Environmental Microbiology

Animal experiments

Effects of Saccharomyces cerevisiae fermentation products on dairy calves: Ruminal fermentation, gastrointestinal morphology, and microbial community
Xiao JX et al. – Journal of Dairy Science

Immunological effects of reduced mucosal integrity in the early life of BALB/c mice
Bendtsen KM et al – PLoS One

Dietary Supplementation with Raspberry Whole Fruit Modifies the Relative Abundance of Fecal Microbial Communities in Obese Diabetic (db/db) Mice
Giuliana Noratto et al – The FASEB Journal

Chemical and pathogen-induced inflammation disrupt the murine intestinal microbiome
Mikayla A. Borton et al – Microbiome

Animal microbiome

Diversity of culturable bacterial communities in the intestinal tracts of goldfish (Carassius auratus) and their ability to produce N-acyl homoserine lactone
Haruo Sugita et al. – Folia Microbiologica

Viral gut metagenomics of sympatric wild and domestic canids, and monitoring of viruses: Insights from an endangered wolf population
Nádia Conceição-Neto et al – Ecology and Evolution

Characterization of the fecal microbiome during neonatal and early pediatric development in puppies
Blake C. Guard et al – PLoS One

The environmental and host-associated bacterial microbiota of Arctic seawater-farmed Atlantic salmon with ulcerative disorders
C Karlsen et al – Journal of Fish Diseases

Pre-print: Caterpillars lack a resident gut microbiome
Tobin J Hammer et al – bioRxiv

Bacterial microbiome of the nose of healthy dogs and dogs with nasal disease
Barbara Tress et al – PLoS One

Plant, root, and soil microbiome

First “charosphere” view towards the transport and transformation of Cd with addition of manure derived biochar
Wang L et al. – Environmental Pollution

Competition drives the response of soil microbial diversity to increased grazing by vertebrate herbivores
Eldridge DJ et al. – Ecology

Soil aggregation and associated microbial communities modify the impact of agricultural management on carbon content
Pankaj Trivedi et al – Environmental Microbiology

Altitudinal, seasonal and interannual shifts in microbial communities and chemical composition of soil organic matter in Alpine forest soils
José A. Siles et al – Soil Biology and Biochemistry

Water, estuarine and sediment microbiome

Pre-peer review: Microbiome succession during ammonification in eelgrass bed sediments
Cassandra L Ettinger et al – PeerJ

Microbial communities in sediment from Zostera marina patches, but not the Z. marina leaf or root microbiomes, vary in relation to distance from patch edge
Cassandra L Ettinger et al – PeerJ

Extremophile and space microbiome

In-depth characterization of bacterial and archaeal communities present in the abandoned Kettara pyrrhotite mine tailings (Morocco)
Odile Bruneel et al – Extremophile
Microbial biotechnology

Impact of selectively enriched microbial communities on long-term fermentative biohydrogen production
Kanniah Goud R. et al – Bioresource Technology

Review: Cooperation in microbial communities and their biotechnological applications
Matteo Cavaliere et al – Environmental Microbiology

Metabolic engineering of Escherichia coli for higher alcohols production: An environmentally friendly alternative to fossil fuels
Ana L. Gonçalves & Manuel Simões – Renewable and Sustainable Energy Reviews

Weak magnetic field: A powerful strategy to enhance partial nitrification
Zhibin Wang et al – Water Research

General microbiology and evolution

Comparative genomics of host-symbiont and free-living Oceanobacillus species
Kumar Mondal A. et al – Genome Biology and Evolution

Draft Genome Sequence of Plantibacter flavus Strain 251 Isolated from a Plant Growing in a Chronically Hydrocarbon-Contaminated Site
Rhea Lumactud et al. – Genome Announcements

HexA is a versatile regulator involved in the control of phenotypic heterogeneity of Photorhabdus luminescens
Langer A. et al – PLoS One

Complete Genome Sequence of the Gamma-Aminobutyric Acid-Producing Strain Streptococcus thermophilus APC151
Daniel M Linares et al – Genome Announcements

Bioinformatics and statistics

MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data
Dhariwal A. et al – Nucleic Acids Research

Techniques and methods

Perspective: The Role of the Negative Control in Microbiome Analyses
Kyle Edmonds & Laura Williams – The FASEB Journal

Perspective: A Robust Framework for Microbial Archaeology
Warinner C. – Annual Review of Genomics and Human Genetics

Microbes in the news

Gut bacteria found to be linked to chronic fatigue syndrome
Victor Marchione – Belmarra Health News

Zapping bacteria with sanitizers made of paper
Phys.org

‘Electric’ bacteria can purify sewage water – fast
EuroNews

How The Gut May Influence Food Choices: Fruit Flies With More Bacteria Had Fewer Cravings
Janissa Delzo – Medical Daily

Harmless Bacteria on Teeth Can Hijack Harmful One That Causes Lung Infections, Study Finds
Magdalena Kegel – Cystic Fibrosis News

Retired US Navy Veteran Comments on Military Microbiome Study
Yahoo News

Microbes In Human Body: Connection Between Abundance Of Various Microbiota Species & Accessibility Of Its Resources
Piyali Roy – The Science Times

A review on how the human microbiome has changed from that of primates, plus articles on biofilm formation in soils, and the influence of microbiomes on bone and psychological health are just a few of the articles highlighted in todays Biks Picks!

Analysis of stability to cheaters in models of antibiotic degrading microbial communities – András Szilágyi – Journal of Theoretical Biology

Human vaginal microbiome

Vaginal ecosystem modeling of growth patterns of anaerobic bacteria in microaerophilic conditions – Audrie A. Medina-Colorado – Anaerobe

Human gut microbiome

Opinion: The shrinking human gut microbiome – Andrew H Moeller – Current Opinion in Microbiology

Review: Osteomicrobiology: The influence of gut microbiota on bone in health and disease – Rheinallt M. Jones – Bone

The Role of the Microbiome in Bipolar Disorder-A New Model – Robert Yolken – Biological Psychiatry

Gut Microbiome and Brain Functional Connectivity in Infants: A Preliminary Study Focusing on the Amygdala – Andrew Salzwedel – Biological Psychiatry

Gut Microbiota Distributions Predict Mood Disorder Symptoms and Mediate Dietary Interactions – Brittany Mason – Biological Psychiatry

Antimicrobial resistance in the Bacteroides fragilis group in faecal samples from patients receiving broad-spectrum antibiotics – Kia Cirkeline Møller Hansen – Anaerobe

Animal experiments

Impact of faecal microbiota transplantation on mouse digestive colonization with two extensively resistant bacteria – Rafael Mahieu – Journal of Infection

Changes of cecal microflora in chickens following Eimeria tenella challenge and regulating effect of coated sodium butyrate – Zuoyong Zhou – Experimental Parasitology

Plant, root, and soil microbiome

Preprint: Bacterial Biofilm Formation On Soil Fungi: A Widespread Ability Under Controls – Cora Miquel Guennoc – BioRxiv

Laboratory persistence in soil of thiacloprid, pendimethalin and fenarimol incubated with treated wastewater and dissolved organic matter solutions. Contribution of soil biota – José Antonio Rodríguez-Liébana – Chemosphere

Food microbiology

Effect of different marinating conditions on the evolution of spoilage microbiota and metabolomic profile of chicken breast fillets – Anastasia E. Lytou – Food Microbiology

Probiotics / prebiotics

A combination of the probiotic and prebiotic product can prevent the germination of Clostridium difficile spores and infection – M. Rätsep – Anaerobe

Gut microbiota-mediated pharmacokinetics of ginseng saponins – Dong-Hyun Kim – Journal of Ginseng Research

Microbes in the news

Rumblings of Parkinson’s: Gut Microbiome Shifts in Early Stage of Disease – ALZFORUM

Yersinia pestis, the plague bacteria, can survive inside Acanthamoeba for protection -OutBreakNewsToday

A bit of a late morning Digest today, as it is packed with articles! Diverse themes, such as rhizosphere microbiome, lots of biotechnology pieces, and insightful reviews on gut microbiota and herbivory, “wild” microbiomes and ecological stoichiometry.

General microbiome

Review: The microbiome in anti-cancer therapy
Stavros Bashiardes et al – Seminars in Immunology

Perspective: Gut Microbiota as a Trigger of Accelerated Directional Adaptive Evolution: Acquisition of Herbivory in the Context of Extracellular Vesicles, MicroRNAs and Inter-Kingdom Crosstalk
Marco Romano – Frontiers in Microbiology

Multi-site human microbiome

Review: Lung Homeostasis: Influence of Age, Microbes, and the Immune System
Clare M. Lloyd & Benjamin J. Marsland – Immunity

Human epitelial microbiome

The oral microbiome community variations associated with normal, potentially malignant disorders and malignant lesions of the oral cavity
Mok Shao Feng et al – Malaysian Journal of Pathology

Human gut microbiome

‘Microbes in sport’ -The potential role of the gut microbiota in athlete health and performance
Rankin A. et al – Journal of Sports Medicine

Effect of pistachio consumption on the modulation of urinary gut microbiota-related metabolites in prediabetic subjects
Hernandéz-Alonso P et al – Journal of Nutritional Biochemistry

Microbial diseases

Alteration of stomach microbiota compositions in the progression of gastritis induces nitric oxide in gastric cell
Tianyi Dong et al – Experimental and Therapeutic Medicine

General environmental microbiome

Review: Evolutionary Biology Needs Wild Microbiomes
Sarah M. Hird – Frontiers in Microbiology

Stratified Bacterial Diversity along Physico-chemical Gradients in High-Altitude Modern Stromatolites
Diego M. Toneatti et al – Frontiers in Microbiology

Origin-Dependent Variations in the Atmospheric Microbiome Community in Eastern Mediterranean Dust Storms
Daniella Gat et al – Environmental Science and Technology

Animal experiments

Urinary and Fecal Metabonomics Study of the Protective Effect of Chaihu-Shu-Gan-San on Antibiotic Induced Gut Microbiota Dysbiosis in Rats
Meng Yu et al – Nature Scientific Reports

Proteomic analysis of a mosquito host cell response to persistent Wolbachia infection
Gerald Baldridge et al – Research in Microbiology

Effect of ensiled mulberry leaves and sun-dried mulberry fruit pomace on the fecal bacterial community composition in finishing steers
Yan Li et al – BMC Microbiology

Effects of various weaning times on growth performance, rumen fermentation and microbial population of yellow cattle calves
Mao H et al – Asian-Australasian Journal of Animal Science

Effects of various levels of dietary copper supplementation with copper sulfate and copper hydroxychloride on Pacific white shrimp Litopenaeus vannamei performance and microbial communities
Yangen Zhou et al – Aquaculture

Plant, root, and soil microbiome

Soil Acidification Aggravates the Occurrence of Bacterial Wilt in South China
Shili Li et al – Frontiers in Microbiology

Interaction between DAPG and HCN producing Pseudomonas brassicacearum LBUM300 and Clavibacter michiganensis subsp. michiganensis in the rhizosphere of tomato
Mélanie M. Paulin et al – Applied and Environmental Microbiology

Distance-dependent varieties of microbial community structure and metabolic functions in the rhizosphere of Sedum alfredii Hance during phytoextraction of a cadmium-contaminated soil
Yang W et al – Environmental Science and Pollution Research

Rhizosphere Engineering: Enhancing Sustainable Plant Ecosystem Productivity in a Challenging Climate
Amirhossein Ahkami et al – Rhizosphere

Influence of red mud on soil microbial communities: Application and comprehensive evaluation of the Biolog EcoPlate approach as a tool in soil microbiological studies
Feigl V et al – Science of the Total Environment

Response of microbial community of organic-matter-impoverished arable soil to long-term application of soil conditioner derived from dynamic rapid fermentation of food waste
Jiaqi Hou et al – Plos One

Effects of adding trace elements on rice straw anaerobic mono-digestion: Focus on changes in microbial communities using high-throughput sequencing
Yafan Cai et al – Bioresource Technology

Cereal-legume intercropping modifies the dynamics of the active rhizospheric bacterial community
E. Taschen et al – Rhizosphere

Water, estuarine and sediment microbiome

Microbial Community Response on Wastewater Discharge in Boreal Lake Sediments
Jatta Saarenheimo et al – Frontiers in Microbiology

Perspective: The Hadal Biosphere: Recent insights and new directions
Rulong Liu et al – Deep Sea Research Part II: Topical Studies in Oceanography

Bacterial community dynamics and functional variation during the long-term decomposition of cyanobacterial blooms in-vitro
Limei Shi et al – Science of the Total Environment

Mixing of water masses caused by a drifting iceberg affects bacterial activity, community composition and substrate utilization capability in the Southern Ocean
Julie Dinasquet et al – Environmental Microbiology

DNA metabarcoding of unfractionated water samples relates phyto-, zoo- and bacterioplankton dynamics and reveals a single-taxon bacterial bloom
Christian Wurzbacher et al – Environmental Microbiology Reports

Shifts in soil microbial metabolic activities and community structures along a salinity gradient of irrigation water in a typical arid region of China
Lijuan Chen et al – Science of the Total Environment

Large-scale seaweed cultivation diverges water and sediment microbial communities in the coast of Nan’ao Island, South China Sea
Xinfei Xie et al – Science of The Total Environment

Extremophile and space microbiome

Review: Toward biotechnology in space: High-throughput instruments for in situ biological research beyond Earth
Fathi Karouia – Biotechnology Advances

Built environment

Diversity changes of microbial communities into hospital surface environments
Rika Yano et al – Journal of Infection and Chemotherapy

Microbial communities in the functional areas of a biofilm reactor with anaerobic-aerobic process for oily wastewater treatment
Li J et al – Bioresource Technology

Dominance of candidate Saccharibacteria in a membrane bioreactor treating medium age landfill leachate: Effects of organic load on microbial communities, hydrolytic potential and extracellular polymeric substances
Remmas N. et al – Bioresource Technology

Microbial biotechnology

Review: Uncovering Potential Applications of Cyanobacteria and Algal Metabolites in Biology, Agriculture and Medicine: Current Status and Future Prospects
Rachana Singh et al – Frontiers in Microbiology

The Ability of Typha angustifolia L. for Degradation of BOD and COD in Wastewater of Tofu Industry Using Phytoremediation
Pertiwi Andarani et al – Advanced Science Letters

Reversible Anaerob-Evapotranspiration Process for Removal of High Strength Ammonium in Leachate from Tropical Landfill
Badrus Zaman et al – Advanced Science Letters

Strain specific variation in plant growth promoting volatile organic compound production by five different Pseudomonas spp. as confirmed by response of Vigna radiata seedlings
Jishma P et al – Journal of Applied Microbiology

Microbial reductive dehalogenation of trihalomethanes by a Dehalobacter-containing co-culture
Zhao S. et al – Applied Microbiology and Biotechnology

Inhibitory effect of coumarin on syntrophic fatty acid oxidizing and methanogenic cultures and biogas reactor microbiomes
Denny Popp et al – Applied and Environmental Microbiology

Food microbiology

Impact of solar radiation exposure on phyllosphere bacterial community of red-pigmented baby leaf lettuce
Pilar Truchado et al – Food Microbiology

Effect of abattoir and cut on variations in microbial communities of vacuum-packaged beef
Mandeep Kaur et al – Meat Science

Smokeless tobacco products harbor diverse bacterial microbiota that differ across products and brands
Smyth EM et al – Applied Microbiology and Biotechnology
General Microbiology

Protein Acetylation and Its Role in Bacterial Virulence
Jie Ren et al – Trends in Microbiology

Perspective: Ecological Stoichiometry beyond Redfield: An Ionomic Perspective on Elemental Homeostasis
Punidan D. Jeyasingh et al – Frontiers in Microbiology

Genomes

Complete Genome Sequence of Pseudomonas protegens H78, a Plant Growth–Promoting Rhizobacterium
Xianqing Huang et al – Genome Announcements

Draft Genome Sequences of Two Hydrogenogenic Carboxydotrophic Bacteria, Carboxydocella sp. Strains JDF658 and ULO1, Isolated from Two Distinct Volcanic Fronts in Japan
Yuto Fukuyama et al – Genome Announcements

The genomic sequence of Exiguobacterium chiriqhucha str. N139 reveals a species that thrives in cold waters and extreme environmental conditions
Ana Gutiérrez-Preciado et al – PeerJ

Phages and viruses

A novel type of polyhedral viruses infecting hyperthermophilic archaea
Ying Liu et al – Journal of Virology

Phage therapy: an alternative or adjunct to antibiotics?
Shawna McCallin & Harald Brüssow – Emerging Topics in Life Sciences

Highlights from the HIV Research for Prevention Conference (R4P)
Sandhya Vasan et al – Journal of Virus Eradication

Bioinformatics and statistics

A powerful microbiome-based association test and a microbial taxa discovery framework for comprehensive association mapping
Hyunwook Koh et al – Microbiome

The BRENDA Enzyme Information System–From a Database to an Expert System
I. Schomburg et al – Journal of Biotechnology

HirBin: high-resolution identification of differentially abundant functions in metagenomes
Tobias Österlund et al – BMC Genomics

A novel genome signature based on inter-nucleotide distances profiles for visualization of metagenomic data
Xian-Hua Xie et al – Physica A: Statistical Mechanics and its Applications

Data Intensive Genome Level Analysis for Identifying Novel,Non-Toxic Drug Targets for Multi Drug Resistant Mycobacterium tuberculosis
Divneet Kaur et al – Nature Scientific Reports

Techniques and methods

Building a Translational Microbiome Toolbox
Payal Joglekar & Julia Segre – Cell

Today’s digest is full of interesting articles on the influence of microbes on chronic diseases, and an interesting article on machine learning predictions of soil microbiomes.

Human gut microbiome

The gut microbiota as a modulator of innate immunity during melioidosis. Lankelma JM. PLoS Neglected Tropical Diseases

Apropos: ‘Gut Microbiota Differences in Children From Distinct Socioeconomic Levels Living in the 1 Same Urban Area in Brazil’. Waugh S. Journal of Pediatric Gastroenterology and Nutrition

Review: Microbiota: Diet can protect against type 1 diabetes. Kugelberg E. Nature Review Immunology

Changes in Composition of the Gut Bacterial Microbiome after Fecal Microbiota Transplantation for Recurrent <i>Clostridium difficile</i> Infection in a Pediatric Heart Transplant Patient. Flannigan KL. Frontiers in Cardiovascular Medicine

Understanding the Gut Microbiota in Inflammatory and Functional Gastrointestinal Diseases. Sundin J. Psychosomatic Medicine

Review: Gut Microbiota Modulation and Its Relationship with Obesity Using Prebiotic Fibers and Probiotics: A Review. Dahiya DK. Frontiers in Microbiology

Microbiota, Environment and Diet. de Morais MB. Journal of Pediatric Gastroenterology and Nutrition

Human lung microbiome

Lung Homeostasis: Influence of Age, Microbes, and the Immune System. Lloyd CM. Immunity

Human microbiome and immune system

Homeostatic Immunity and the Microbiota. Belkaid Y. Immunity

Review: Regionalized Development and Maintenance of the Intestinal Adaptive Immune Landscape. Agace WW. Immunity

Human vaginal microbiome

Antimicrobial Compounds Produced by Vaginal <i>Lactobacillus crispatus</i> Are Able to Strongly Inhibit <i>Candida albicans</i> Growth, Hyphal Formation and Regulate Virulence-related Gene Expressions. Wang S. Frontiers of Microbiology

Human liver microbiome 

β-Klotho deficiency protects against obesity through a crosstalk between liver, microbiota, and brown adipose tissue. Somm E. JCI Insight

Animal and insect microbiome

Honeybee gut microbiota promotes host weight gain via bacterial metabolism and hormonal signaling. Zheng H. PNAS.

Comparative Analysis of the Gut Microbial Communities in Forest and Alpine Musk Deer Using High-Throughput Sequencing. Hu X. Frontiers of Microbiology

Mosquito Microbiome Dynamics, a Background for Prevalence and Seasonality of West Nile Virus. Novakova E. Frontiers of Microbiology

Newer Insights into the Antidiarrheal Effects of Acacia catechu Willd. Extract in Guinea Pig.Micucci M. Journal of Medicinal Food

Plant, soil, and air microbiome

Elevated Air Humidity Changes Soil Bacterial Community Structure in the Silver Birch Stand.Truu M. Frontiers of Microbiology

Distance-dependent varieties of microbial community structure and metabolic functions in the rhizosphere of Sedum alfredii Hance during phytoextraction of a cadmium-contaminated soil. Yang W. Environmental science and pollution research

Metagenome-Wide Association Study and Machine Learning Prediction of Bulk Soil Microbiome and Crop Productivity. Chang HX. Frontiers of Microbiology

Origin-Dependent Variations in the Atmospheric Microbiome Community in Eastern Mediterranean Dust Storms.Gat D. Environmental science and technology

Faecal microbiome 

Fecal microbiota transplantation is a rescue treatment modality for refractory ulcerative colitis. Uygun A. Medicine (Baltimore)

Probiotics

Mismatch between Probiotic Benefits in Trials versus Food Products. Scourboutakos MJ. Nutrients

A light digest for Marathon Monday. For me, the highlights today are under “Microbes in the News”, with amazing papers on viral/bacterial detection, bacterial cell size, and cluster regulation!

Human nearly-sterile sites
Evidence for polymicrobial communities in explanted vascular filters and atheroma debris – Jeremy E. Ellis – Molecular and Cellular Probes

Plant, root, and soil microbiome
Global-scale structure of the eelgrass microbiome – Ashkaan K. Fahimipour – Applied Environmental Microbiology
Note: Published as a pre-print back on November 28, 2016

Built environment
Comparing the impact of ultrafine particles from petrodiesel and biodiesel combustion to bacterial metabolism by targeted HPLC-MS/MS metabolic profiling – Fanyi Zhong – Ecotoxicology and Environmental Safety

Revealing the bacterial profile of an anoxic-aerobic moving-bed biofilm reactor system treating a chemical industry wastewater – Joao P Bassin – International Biodeterioration & Biodegradation

Probiotics / prebiotics
An extracellular cell-attached pullulanase confers branched α-glucan utilization in human gut Lactobacillus acidophilus – Marie S Moller – Applied and Environmental Microbiology

Phages and viruses (and transfers)
Class 1 integrons as invasive species – Michael R Gillings – Current Opinion in Microbiology

Bioinformatics
MaxTiC: Fast Ranking Of A Phylogenetic Tree By Maximum Time Consistency With Lateral Gene Transfers – Cedric Chauve – bioRxiv

Techniques
Validation and application of an ultrahigh-performance liquid chromatographic-Orbitrap mass spectrometric method for the simultaneous detection and quantification of volatile and non-volatile organic acids in human faecal samples – Claudio Gardana – Journal of Pharmaceutical and Biomedical Analysis

Impact of wet aerobic pretreatments on cellulose accessibility and bacterial communities in rape straw – Jiang-Hao Tian – Bioresource Technology

Nanopore detection of bacterial DNA base modifications – Alexa B.R. McIntyre – bioRxiv

Microbes in the news
Novel CRISPR Tool Rapidly Detects Viruses And Bacteria – Milla Bengtsson – ReliaWire
Original paper: Nucleic acid detection with CRISPR-Cas13a/C2c2 – Jonathan S. Gootenberg – Science

Study discovers fundamental unit of cell size in bacteria – UCSD – EurekAlert
Invariance of Initiation Mass and Predictability of Cell Size in Escherichia coli – Fangwei Si – Current Biology

Mini-Factories For Drugs? Researchers Find A Way To Switch On ‘Silent’ Gene Clusters In Bacteria – Avaneesh Pandey – International Business Times
Original paper: Discovery of scmR as a global regulator of secondary metabolism and virulence in Burkholderia thailandensis E264 – Dainan Mao – PNAS