August 13, 2018

Today’s Digest is full of amazing research from focusing on causation in microbiome studies to increased efficacy of BLAST searches in the age of high throughput sequencing.

General Microbiome

Microbiome: Focus on Causation and Mechanism.Fischbach MA. Cell.

Effect of Antibiotic-Mediated Microbiome Modulation on Rotavirus Vaccine Immunogenicity: A Human, Randomized-Control Proof-of-Concept Trial.Harris VC. Cell Host and Microbe

Enhancing Rotavirus Vaccination: A Microbial Fix? Parker EPK. Cell Host and Microbe

Snapshot of an early Paleoproterozoic ecosystem: Two diverse microfossil communities from the Turee Creek Group, Western Australia. Barlow EV. Geobiology.

Background levels of microorganisms in the busy urban environment of transport hubs.Patel KV. Journal of Applied Microbiology.

Immunomodulation as Therapy for Fungal Infection: Are We Closer?Sam QH. Frontiers in Microbiology

Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA.Grahl N. mSphere.

Oral Microbiome

Comparison of oral microbiota in orthodontic patients and healthy individuals.Sun F. Microbial Pathogenesis

Skin Microbiome

Mud therapy and skin microbiome: a review.Antonelli M. International Journal of Biometeorology

Gut Microbiome

Phylogeny-corrected identification of microbial gene families relevant to human gut colonization.Bradley PH. PLoS Computational Biology

Dynamic changes in human-gut microbiome in relation to a placebo-controlled anthelminthic trial in Indonesia.Martin I. PLoS Neglected Tropical Disease.

Faecal Microbiome

Effects of metal and metalloid pollutants on the microbiota composition of feces obtained from twelve commercial pig farms across China.Peng Z. Science Total Environment

Fecal Microbiota Alterations Associated With Diarrhea-Predominant Irritable Bowel Syndrome.Zhuang X. Frontiers in Microbiology.

Plant, Soils, and Air Microbiome

Environmental variables better explain changes in potential nitrification and denitrification activities than microbial properties in fertilized forest soils.Tang Y. Science of Total Environment

Metagenomic analysis of rhizosphere microflora of oil-contaminated soil planted with barley and alfalfa. Kumar V. PLoS One.

Trichoderma polysporum selectively inhibits white-nose syndrome fungal pathogen Pseudogymnoascus destructans amidst soil microbes.Singh A. Microbiome.

Tissue Microbiome of Norway Spruce Affected by Heterobasidion-Induced Wood Decay.Ren F. Microbial Ecology

Evidence for complete nitrification in enrichment culture of tidal sediments and diversity analysis of clade a comammox Nitrospira in natural environments. Yu C. Applied Microbiology and Biotechnology.

Traits-Based Integration of Multi-Species Inoculants Facilitates Shifts of Indigenous Soil Bacterial Community.Wang J. Frontier in Microbiology

Spatial Patterns and Drivers of Microbial Taxa in a Karst Broadleaf Forest.Song M. Frontiers in Microbiology

Water Microbiome

Response of Microbial Communities to Changing Climate Conditions During Summer Cyanobacterial Blooms in the Baltic Sea.Berner C. Frontiers in Microbiology

Coral Microbiome Database: Integration of sequences reveals high diversity and relatedness of coral-associated microbes.Huggett MJ. Environmental Microbiology Reports

Animal Experiments and Microbiome

Diet and other environmental factors shape the bacterial communities of fish gut in an eutrophic lake. Kashinskaya EN. Journal of Applied Microbiology

Yeast-like microorganisms in the scale insect Kermes quercus (Insecta, Hemiptera, Coccomorpha: Kermesidae). Newly acquired symbionts?Podsiadło E. Arthropod Structure and Development

Initial description of the core ocular surface microbiome in dogs: Bacterial community diversity and composition in a defined canine population.Leis ML. Veterinary Ophthalmology

High-Throughput Analysis Reveals Seasonal Variation of the Gut Microbiota Composition Within Forest Musk Deer (<i>Moschus berezovskii</i>).Hu X. Frontiers in Microbiology

A Comprehensive Research on Antibiotic Resistance Genes in Microbiota of Aquatic Animals.Hong B. Frontiers in Microbiology

Identification of spider-mite species and their endosymbionts using multiplex PCR.Zélé F. Experimental and Applied Acarology

Soil microarthropods alter the outcome of plant-soil feedback experiments.Kuťáková E. Scientific Reports

Techniques/Bioinformatics 

Metagenome complexity and template length are the main causes of bias in PCR-based bacteria community analysis.Peng W. Journal of Basic Microbiology

Single-cell RNA sequencing technologies and bioinformatics pipelines.Hwang B. Experimental and Molecular Medicine

Negative Binomial Mixed Models for Analyzing Longitudinal Microbiome Data.Zhang X. Frontiers in Microbiology

Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems. Hu Y. Scientific Reports

CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing.Tristão Ramos RJ. Bioinformatics

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August 2, 2018

In today’s Microbiome Digest you can read about: the connection of mother’s microbiota and development of psychiatric disorders by M.G. Codagnone; pulmonary microbiome by A.N. Costa; microbiome and allergic diseases by M.Pascal; olfactory communication via microbiota in birds by O. Maraci; global topsoil microbiome by M. Bahram and many more. Enjoy your hot summer read!

Pregnancy and early life

Review: Programming Bugs: Microbiota and the Developmental Origins of Brain Health and Disease – Martin G.Codagnone – Biological Psychiatry

Human respiratory microbiome

The pulmonary microbiome: challenges of a new paradigm – André Nathan Costa – Jornal Brasileiro de Pneumologia

Oral microbiology

Are the mutans streptococci still considered relevant to understanding the microbial etiology of dental caries? – Jeffrey A. Banas – BMC Oral Health

Predicting oral malodour based on the microbiota in saliva samples using a deep learning approach – Yoshio Nakano – BMC Oral Health

Human skin microbiome

The Environmental Exposures and Inner- and Intercity Traffic Flows of the Metro System May Contribute to the Skin Microbiome and Resistome – Kang Kang – Cell Reports

Human gut microbiome

Alterations in the Gut Microbiota of Rats Chronically Exposed to Volatilized Cocaine and Its Active Adulterants Caffeine and Phenacetin – Cecilia Scorza – Neurotoxicity Research

Origination, change, and modulation of geriatric disease-related gut microbiota during life – Muhammad Shahid Riaz Rajoka – Applied Microbiology and Biotechnology

Rapid gastrointestinal loss of Clostridial Clusters IV and XIVa in the ICU associates with an expansion of gut pathogens – Alexandra E. Livanos – PLOS One

Minireview: Microbiome and Allergic Diseases – Mariona Pascal – Frontiers in Immunology / Mucosal Immunity

Comparison of Microbiota in Patients Treated by Surgery or Chemotherapy by 16S rRNA Sequencing Reveals Potential Biomarkers for Colorectal Cancer Therapy – Xingming Deng – Frontiers in Microbiology / Antimicrobials, Resistance and Chemotherapy

Moxibustion treatment modulates the gut microbiota and immune function in a dextran sulphate sodium-induced colitis rat model – Qin Qi – World Journal of Gastroenterology

Helicobacter pylori in human health and disease: Mechanisms for local gastric and systemic effects – Denisse Bravo – World Journal of Gastroenterology

Acquisition of MACPF domain-encoding genes is the main contributor to LPS glycan diversity in gut Bacteroides species – Valentina Laclare McEneany – The ISME Journal

Drivers of Microbiome Biodiversity: A Review of General Rules, Feces, and Ignorance – Aspen T. Reese – mBio

Effects of prebiotic inulin-type fructans on blood metabolite and hormone concentrations and faecal microbiota and metabolites in overweight dogs – Celeste Alexander – British Journal of Nutrition

Standardization of gut microbiota analysis: Variability in samples taken at different times from single case and the effect of the freezing the sample – F. Saglam – International Journal of Infectious Diseases

Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size – Emily C. Hoedt – The ISME journal

Animal experiments 

A Polysaccharide Isolated from Dictyophora indusiata Promotes Recovery from Antibiotic-Driven Intestinal Dysbiosis and Improves Gut Epithelial Barrier Function in a Mouse Model – Sadia Kanwal – Nutrients

High Dose Vitamin D supplementation alters faecal microbiome and predisposes mice to more severe colitis – Simon Ghaly – Scientific Reports

Treatment with camu camu (Myrciaria dubia) prevents obesity by altering the gut microbiota and increasing energy expenditure in diet-induced obese mice – Fernando F Anhê – Gut Microbiota

Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures – Matej Medvecky – BMC Genomics

Addition of arabinoxylan and mixed linkage glucans in porcine diets affects the large intestinal bacterial populations – John B. Gorham – European Journal of Nutrition

Animal microbiome 

A prokaryotic-eukaryotic relation in the fat body of Bombus terrestris – Anneleen Parmentier – Environmental Microbiology Reports

Olfactory Communication via Microbiota: What Is Known in Birds? – Öncü Maraci – Genes

Unprecedented Diversity of ssDNA Phages from the Family Microviridae Detected within the Gut of a Protochordate Model Organism (Ciona robusta) – Alexandria Creasy – Viruses

Plant, root, and soil microbiome

Description of ‘Candidatus Methylocucumis oryzae’, a novel Type I methanotroph with large cells and pale pink colour, isolated from an Indian rice field – Pranitha S. Pandit – Antonie van Leeuwenhoek

Long-term effects of untreated wastewater on soil bacterial communities – Tianlin Shen – Science of The Total Environment

Minireview: Rhizoremediation of petroleum hydrocarbons: a model system for plant microbiome manipulation – Sara Correa-García – Microbial Biotechnology

Soil pre-fumigation could effectively improve the disease suppressiveness of biofertilizer to banana Fusarium wilt disease by reshaping the soil microbiome – Zongzhuan Shen – Biology and Fertility of Soils

Structure and function of the global topsoil microbiome – Mohammad Bahram – Nature

Globally rising soil heterotrophic respiration over recent decades – Ben Bond-Lamberty – Nature

Water and extremophile microbiome

Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar Current – Flavia Flaviani – Frontiers in Microbiology / Aquatic Microbiology

Evaluation of biomethane potential of waste algal biomass collected from eutrophied lake: effect of source of inocula, co-substrate, and VS loading – Pushpendar Kumar – Journal of Applied Phycology

Distinct molecular signatures in dissolved organic matter produced by viral lysis of marine cyanobacteria – Xiufeng Ma – Environmental Microbiology

Increased biofilm formation due to high-temperature adaptation in marine Roseobacter – Alyssa G. Kent – Nature Microbiology

Adaptive mechanisms that provide competitive advantages to marine bacteroidetes during microalgal blooms – Frank Unfried – The ISME Journal

The anchoring effect—long-term dormancy and genetic population structure – Lisa Sundqvist – The ISME Journal

Genome biology of a novel lineage of planctomycetes widespread in anoxic aquatic environments – Stefan Spring – Environmental Microbiology

The distribution of active iron‐cycling bacteria in marine and freshwater sediments is decoupled from geochemical gradients – Julia M. Otte – Environmental Microbiology

Temporal and spatial dynamics in microbial community composition within a temperate stream network – Norman Hassell – Environmental Microbiology

Diel dynamics and coupling of heterotrophic prokaryotes and dissolved organic matter in epipelagic and mesopelagic waters of the central Red Sea – Francisca C. García – Environmental Microbiology

Probiotics / prebiotics

The effects of a multispecies probiotic on migraine and markers of intestinal permeability–results of a randomized placebo-controlled study – N M de Roos – European Journal of Clinical Nutrition

Phages and viruses

Eicosanoid biosynthesis influences the virulence of Candida parapsilosis – Tanmoy Chakraborty – Virulence

Competition between mobile genetic elements drives optimization of a phage-encoded CRISPR-Cas system: Insights from a natural arms-race – Amelia McKitterick – bioRxiv

Bioinformatics

BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea – Johannes Alneberg – Scientific Data

Bacteria & Art

The Beautiful World of Bacteria

 

July 28, 2018

Have a good weekend! For this Saturday, we have more than 60 articles! 

Including: A set of reviews about mother, delivery and neonate microbiome; relationship between microbiome and cancer and Alzheimer; microbiome in primate models, reviews about pathogens and more…

 

Human and General Microbiome

Review: Gut Mycobiota and Fungal Metabolites in Human Homeostasis – Izabella Mogilnicka – Current Drug Targets

Review: Dietary Protein and Muscle in Aging People: The Potential Role of the Gut Microbiome – Mary Ni Lochlainn – Nutrients

Review: The interplay between neutrophils and microbiota in cancer – Carolyne K. Smith – Journal of Leukocyte Biology

Review: Flux, Impact, and Fate of Halogenated Xenobiotic Compounds in the Gut – Siavash Atashgahi – Frontiers in Physiology

Review: Akkermansia muciniphila in the Human Gastrointestinal Tract: When, Where, and How? – Sharon Y. Geerlings – Microorganisms

Review: Considering gut microbiota disturbance in the management of Helicobacter pylori infection – Loris R. Lopetuso – Expert Review of Gastroenterology & Hepatology

Microbiome Analyses for Toxicological Studies – Jacquelynn Benjamino – Current Protocols in Toxicology

Editorial: Caesarean-Section and Neonatal Gut Microbiome: Short and Long Term Effects and New Targets for Early Prevention – Giannattasio A. – Annals of Nutrition and Metabolism

Review: C-section and the Neonatal Gut Microbiome Acquisition: Consequences for Future Health – Arboleya S. – Annals of Nutrition and Metabolism

Review: Birth Mode-Related Differences in Gut Microbiota Colonization and Immune System Development – Francino M.P.  – Annals of Nutrition and Metabolism

Review: Intervention for Dysbiosis in Children Born by C-Section – Francavilla R. – Annals of Nutrition and Metabolism

Review: Gut Microbiota Composition in Healthy Japanese Infants and Young Adults Born by C-Section – Nagpal R. – Annals of Nutrition and Metabolism

Review: Dysbiosis in Children Born by Caesarean Section – Salas Garcia M.C. – Annals of Nutrition and Metabolism

 

Human Gut

Association between Alzheimer’s Disease and Oral and Gut Microbiota: Are Pore Forming Proteins the Missing Link? – Aguayo, Sebastian –  Journal of Alzheimer’s Disease

Gut microbiome analysis as a tool towards targeted non-invasive biomarkers for early hepatocellular carcinoma – Zhigang Ren – Gut

A Multi-omic Association Study of Trimethylamine N-Oxide – Ohad Manor – Cell Reports

Gut Bacterial Microbiota and its Resistome Rapidly Recover to Basal State Levels after Short-term Amoxicillin-Clavulanic Acid Treatment in Healthy Adults – Chad W. MacPherson – Scientific Reports

Cost-effectiveness analysis of ribotype-guided fecal microbiota transplantation in Chinese patients with severe Clostridium difficile infection – Minghuan Jiang – PLoS ONE

Microbiota Quality and Mitochondrial Activity Link with Occurrence of Muscle Cramps in Hemodialysis Patients using Citrate Dialysate: A Pilot Study – Durand P.-Y. – Blood Purification

Gut microbiota, dietary intakes and intestinal permeability reflected by serum zonulin in women – S. Mörkl – European Journal of Nutrition

Analysis of the Enteric Microbiome: First Tentative Steps Towards a Comprehensive Work-up of Prostate Cancer? – Ilaria Cavarretta – European Urology

 

Human Respiratory Tract

Respiratory Microbiome Profiling for Etiologic Diagnosis of Pneumonia in Mechanically Ventilated Patients – Georgios D. Kitsios – Frontiers in Microbiology

Oropharyngeal microbiome evaluation highlights Neisseria abundance in active celiac patients – Laura Iaffaldano – Scientific Reports

 

Newborn and Mother Microbiome

Maternal antimicrobial use at delivery has a stronger impact than mode of delivery on bifidobacterial colonization in infants: a pilot study – Naruaki Imoto – Journal of Perinatology

 

Human Urinary/Reproductive Tract

Endocervical and vaginal microbiota in South African adolescents with asymptomatic Chlamydia trachomatis infection – Christina Balle – Scientific Reports

Introduction: Microbes in the female reproductive function, do they matter? – Carlos Simon – Fertility and Sterility

 

Human Skin

Relations between epidermal barrier dysregulation and staphylococci-dominated microbiome dysbiosis in atopic dermatitis – Can Altunbulakli – Atopic Dermatitis Research

 

Animal Microbiome / Animal Experiments

Associations Between Nutrition, Gut Microbiome, and Health in A Novel Nonhuman Primate Model – Jonathan B. Clayton – Scientific Reports

Diarrhea-Associated Intestinal Microbiota in Captive Sichuan Golden Snub-Nosed Monkeys (Rhinopithecus roxellana) – Hui Zhu – Microbes and Environments

An orally administered oral pathobiont and commensal have comparable and innocuous systemic effects in germ-free mice – Keisuke Sato – Journal of Periodontal Disease

Effects of dietary tryptophan supplementation in the acetic acid-induced colitis mouse model – Shuai Chen – Food and Nutrition

Early-life stress leads to sex-dependent changes in pubertal timing in rats that are reversed by a probiotic formulation – Caitlin S. M. Cowan – Developmental Psychobiology

A Comparative Study on the Faecal Bacterial Community and Potential Zoonotic Bacteria of Muskoxen (Ovibos moschatus) in Northeast Greenland, Northwest Greenland and Norway – Emilie U. Andersen-Ranberg – Microorganisms

Gut microbiota influences Alzheimer’s disease pathogenesis by regulating acetate in Drosophila model – Yan Kong – Future Microbiology

Elevated Seawater Temperatures Decrease Microbial Diversity in the Gut of Mytilus coruscus – Yi-Feng Li – Frontiers in Physiology

Microbiome-metabolomics Analysis of the Impacts of Long-term Dietary Advanced Glycation End Products Consumption on the C57BL/6 Mouse Fecal Microbiota and Metabolite Perturbation – Wanting Qu – Journal of Agricultural and Food Chemistry

Papio spp. Colon microbiome and its link to obesity in pregnancy – XuanJi Li – Journal of Medical Primatology

Combination of Aronia, Red Ginseng, Shiitake Mushroom and Nattokinase Potentiated Insulin Secretion and Reduced Insulin Resistance with Improving Gut Microbiome Dysbiosis in Insulin Deficient Type 2 Diabetic Rats – Hye Jeong Yang – Nutrients

Short and long-term effects of a synbiotic on clinical signs, the fecal microbiome, and metabolomic profiles in healthy research cats receiving clindamycin: a randomized, controlled trial – Jacqueline C. Whittemore​ – PeerJ

Lactobacillus plantarum ZDY04 exhibits a strain-specific property of lowering TMAO via the modulation of gut microbiota in mice – Liang Qiu – Food and Function

Diet induced maternal obesity affects offspring gut microbiota and persists into young adulthood – Yanjie Guo – Food and Function

Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity – Xue-Song Zhang – eLife

Clostridium butyricum Attenuates Chronic Unpredictable Mild Stress-Induced Depressive-Like Behavior in Mice via the Gut-Brain Axis – Jing Sun – Journal of Agricultural and Food Chemistry

 

Food Microbiome

Analysis of Fish Commonly Sold in Local Supermarkets Reveals the Presence of Pathogenic and Multidrug-Resistant Bacterial Communities – Ama Okyere – Microbiology Insights

Short communication: Profiling white wine seed vinegar bacterial diversity through viable counting, metagenomic sequencing and PCR-DGGE – Vesna Milanović – International Journal of Food Microbiology

Acyl-homoserine-lactones receptor LuxR of Shewanella baltica involved in the development of microbiota and spoilage of refrigerated shrimp – Jinxin Jie – Journal of Food Science and Technology

 

Beneficial Microbes and Compounds

Review: Probiotics against airway allergy: host factors to consider – Irina Spacova – Disease Model and Mechanisms

Abundance of gut Prevotella at baseline and metabolic response to barley prebiotics – Jonna Sandberg – European Journal of Nutrition

Letter: Effect of Metformin or Chinese Herbal Formula in Patients with Type 2 Diabetes Mellitus and Hyperlipidemia: A Reassessment – Venu Gopal Jonnalagadda – mBio

Coreopsis Tinctoria Modulates Lipid Metabolism by Decreasing Low-Density Lipoprotein and Improving Gut Microbiota – Ren Z. – Cellular Physiology and Biochemistry

 

Pathogen Research

Review: Recent insights into Shigella – Stephen Baker – Current Opinion in Infectious Diseases

Review: Cholera: recent updates – Ana A. Weil – Current Opinion in Infectious Diseases

 

Soil and Plant Microbiome

Microbial community assembly differs across minerals in a rhizosphere microcosm – Thea Whitman – Environmental Microbiology

Bipartite interactions, antibiotic production and biosynthetic potential of the Arabidopsis leaf microbiome – Eric J. N. Helfrich – Nature Microbiology

Vineyard under-vine floor management alters soil microbial composition, while the fruit microbiome shows no corresponding shifts – Ming-Yi Chou – Scientific Reports

 

Methods

Methodology: A two-stage microbial association mapping framework with advanced FDR control – Jiyuan Hu – Microbiome

A Comprehensive Study on Predicting Functional Role of Metagenomes Using Machine Learning Methods – Jyotsna Talreja Wassan – IEEE/ACM Transactions on Computational Biology and Bioinformatics

Generalized Linear Models with Linear Constraints for Microbiome Compositional Data – Jiarui Lu – Biometrics

Analyzing differences between microbiome communities using mixture distributions – Konstantin Shestopaloff – Statistics in Medicine

Pathomimetic modeling of human intestinal diseases and underlying host-gut microbiome interactions in a gut-on-a-chip – Woojung Shin – Methods in Cell Biology

 

Other

A year of monitoring 20 mesophilic full-scale bioreactors reveals the existence of stable but different core microbiomes in bio-waste and wastewater anaerobic digestion systems – Magdalena Calusinska – Biotechnology for Biofuels

 

11 July, 2018

Today’s digest is short but full of exciting research. Firstly, a look at how maternal diet can influence infant microbiome and a brilliant preprint highlighting the role women have played in science

General Microbiome

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

Oral Microbiome

Dysbiosis of oral microbiota and its association with salivary immunological biomarkers in autoimmune liver disease.Kazumichi Abe. PLos ONE

Gut Microbiome

Gut microbiota-immune-brain interactions in chemotherapy-associated behavioral comorbidities.Jordan KR Cancer

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

Commentary:Reducing Viability Bias in Analysis of Gut Microbiota in Preterm Infants at Risk of NEC and Sepsis.Agustí G. Frontier in Cellular and Infection Microbiology .

Animal Experiments and Microbiome

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

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

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

Plant, Soil, and Water Microbiome

Microbial community of tannery wastewater involved in nitrification revealed by Illumina MiSeq sequencing.Ma X. Journal of Microbiology and Biotechnology

Rhizosphere fungal community dynamics associated with Rehmannia glutinosa replant disease in a consecutive monoculture regime. Wu L Phytopathology.

Effects of soil erosion on agro-ecosystem services and soil functions: A multidisciplinary study in nineteen organically farmed European and Turkish vineyards. Costantini EAC. Journal of Environmental Management

Virome

Temporal dynamics of the lung and plasma viromes in lung transplant recipients Maia Segura-Wang. PLos ONE

Techniques

Mining Novel Constitutive Promoter Elements in Soil Metagenomic Libraries in <i>Escherichia coli</i>.Westmann CA. Frontier in Microbiology.

Taxonomic and Functional Compositions Impacted by the Quality of Metatranscriptomic Assemblies.Lau MCY. Frontiers in Microbiology.

Preprint

Illuminating women’s hidden contribution to the foundation of theoretical population genetics. Samantha Dung. bioRxiv

July 8, 2018

Today’s Microbiome Digest blog comes up with the current research articles on the microbiome of GIT, Respiratory, UT, Vagina, Infant, Oral, Marine, Plant-Soil and Animal- Bird. It also features the articles on the bioremediation, pre/pro-biotics, nutrient and dietary effects on microbiome, the potential prognosis, biofilm reduction and multi-omics study of pregnancy cohort, role of Environmental Contaminants(ECs), spore-forming bacteria, attenuation of colitis score, systematic repercussions by antibiotics, glucocorticoid signaling, TMAO, drug-induced liver injury (DILI), neurotransmitter interactions, effect of glycation of fish proteins, NOD2-IBD, Carbapenemase-producing Enterobacteriaceae (CPE).

Have a look and enjoy SUNDAY!

EVENTS, JOBS, PhD POSITIONS:

EVENT – Third Annual Microbiome Symposium on September 24 , 8:00AM – 7:00PM at the Stanford Faculty Club

 

GASTRO-INTESTINAL MICROBIOME: 

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

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

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

Absence of NOD2 receptor predisposes to intestinal inflammation by a deregulation in the immune response in hosts that are unable to control gut dysbiosis – Patrícia Reisde Souza – Immunobiology

Review – Outside the liver box: The gut microbiota as pivotal modulator of liver diseases – Annika Wahlström – Biochimica et Biophysica Acta (BBA) – Molecular Basis of Disease

 

RESPIRATORY MICROBIOME:

Review – Microbiome in the primary prevention of allergic diseases and bronchial asthma – B.Sozańska – Allergologia et Immunopathologia

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

URINARY TRACT MICROBIOME:

Review – Infections – The Urinary Tract Microbiome: The Answer to All Our Open Questions? – Giuseppe Magistro – European Urology focus

VAGINAL MICROBIOME:

Anti-HIV-1 Activity of Lactic Acid in Human Cervicovaginal Fluid – Tyssen D – mSphere

INFANT MICROBIOME:

Bifidobacterium longum subsp. infantis EVC001 stably restores the infant gut microbiome over the first year of life in breastfed infants – Jennifer Smilowitz – Pediatrics

Review – Does antibiotic choice for the treatment of suspected late-onset sepsis in premature infants determine the risk of developing necrotising enterocolitis? A systematic review – Josephine V.Seale – Early Human Developmment

ORAL MICROBIOME: 

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

Differential preservation of endogenous human and microbial DNA in dental calculus and dentin – Mann AE – Scientific Reports

Distinctions and associations between the microbiota of saliva and supragingival plaque of permanent and deciduous teeth – Shi W – PLoS One

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

GENERAL HUMAN MICROBIOME:

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

Book chapter – Genomics and Drug-Metabolizing Enzymes and Its Application in Drug Delivery: Evaluating the Influence of the Microbiome – Sheeba Varghese Gupta

Effects of Substance Use and Sex Practices on the Intestinal Microbiome During HIV-1 Infection – Jennifer A Fulcher –The Journal of Infectious Diseases

Preview – Interactions between Clostridioides difficile and fecal microbiota in in vitro batch model: growth, sporulation and microbiota changes – Sabina Horvat – Frontiers in Microbiology

Review – Metagenomic and clinical microbiology – Sophie Amrane – Human Microbiome

Implants induce a new niche for microbiomes – Tim H. Jakobsen – Wiley Online Library

Short Communication Transmission of IMI-2 carbapenemase-producing Enterobacteriaceae from river water to human – Chrislène Laurens – Journal of Global Antimicrobial Resistance

Review – The hygiene hypothesis: immunological mechanisms of airway tolerance – Eline Haspeslagh – Current Opinion in Immunology

Microbiota affects the expression of genes involved in HPA axis regulation and local metabolism of glucocorticoids in chronic psychosocial stress – M. Vodička – Brain, Behavior, and Immunity

Review – The Role of Microbiota in Cardiovascular Risk: Focus on Trimethylamine Oxide – HusseinAl-Rubaye – Current Problems in Cardiology

 

HUMAN-MICROBE CROSS-TALK:

Gut Microbiota-Dependent Trimethylamine N-Oxide Predicts Risk of Cardiovascular Events in Patients With Stroke and Is Related to Proinflammatory Monocytes – Haghikia A – Arterioscler Thromb Vasc Biol.

Cutting Edge: Critical Roles for Microbiota-Mediated Regulation of the Immune System in a Prenatal Immune Activation Model of Autism – Catherine R. Lammert – J Immunol

Critical Role for the Microbiota in CX3CR1+ Intestinal Mononuclear Phagocyte Regulation of Intestinal T Cell Responses – Myunghoo Kim – Immunity

 

MARINE/WATER MICROBIAL ECOLOGY:

Review – Ecology and evolution of seafloor and subseafloor microbial communities – WD Orsi – Nature Reviews Microbiology

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

Metagenomic analysis of basal ice from an Alaskan glacier – Kayani MUR – Microbiome

Patterns of Change in Metabolic Capabilities of Sediment Microbial Communities in River and Lake Ecosystems – Oest A1 – Int J Microbiol

Succession of toxicity and microbiota in hydraulic fracturing flowback and produced water in the Denver–Julesburg Basin – Natalie M Hull – Science of The Total Environment

 

PLANT or SOIL MICROBIOME:

Preview – New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes – Marie E. Kroeger – Frontiers in Microbiology

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

Preview – Unravelling the composition of the root-associated bacterial microbiota of Phragmites australis and Typha latifolia – Laura Pietrangelo – Frontiers in Microbiology

 

BIOREMEDIATION:

Characterization and Dynamic Shift of Microbial Communities during Start-Up, Overloading and Steady-State in an Anaerobic Membrane Bioreactor – Nsanzumukiza Martin Vincent – Int. J. Environ. Res. Public Health

Review – Response of microbial communities to oil spill in the Gulf of Mexico: A review – Linda Adzigbli – Afr. J. Microbiol. Res

A two-staged system to generate electricity in microbial fuel cells using methane – Jaewook Myung – Chemical Engineering Journal

The influence of pressure on crude oil biodegradation in shallow and deep Gulf of Mexico sediments – Nguyen UT – PLoS One

Microbial Community Cohesion Mediates Community Turnover in Unperturbed Aquifers – Robert E. Danczak – mSystems

Energy efficiency: Importance of indigenous microorganisms contained in the municipal solid wastes – S.Zahedi – Waste management

Systematic characterization and proposed pathway of tetracycline degradation in solid waste treatment by Hermetia illucens with intestinal microbiota – Minmin Cai – Environmental Pollution

 

NUTRITION or DIET and TREATMENTS:

Functional Effects of the Buckwheat Iminosugar d-Fagomine on Rats with Diet-Induced Prediabetes – Ramos-Romero S – Mol Nutr Food Res

Long-Term Genistein Consumption Modifies Gut Microbiota, Improving Glucose Metabolism, Metabolic Endotoxaemia and Cognitive Function in Mice Fed a High-Fat Diet – López P – Mol Nutr Food Res

Brown rice-specific γ-oryzanol as a promising prophylactic avenue to protect against diabetes mellitus and obesity disease in humans – Masuzaki H – J Diabetes Investig

Intestinal Inflammation in Chilean Infants Fed With Bovine Formula vs. Breast Milk and Its Association With Their Gut Microbiota – Ossa JC – Front Cell Infect Microbiol.

Trigonelline inhibits intestinal microbial metabolism of choline and its associated cardiovascular risk – Anwar S – J Pharm Biomed Anal

Off-target effects of tribendimidine, tribendimidine plus ivermectin, tribendimidine plus oxantel-pamoate, and albendazole plus oxantel-pamoate on the human gut microbiota – Pierre H.H.Schneeberger – International Journal for Parasitology: Drugs and Drug Resistance

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

Glycation of fish protein impacts its fermentation metabolites and gut microbiota during in vitro human colonic fermentation – Yuhong Yang – Food Research International

Correlation between microbiota and flavours in fermentation of Chinese Sichuan Paocai – YangshengXiao – Food Research International

Review – Relationship between fatty acids intake and Clostridium coccoides in obese individuals with metabolic syndrome – Giovana Jamar – Food Research International

Review – Microbiota of milk powders and the heat resistance and spoilage potential of aerobic spore-forming bacteria – Faizan A.Sadiq – International Diary Journal

Review – The debate over neurotransmitter interaction in aspartame usage – Arbind Kumar Choudhary – Journal of Clinical Neuroscience

 

METHODS:

Reevaluating approaches to cystic fibrosis pulmonary exacerbations – Schechter MS – Pediatr Pulmonol

Review – Bioresponsive drug delivery systems in intestinal inflammation: State-of-the-art and future perspectives – Niranjan G.Kotla – Advance Drug Delivery Reviews

Rapid analysis of photoautotroph microbial communities in soils by flow cytometric barcoding and fingerprinting – László Menyhárt – Applied Soil Ecology

Degradation studies of modified inulin as potential encapsulation material for colon targeting and release of mesalamine – MichaelWalz – Carbohydrate Polymers

Review – Advances in drug-induced cholestasis: Clinical perspectives, potential mechanisms and in vitro systems – M. LeonorFernández-Murga – Food and Chemical Toxicology

 

ANIMAL and BIRD MICROBIOME:

Characteristics of microbial communities and intestinal pathogenic bacteria for migrated Larus ridibundus in southwest China – Liao F – Microbiology Open

Gut microbiota correlates with fiber and apparent nutrients digestion in goose – Guojun Liu – Poultry Science

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

Analysis of temporal fecal microbiota dynamics in weaner pigs with and without exposure to enterotoxigenic Escherichia coli – J. Pollock – Journal of Animal Science

 

ANIMAL EXPERIMENTS:

Aryl hydrocarbon receptor/IL-22/Stat3 signaling pathway is involved in the modulation of intestinal mucosa antimicrobial molecules by commensal microbiota in mice – Wang J – Innate Immun.

Oral infection of mice with Fusobacterium nucleatum results in macrophage recruitment to the dental pulp and bone resorption – Larry Johnson – Biomedical Journal

Preview – Fecal Microbiota Transplantation is Associated with Reduced Morbidity and Mortality in Porcine Circovirus Associated Disease – Megan C. Niederwerder – Frontiers in Microbiology

Oral treatment with Lactobacillus rhamnosus 64 during the early postnatal period improves the health of adult rats with TNBS-induced colitis – Stanislava Stanojević – Journal of Functional Foods

Antibiotic-induced dysbiosis effects on the murine gastrointestinal tract and their systemic repercussions – Caio PupinRosa – Life Sciences

 

MICROBIOLOGY:

N-Acetyl-glucosamine influences the biofilm formation of Escherichia coli – Sicard JF – Gut Pathog

Benzoyl Peroxide Inhibits Quorum Sensing and Biofilm Formation by Gardnerella vaginalis 14018 – Ammar Algburi – Infectious Diseases in Obstetrics and Gynecology

 

PRE/PRO – BIOTICS:

Review : Benefaction of probiotics for human health: A review – George Kerry R – J Food Drug Anal

Review – Role of prebiotics in regulation of microbiota and prevention of obesity – Grethel T.Choque Delgado – Food Research International

Effects of the Administration of Probiotics on Fecal Microbiota Diversity and Composition in Healthy Individuals – Choong-Kyun Noh – J Neurogastroenterol Motil

 

METABOLOMICS:

Microbiome-related metabolite changes in gut tissue, cecum content and feces of rats treated with antibiotics – C.Behr – Toxicology and Applied Pharmacology

 

MULTI-OMICS PICKS:

Multiomics Modeling of the Immunome, Transcriptome, Microbiome, Proteome, and Metabolome Adaptations During Human Pregnancy – Mohammad Sajjad Ghaemi – Bioinformatics

July 03, 2018

In today’s Digest you can read about: soil microbes regulating forest succession by H. Liao,  sinking particles in the ocean microbiome by M. Mestre, ecology and evolution of seafloor and subseafloor microbial communities by W. D. Orsi, biotechnological potentials of marine bacteria by A. K.  Farha, differentiation of Candida species Raman spectroscopy by A. Silge. Enjoy your summer read!

General microbiome

Signatures of ecological processes in microbial community time series – Karoline Faust – Microbiome

Review: Metabolic reprogramming for cancer cells and their microenvironment: Beyond the Warburg Effect – Linchong Sun – Biochimica et Biophysica Acta (BBA) – Reviews on Cancer

Oral microbiota

Microbial similarity and preference for specific sites in healthy oral cavity and esophagus – Li Dong – Frontiers in Microbiology / Microbial Symbioses

Human gut microbiome

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

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

Plant, root, and soil microbiome

Trait-based patterns of microbial dynamics in dormancy potential and heterotrophic strategy: case studies of resource-based and post-press succession – Patrick J. Kearns – The ISME Journal

Links among warming, carbon and microbial dynamics mediated by soil mineral weathering – S. Doetterl – Nature Geoscience

In Planta Bacterial Transcriptomics Predict Plant Disease Outcomes – Stephen P.Cohen – Trends in Plant Science

Hymenobacter jeollabukensis sp. nov., isolated from soil – Leonid N. Ten -Journal of Microbiology

Ruegeria kandeliae sp. nov., isolated from the rhizosphere soil of a mangrove plant Kandelia candel – Lv Zhang –  International Journal of Systematic and Evolutionary Microbiology

Soil microbes regulate forest succession in a subtropical ecosystem in China: evidence from a mesocosm experiment – Huixuan Liao – Plant and Soil

Solubilization of insoluble zinc compounds by zinc solubilizing bacteria (ZSB) and optimization of their growth conditions – Mohammad Yaghoubi Khanghahi – Environmental Science and Pollution Research

Soil microbial communities differ according to fertiliser regimes and cabbage (Brassica oleracea var. capitata L.) growth, but not aphid herbivory – Flora J. O’Brien – Frontiers in Microbiology / Terrestrial Microbiology

Paenibacillus elymi sp. nov., isolated from the rhizosphere of Elymus tsukushiensis, a plant native to the Dokdo Islands, Republic of Korea – Ye-Ji Hwang – International Journal of Systematic and Evolutionary Microbiology

Changes in rhizosphere microbial communities in potted cucumber seedlings treated with syringic acid – Zhilin Wang – PLOS One

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

Isolation of Pseudomonas putida from Harir/Erbil soil and screening for the presence of phosphate solubilizing genes – Aras Mohammed Khudhur – Polytechnic Journal

Environmental controls on soil microbial communities in a seasonally dry tropical forest – Silvia Pajaresa – Applied and Environmental Microbiology

Temperature effects on structure and function of the methanogenic microbial communities in two paddy soils and one desert soil – Pengfei Liu – Soil Biology and Biochemistry

Soil microbial communities differ according to fertiliser regimes and cabbage (Brassica oleracea var. capitata L.) growth, but not aphid herbivory – Flora J. O’Brien – Frontiers in Microbiology

Natural forests maintain a greater soil microbial diversity than that in rubber plantations in Southwest China –  Jutamart Monkai – Agriculture, Ecosystems & Environment

Water and extremophile microbiome 

Sinking particles promote vertical connectivity in the ocean microbiome – Mireia Mestre – PNAS

Filtering artefacts in bacterial community composition can affect the outcome of dissolved organic matter biolability assays – Joshua F. Dean – Biogeosciences

Review: Ecology and evolution of seafloor and subseafloor microbial communities – William D. Orsi  – Nature Reviews Microbiology

The unexpected diversity of microbial communities associated with black corals revealed by high-throughput Illumina sequencing – Yong-Chun Liu  – FEMS Microbiology Letters

Effect of spatial origin and hydrocarbon composition on bacterial consortia community structure and hydrocarbon biodegradation rates – Lloyd D Potts – FEMS Microbiology Ecology

Microbial distribution and turnover in Antarctic microbial mats highlight the relevance of heterotrophic bacteria in low-nutrient environments – Patricia M Valdespino-Castillo – FEMS Microbiology Ecology

Cultivation and characterization of Candidatus Nitrosotenuis aquariensis, an ammonia-oxidizing archaeon from a freshwater aquarium biofilter – Laura A. Sauder – Applied and Environmental Microbiology

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

Hydrocarbon degradation and response of seafloor sediment bacterial community in the northern Gulf of Mexico to light Louisiana sweet crude oil  – Hernando P. Bacosa – The ISME Journal

A closely-related clade of globally distributed bloom-forming cyanobacteria within the Nostocales – Connor B.Driscoll – Harmful Algae

Review: Recent developments in synthetic biology and metabolic engineering in microalgae towards biofuel production – Sheeja Jagadevan – Biotechnology for Biofuels

Phylogenetic diversity and biotechnological potentials of marine bacteria from continental slope of eastern Arabian Sea – Arakkaveettil Kabeer Farha – Journal of Genetic Engineering and Biotechnology

Biochemical methane potential of microalgae biomass using different microbial inocula – Cristina Gonzalez-Fernandez – Biotechnology for Biofuels

Quorum sensing in thermophiles: prevalence of autoinducer-2 system – Amandeep Kaur – BMC Microbiology

Molecular Cloning and Characterization of a Novel α-Amylase from Antarctic Sea Ice Bacterium Pseudoalteromonas sp. M175 and Its Primary Application in Detergent – Xiaofei Wang – BioMed Research International

Low-temperature sulfidic-ice microbial communities, Borup Fiord Pass, Canadian high Arctic – Christopher B. Trivedi – Frontiers in Microbiology / Extreme Microbiology

Phages and viruses

Beyond members of the Flaviviridae family, sofosbuvir also inhibits chikungunya virus replication – Andre Ferreira – bioRxiv

Evaluation of bias induced by viral enrichment and random amplification protocols in metagenomic surveys of saliva DNA viruses – Marcos Parras-Moltó – Microbiome

Immuno-metabolic changes in herpes virus infection – Debprasa Chattopadhyay – Cytokine

Emergence of a Virulent Genotype VIIi of Newcastle Disease Virus in Iran – Arash Ghalyanchilangeroudi – Avian Pathology

Techniques

High-throughput microfluidic sorting of live magnetotactic bacteria – Andy Tay – Applied and Environmental Microbiology

The application of UV resonance Raman spectroscopy for the differentiation of clinically relevant Candida species – Anja Silge – Analytical and Bioanalytical Chemistry

June 27, 2018

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

General microbiome

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

Pregnancy and early life

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

Human ear microbiota

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

Human respiratory microbiome

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

Human gut microbiome

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

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

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

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

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

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

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

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

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

Animal experiments 

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

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

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

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

Animal microbiome

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

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

Plant, root, and soil microbiome

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

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

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

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

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

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

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

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

Water and extremophile microbiome

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

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

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

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

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

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

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

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

Review: Cyanobacterial blooms – Jef Huisman – Nature Reviews Microbiology

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

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

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

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

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

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

Built environment 

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

Phages and viruses

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

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

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

Host-microbiome interactions

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

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

Bioinformatics

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

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

Science, publishing, and career 

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

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