April 17, 2019

Today’s Digest contains quite a few news articles. Features for today include a review on the importance of proper controls in microbiome studies, a patent for one method of analyzing microbiome dynamics (really?), and the NASA Twins Study, how can one year in space change your gut microbiota and much more? Enjoy reading!

General microbiology

Guideline: Microbiology Investigation Criteria for Reporting Objectively (MICRO): a framework for the reporting and interpretation of clinical microbiology data – Paul Turner & Andrew Fox-Lewis et al. – BMC Medicine

** Patent: Method of analyzing microbiome – E Segal & E Elinav

Combined deterministic and stochastic processes control microbial succession in replicate granular biofilm reactors – R Liébana et al. – Environmental Science & Technology

** Uncorrected proof: Issues and current standards of controls in microbiome research – Bastian V.H. Hornung et al. – FEMS Microbiology Ecology

Pregnancy and early life

Review: Intestinal Microbiota in Early Life and Its Implications on Childhood Health – Lu Zhuang et al. – Genomics, Proteomics & Bioinformatics

Cancer microbiome

PDF: Gastric Microbiota in Helicobacter pylori-Negative and -Positive Gastritis Among High Incidence of Gastric Cancer Area – Boldbaatar Gantuya et al. – Cancers

Human respiratory microbiome

Review: Microbes, metabolites, and the gut–lung axis – Anh Thu Dang & Benjamin J. Marsland – Mucosal Immunology

Microbial contributions to bronchial asthma occurrence in children: A metagenomic study – Man Tian et al. – Journal of Cellular Biochemistry

Human gut microbiome

Review: A Review on Bile Acids: Effects of the Gut Microbiome, Interactions with Dietary Fiber, and Alterations in the Bioaccessibility of Bioactive Compounds – Jashbir Singh et al. – Journal of Agricultural and Food Chemistry

Increased mucosal neutrophil survival is associated with altered microbiota in HIV infection – Tiffany Hensley-McBain et al. – PLoS Pathogens

Review: Thinking bigger: How early life environmental exposures shape the gut microbiome and influence the development of asthma and allergic disease – Hind Sbihi et al. – Allergy

** The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight – Francine E. Garrett-Bakelman et al. – Science

Metabolomics

Review: Changes in the Human Metabolome Associated With Alcohol Use: A Review – Taija Voutilainen & Olli Kärkkäinen – Alcohol and Alcoholism

Animal microbiome

Dynamic changes in rumen fermentation and bacterial community following rumen fluid transplantation in a sheep model of rumen acidosis: implications for rumen health in ruminants – Junhua Liu et al. – The FASEB Journal

Rainbow trout (Oncorhynchus mykiss) gut microbiota is modulated by insect meal from Hermetia illucens prepupae in the diet – Genciana Terova et al. – Reviews in Fish Biology and Fisheries

Plant, root and soil microbiome

Effects of mycorrhizae and water conditions on perennial ryegrass growth in rare earth tailings – Qiao Yang et al. – RSC Advance

Niche separation of species of entomopathogenic fungi within the genera Metarhizium and Beauveria in different cropping systems in Mexico – J.A. Cabrera-Mora et al. – Fungal Ecology

Soil abiotic properties and plant functional traits mediate associations between soil microbial and plant communities during a secondary forest succession on the Loess Plateau – Yongfu Chai et al. – Frontiers in Microbiology

Microbial Diversity and Antimicrobial Resistance Profile in Microbiota from Soils of Conventional and Organic Farming Systems – Julija Armalytė et al. – Frontiers in Microbiology

Effects of elevated temperature and elevated CO2 on soil nitrification and ammonia-oxidizing microbial communities in field-grown crop – Linh T.T. Nguyen et al. – Science of The Total Environment

Tropical forest conversion to rubber plantation affects soil micro- & mesofaunal community & diversity – Dharmesh Singh et al. – Scientific Reports

Water and extremophile microbiome

Sulfate reduction by a haloalkaliphilic bench-scale sulfate-reducing bioreactor and its bacterial communities at different depths – Tingzhen Mu et al. – Biochemical Engineering Journal

Extremely acidic environment: Biogeochemical effects on algal biofilms – Ana Teresa Luís et al. – Ecotoxicology and Environmental Safety

Proliferation of hydrocarbon-degrading microbes at the bottom of the Mariana Trench – Jiwen Liu & Yanfen Zheng et al. – Microbiome

Metagenomic insights to understand transient influence of Yamuna River on taxonomic and functional aspects of bacterial and archaeal communities of River Ganges – Rachel Samson et al. – Science of The Total Environment

Distribution of microbial communities in metal-contaminated nearshore sediment from Eastern Guangdong, China – Mei Zhuang et al. – Environmental Pollution

Phages and viruses

Diversities and potential biogeochemical impacts of mangrove soil viruses – Min Jin et al. – Microbiome

Technology

Explore mediated co-varying dynamics in microbial community using integrated local similarity and liquid association analysis – Dongmei Ai et al. – BMC Genomics

Microbes in the news

Can changing the microbiome reverse lactose intolerance? – PATRICIA L. FOSTER – PhillyVoice

A Look at the Trillions of Microorganisms That Live in and on You – Shayla Love – Vice

Mode of delivery alters infants’ gut microbiota and this may impact respiratory health in first year of life – EurekAlert!

Fecal Transplant Reduces Nearly 50 Percent Of Autism Symptoms In Children – Allan Adamson – Tech Times

Edinburgh Science Festival: from gut bacteria and depression to how rice is risking the planet – Helen McArdle – The Herald

Gut microbiome changes emerge as a potential modulator of age-associated cardiovascular disease risk – Andreu Prados – Gut Microbiota for Health

The Gut Microbiome & Cancer Immunotherapy – Osman, Afaf E. G. & Luke, Jason J. – Oncology Times

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April 16, 2019

Good morning everyone! Today’s digest will deal a lot of disturbance in various ecosystems- starvation of the oral microbiota, forest fires, elevated CO2 levels and rising temperatures and more. Additionally, interesting pieces about science communication and education are recommended (bottom of the post).

Animal microbiome

Effects of diet on gut microbiota of soil collembolans– Qian Xiang- Science of the Total Environment

Diel population and functional synchrony of microbial communities on coral reefs– Winda Wegley-Kelly- Nature Communications

Human microbiome

Klebsiella and Providencia emerge as lone survivors following long-term starvation of oral microbiota– Jonathon L. Baker- PNAS

Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation– Hyeonsoo Jeong- Scientific Reports

Dysbiosis patterns during re-induction/salvage versus induction chemotherapy for acute leukemia– Armin Rashidi- Scientific Reports

The personalized temporal dynamics of microbiome in the airways of cystic fibrosis patients– Giovanni Baci- bioRxiv

Plant, root and soil microbiome

Maize synthesized benzoxazinoids affect the host associated microbiome- Enoch Narh Kodjordjie- Microbiome

Utilization of carbon sources in the rice rhizosphere and non-rhizosphere soils with different long-term fertilization management– Tang H- J of Basic Microbiology

Effect of forest fire prevention treatments on bacterial communities associated with productive Boletus edulis sites- Olaya Mediavilla- Microbial Biotechnology

Effects of elevated temperature and elevated CO2 on soil nitrification and ammonia-oxidizing microbial communities in field-grown crop– Linh T.T Nguyen- Science of the Total Environment

Phyllosphere epiphytic and endophytic fungal community and network structures differ in a tropical mangrove ecosystem– Hui Yao- Microbiome

Changes in fungal communities across a forest disturbance gradient– Lingling Shi- AEM

Water microbiome

Wetland sediments host diverse microbial taxa capable of cycling alchohols- Paula Dalcin Martins- AEM

Review- The microbiomes of deep-sea hydrothermal vents: distributed globally, shaped locally– Gregory J. Dick- N. Reviews Microbiology

Bioinformatics

DeeplyEssential: A Deep Neural Network for Predicting Essential Genes in Microbes- Md Abid Hassan- bioRxiv

Microbiome news and science communication

Biotech company launches animal models with custom microbiome profiles

Microbial biotechnology for water treatment- A collection of high-quality websites (from Microbial Biotechnology)

Thematic series on scholarly communications in the digital age

The urgent need for microbiology literacy in society

April 15, 2019

Today’s Monday morning digest covers reviews on different aspects of human microbiome, interesting articles about effects of early life treatments in rodents and news updates on market prediction of microbiome sequencing and therapeutics.

General microbiome

Current understanding of the human microbiome – Jack A Gilbert – Nature Communications

The Importance of the Microbiome in Bariatric Surgery: a Systematic Review – Josianne C. H. B. M. Luijten – Obesity surgery

A potential role for the gut microbiome in substance use disorders – Katherine R. Meckel – Psychopharmacology

The power of small changes: Comprehensive analyses of microbial dysbiosis in breast cancer – Sheetal Parida -Biochimica et Biophysica Acta

The lung microbiome and transplantation –  Alicia B. Mitchell – Current Opinion in Organ Transplantation

Human gut microbiome

Encrustations on ureteral stents from patients without urinary tract infection reveal distinct urotypes and a low bacterial load – Matthias T. Buhmann – Microbiome

Overuse of anti‐anaerobic drug is associated with poor post‐chemotherapy prognosis of patients with hepatocellular carcinoma – Noriho Lida – International Journal of Cancer

Antibiotic-induced shifts in fecal microbiota density and composition during hematopoietic stem cell transplantation – Sejal Morjaria – BioRxiv

Surveillance-embedded genomic outbreak resolution of methicillin-susceptible Staphylococcus aureus in a neonatal intensive care unit – AJH Cremers – BioRxiv

Animal experiments

Antidepressants affect gut microbiota and Ruminococcus flavefaciens is able to abolish their effects on depressive-like behavior – Iva Lukić – Translational Psychiatry

Early life stress induces type 2 diabetes-like features in ageing mice – Hanna Ilchmann-Diounou – Brain, Behavior and Immunity

Early-life vancomycin treatment promotes airway inflammation and impairs microbiome homeostasis – Xin Yang – Aging

Early-life stress, microbiota, and brain development: probiotics reverse the effects of maternal separation on neural circuits underpinning fear expression and extinction in infant rats – Caitlin S.M. Cowan – Developmental Cognitive Neuroscience

Commensal Escherichia coli aggravates acute necrotizing pancreatitis through targeting intestinal epithelial cells – Junyuan Zheng – Applied and Environmental Microbiology

Host-Microbiome Synergistic Control on Sphingolipid Metabolism by Mechanotransduction in Model Arthritis – Xiaoyuan Zhou – Biomolecules

Plant, root, soil microbiome

Bacterial community diversity associated with the severity of bacterial wilt disease in tomato fields in south-east China – Xuefang Zheng – Canadian Journal of Microbiology

Bacterial disease induced changes in fungal communities of olive tree twigs depend on host genotype – Teresa Gomes – Scientific Reports

Co‐inoculation of Bacillus spp. and Pseudomonas putida at different development stages acts as a biostimulant to promote growth, yield and nutrient uptake of tomato – Yanhui He – Journal of Applied Microbiology

Water microbiome and extremophiles

Extant microbial communities in the partially desiccated Rincon de Parangueo maar crater lake in Mexico – Janet Sánchez-Sánchez – Fems Microbiology Ecology

Novosphingobium meiothermophilum sp. nov., isolated from a hot spring – Wen-Dong Xian – International Journal of Systematic and Evolutionary Microbiology

Built Environment

Impacts of Indoor Surface Finishes on Bacterial Viability – Jinglin Hu – Indoor air

Probiotics

Probiotics: If It Does Not Help It Does Not Do Any Harm. Really? – Aaron Lerner – Microorganisms

Effects of Lactobacillus plantarum PS128 on Children with Autism Spectrum Disorder in Taiwan: A Randomized, Double-Blind, Placebo-Controlled Trial – Yen-Wenn Liu – Nutrients

Microbes in the news

Global Human Microbiome Therapeutics Market Outlook 2019-2024: ENTEROME Bioscience, Rebiotix, Seres Therapeutics – NewsPrimo

Caesarean babies slower to acquire ‘good’ gut bacteria: study – PanArmenian Net

Mode of delivery has substantial impact on infants’ health – Business Standard

Newborn’s ‘Microbiome’ Could Give Clues to Weight Later – Doctors Lounge

Microbiome Sequencing Services Market is expected to grow at a CAGR of 18% during the forecast period of (2018 – 2023) – Redfield Report

Human Microbiome Market boosting the growth Worldwide – Business Herald

April 13, 2019

In today’s digest read about diverse population of bacteria and fungi on the International Space Station, how antidepressants affect gut microbiota, and check out a new framework for comparing and assessing taxonomic profilers (OPAL). Happy weekend!

Vaginal microbiome

Defining characteristics of genital health in South African adolescent girls and young women at high risk for HIV infection – Smritee Dabee – PlosOne

Detection of ureaplasmas and bacterial vaginosis associated bacteria and their association with non-gonococcal urethritis in men – Maria Frølund – PlosOne

Group B streptococcal screening, intrapartum antibiotic prophylaxis, and neonatal early-onset infection rates in an Australian local health district: 2006-2016 – Kathryn Braye – PlosOne

Gut microbiome

Long-term benefit of Microbiota Transfer Therapy on autism symptoms and gut microbiota – Dae-Wook Kang – Scientific Reports

The Prevotella copri complex comprises four distinct clades that are underrepresented in Westernised populations – Adrian Tett – bioRxiv

Fecal short-chain fatty acids are not predictive of colonic tumor status and cannot be predicted based on bacterial community structure – Marc A. Sze – bioRxiv

Evidence for a multi-level trophic organization of the human gut microbiome – Tong Wang – bioRxiv

Animal microbiome

Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms – Philipp Rausch – bioRxiv

Metagenomic Analysis of the Whole Gut Microbiota in Brazilian Termitidae Termites Cornitermes cumulans, Cyrilliotermes strictinasus, Syntermes dirus, Nasutitermes jaraguae, Nasutitermes aquilinus, Grigiotermes bequaerti, and Orthognathotermes mirim – Maria B. Grieco – Current Microbiolgy

The sponge microbiome within the greater coral reef microbial metacommunity – Daniel F. R. Cleary – Nature Communications

Insights into the intestinal microbiota of several aquatic organisms and association with the surrounding environment – Fulin Sun – Aquaculture

Animal experiments

*Antidepressants affect gut microbiota and Ruminococcus flavefaciens is able to abolish their effects on depressive-like behavior – Iva Lukić – Translational Psychiatry

Chronic paradoxical sleep deprivation-induced depression­like behavior, energy metabolism and microbial changes in rats – Weini Ma – Life Sciences

Ability of bifidobacteria to metabolize chitin-glucan and its impact on the gut microbiota – Giulia Alessandri – Scientific Reports

Probiotics

Fasting breath H2 and gut microbiota metabolic potential are associated with the response to a fermented milk product in irritable bowel syndrome – Boris Le Nevé – PlosOne

Lactobacillus fermentum and Lactobacillus plantarum increased gut microbiota diversity and functionality, and mitigated Enterobacteriaceae, in a mouse model – C. Linninge – Beneficial Microbes

Complex responses to inflammatory oxidants by the probiotic bacterium Lactobacillus reuteri – Poulami Basu Thaku – bioRxiv

Plant/root/soil microbiome

Urban traffic changes the biodiversity, abundance, and activity of phyllospheric nitrogen-fixing bacteria – Yang Li – Environmental Science and Pollution Research

Comparative analysis of the rhizomicrobiome of the wild versus cultivated crop: insights from rice and soybean – Shaohua Shi – Archives of Microbiology

Copper and zinc in rhizospheric soil of wild plants growing in long-term acid vineyard soils – C.Campillo-Cora – Science of The Total Environment

Review: Soil microbiome: a key player for conservation of soil health under changing climate – Anamika Dubey – Biodiversity and Conservation

Rhizosphere microbiota compositional changes reflect potato blackleg disease – Lutian Mao – Applied Soil Ecology

Pseudomonas urumqiensis sp. nov., isolated from rhizosphere soil of Alhagi sparsifolia – Yuanyuan Zou – International Journal of Systematic and Evolutionary Microbiology

Insights gained from metagenomic shotgun sequencing of apple fruit epiphytic microbiota – Dario Angeli – Postharvest Biology and Technology

Extremophile microbiome

*Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces – Aleksandra Checinska Sielaff – Microbiome

Techniques

Review: Untargeted LC/MS-based metabolic phenotyping (metabonomics/metabolomics): The state of the art – Helen Gika – Journal of Chromatography B

Bioinformatics

*Assessing taxonomic metagenome profilers with OPAL – Fernando Meyer – Genome Biology

Analysis of error profiles in deep next-generation sequencing data – Xiaotu Ma – Genome Biology

clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers – Kieran R. Campbell – Genome Biology

RnBeads 2.0: comprehensive analysis of DNA methylation data – Fabian Müller – Genome Biology

Review: Big data analytics for personalized medicine – Davide Cirillo and Alfonso Valencia – Current Opinion in Biotechnology

Meta-network: optimized species-species network analysis for microbial communities – Pengshuo Yang – BMC Genomics

8 April, 2019

General Microbiome

Coevolutionary dynamics shape the structure of bacteria-phage infection networks. Fortuna MA.Evolution.

High proportions of bacteria are culturable across major biomes. Martiny AC. ISME Journal

The complexity of an optimal vaginal biome. Eschenbach DA. BJOG

The lung microbiome, vitamin D, and the tuberculous granuloma: A balance triangle. Balcells ME. Microbial Pathogenesis

Gut Microbiome

The parasitic worm product ES-62 normalises the gut microbiota bone marrow axis in inflammatory arthritis. Doonan J. Nature Communications

Culture-enriched human gut microbiomes reveal core and accessory resistance genes. Raymond F.Microbiome.

Plant, Soil, Water, and Air Microbiome

Temperature and soil moisture control microbial community composition in an arctic-alpine ecosystem along elevational and micro-topographic gradients.Frindte K. ISME Journal

Root traits and belowground herbivores relate to plant-soil feedback variation among congeners.Wilschut RA. Nature Communications

A Polyphasic Approach for Assessing Eco-System Connectivity Demonstrates that Perturbation Remodels Network Architecture in Soil Microcosms.Stamou GP. Microbial Ecology

Effect of stock density on the microbial community in biofloc water and Pacific white shrimp (Litopenaeus vannamei) gut microbiota.Deng Y. Applied Microbiology Biotechnology

Rapid and stable microbial community assembly in the headwaters of third-order stream. Teachey ME. Applied Environmental Microbiology

Comparative Metagenomics Reveals Enhanced Nutrient Cycling Potential After Two Years of Biochar Amendment in a Tropical Oxisol. Yu J. Applied Environmental Microbiology

Animal Experiments and Microbiome

Effect of a low protein diet on chicken ceca microbiome and productive performances. De Cesare A. Poultry Science

Impact of a probiotic-based cleaning product on the microbiological profile of broiler litters and chicken caeca microbiota.De Cesare P. Poultry Science

Metagenomic Analysis of the Whole Gut Microbiota in Brazilian Termitidae Termites Cornitermes cumulans, Cyrilliotermes strictinasus, Syntermes dirus, Nasutitermes jaraguae, Nasutitermes aquilinus, Grigiotermes bequaerti, and Orthognathotermes mirim. Grieco MB. Current Microbiology.

The hemolymph microbiome of insects. Blow F. Journal Of Insect Physiology

Musa basjoo regulates the gut microbiota in mice by rebalancing the abundance of probiotic and pathogen. Wei T. Microbial Pathogenesis

Investigating the influence of organic acid marinades, storage temperature and time on the survival/inactivation interface of Salmonella on chicken breast fillets.

Lytou AE. International Journal of Food Microbiology.

April 6, 2019

Highlights: Inferring absolute species concentration in vaginal microbiome, transcriptomics of Arctic Tundra soils, successional traits of prokaryotic communities in Tundra soil, Modulation of plant microbial community by fungal endophyte Epichloë and many more.

General microbiome

Microbial community design: methods, applications, and opportunities –  A Eng – Current Opinion in Biotechnology

Human vaginal microbiome

Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: implications for in vivo dominance of the vaginal microbiota – Charlotte van der Veer – Microbiome

Complementing 16S rRNA gene amplicon sequencing with estimates of total bacterial load to infer absolute species concentrations in the vaginal microbiome – Florencia Tettamanti Boshier – bioRxiv

Human gut microbiome

Perturbation of the human gut microbiome by a non-antibiotic drug contributes to the resolution of autoimmune disease – Renuka R Nayak – bioRxiv

Gut microbiota from high-risk men who have sex with men drive immune activation in gnotobiotic mice and in vitro HIV infection – SX Li – PLoS Pathogens

Distinct gut microbiota profile in antiretroviral therapy-treated perinatally HIV-infected patients associated with cardiac and inflammatory biomarkers – L Sessa – AIDS

The relationship between gastric microbiota and gastric disease – S Zhang – Scandinavian Journal of Gastroenterology

The Gut Microbiome Says NO to microRNA-Mediated Gene Silencing – Z Wei – Biochemistry

Functional diversity and metabolic profile of microbial community of mine soils with different levels of chromium contamination – SK Pradhan – International Journal of Environmental Health Research

16S rRNA/rRNA Gene Ratios and Cell Activity Staining Reveal Consistent Patterns of Microbial Activity in Plant-Associated Soil – AW Bowsher – mSystems

Spatial segregation of the biological soil crust microbiome around its foundational cyanobacterium, Microcoleus vaginatus, and the formation of a nitrogen-fixing cyanosphere – E Couradeau – Microbiome

 

Plant, root, and soil microbiome

A long-term field experiment demonstrates the influence of tillage on the bacterial potential to produce soil structure-stabilizing agents such as exopolysaccharides and lipopolysaccharides – Barbara Cania – Environmental Microbiome

Heritable Epichloë symbiosis shapes fungal but not bacterial communities of plant leaves – Riitta Nissinen – Scientific Reports

Prokaryotic community shifts during soil formation on sands in the tundra zone – Alena Zhelezova – PLoS ONE

The epiphytic microbiota of sour rot-affected grapes differs minimally from that of healthy grapes, indicating causal organisms are already present on healthy berries – Megan E Hall – PLoS ONE

Transcriptomic responses to warming and cooling of an Arctic tundra soil microbiome – Morten Dencker Schostag – bioRxiv

Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil – Evan P. Starr – bioRxiv

Comparison of prokaryotic communities between the fields showing different disinfestation effects by anaerobic soil disinfestation – Chol Gyu Lee – bioRxiv

Long-term urea fertilization alters the composition and increases the abundance of soil ureolytic bacterial communities in an upland soil – R Sun – FEMS Microbial Ecology

Water and extremophile microbiome 

Diversity and shifts of the bacterial community associated with Baikal sponge mass mortalities – Sergei Belikov – PLoS ONE

Temporal covariation of epibacterial community and surface metabolome in the Mediterranean seaweed holobiont Taonia atomaria – B Paix – Environmental Microbiology

Monitoring Microbial Communities in the Marine Environment – Ger van den Engh – Cytometry Part A

Microbes in the news

Evidence for link between ‘leaky gut’ and autoantibody production in HIV-positive patients – Science Daily

Eden Project hosts bacteria filled art exhibition – The Packet

April 05, 2019

Good morning everyone! In today’s microbiome digest, we have multiple research and review articles focusing on the role of microbiome in Prostate Cancer, Breast Cancer, Gastric Cancer, Allergy, Gut-Brain axis, Schizophrenia, Paediatric Crohn’s Disease, Nonalcoholic Fatty Liver Disease, Alveolar Osteitis, Renal Failure, Cholecystokinin Expression, Lipid Metabolism Disorder, Regulation of Blood Pressure and an independent section on Fecal Microbiota Transplantation. Additionally, two very interesting metagenomic studies have discovered specific microbial signature as well as link with choline degradation in the colorectal cancer patients. Enjoy reading.

General microbiome

Reivew: The Human Microbiota and Prostate Cancer: Friend or Foe? – Francesco Massari – Cancers

Microbiome—Microbial Metabolome—Cancer Cell Interactions in Breast Cancer—Familiar, but Unexplored – Edit Miko – Cells

Review: Fighting AMR in the Healthcare Environment: Microbiome-Based Sanitation Approaches and Monitoring Tools – Maria D’Accolti – Molecular Sciences

Gut microbiome

Gut microbial dysbiosis is associated with allergen-specific IgE responses in young children with airway allergies – Chih-Yung Chiu – World Allergy Organization Journal

Review: The gut virome: the ‘missing link’ between gut bacteria and host immunity? – Indrani Mukhopadhya – Therapeutic Advances in Gastroenterology

Regulatory T Cells and Plasmacytoid Dendritic Cells Within the Tumor Microenvironment in Gastric Cancer Are Correlated With Gastric Microbiota Dysbiosis: A Preliminary Study – Zongxin Ling – Frontiers in Immunology

Review: Impact of Different Types of Diet on Gut Microbiota Profiles and Cancer Prevention and Treatment – Rainer J. Klement – Medicina

Review: Glutamatergic Signaling Along The Microbiota-Gut-Brain Axis – Andreina Baj – Molecular Sciences

Investigation of the Gut Microbiome in Patients with Schizophrenia and Clozapine-Induced Weight Gain: Protocol and Clinical Characteristics of First Patient Cohorts –Gorbovskaya I. –  Neuropsychobiology

Review: Sex Differences in Gut Microbiota – Yong Sung Kim – The World Journal of MEN’s HEALTH

The Microbiome in Paediatric Crohn’s Disease—A Longitudinal, Prospective, 
Single-Centre Study – Shivani Kansal – Journal of Crohn’s and Colitis

A gut microbiome signature for cirrhosis due to nonalcoholic fatty liver disease – Cyrielle Caussy – Nature Communications

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation – Andrew Maltez Thomas – Nature Medicine

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer – Jakob Wirbel – Nature Medicine

Ceftriaxone and cefotaxime have similar effects on the intestinal microbiota in human volunteers treated by standard doses regimens – Charles Burdet – Antimicrobial Agents and Chemotherapy

Human respiratory microbiome

Mycobiome Sequencing and Analysis Applied to Fungal Community Profiling of the Lower Respiratory Tract During Fungal Pathogenesis – Lisa R. McTaggart – Frontiers in Microbiology

Reproductive tract microbiome

Identification and evaluation of the microbiome in the female and male reproductive tracts – Rivka Koedooder – Human reproduction update

Skin microbiome

Mast cell recruitment is modulated by hairless skin microbiome – Chia-Chi Wu – The Journal of Allergy and Clinical Immunology

Oral microbiome

A metagenomic study of patients with alveolar osteitis after tooth extraction. A preliminary case-control study – Laura Aguilar-Duran – Clinical Oral Investigations

Animal microbiome / Animal experiments

Interactions Between Commensal Bacteria and Enteric Neurons, via FPR1 Induction of ROS, Increase Gastrointestinal Motility in Mice – Bindu Chandrasekharan – Gastroenterology

Danshen can interact with intestinal bacteria from normal and chronic renal failure rats – Hongdie Cai – Biomedicine and Pharmacotherapy

Review: A place for taxonomic profiling in the study of the coral prokaryotic microbiome – Alejandra Hernandez-Agreda – FEMS Microbiology Letters

Fructose malabsorption induces cholecystokinin expression in the ileum and cecum by changing microbiota composition and metabolism – Xufei Zhang – THE FASEB JOURNAL

Spinach consumption ameliorates the gut microbiota and dislipaemia in rats with diet-induced non-alcoholic fatty liver disease (NAFLD) – Elvira-Torales LI – Food and Functions

Microbial Colonization in Adulthood Shapes the Intestinal Macrophage Compartment – Franziska Schmidt – Journal of Chron’s and Colitis

Feeding modes shape the acquisition and structure of the initial gut microbiota in newborn lambs – Yanliang Bi – Environmental Microbiology

Effects of dietary lipid sources on the intestinal microbiome and health of golden pompano (Trachinotus ovatus) – Cuihong You – Fish & Shellfish Immunology

Gut microbiota characterization and lipid metabolism disorder found in PCB77-treated female mice – Chi Y – Toxicology

Changes of gut microbiota between different weight reduction programs – Belle Yanyu Lin – Surgery for Obesity and Related Diseases

Microbiome-metabolomic analysis of the impact of Zizyphus jujuba cv. Muzao polysaccharides consumption on colorectal cancer mice fecal microbiota and metabolites – Xiaolong Ji – International Journal of Biological Macromolecules

Fecal Microbiota Transplantation

Critical Role of the Interaction Gut Microbiota – Sympathetic Nervous System in the Regulation of Blood Pressure – Marta Toral – Frontiers in Physiology

Faecal microbiota transplantation for the decolonisation of antibiotic-resistant bacteria in the gut: a systematic review and meta-analysis – Vera Tavoukjian – The Journal of Hospital Infection

Prebiotics/Probiotics

Effect of a multistrain probiotic (Lactoflorene®Plus) on inflammatory parameters and microbiota composition in subjects with stress-related symptoms – Sara Soldi – Neurobiology of Stress

Probiotics, prebiotics, and low FODMAP diet for irritable bowel syndrome – What is the current evidence? – Soo Liang Ooi – Complementary Therapies in Medicine

Water and extremophile microbiome

Microbial Community of Saline, Alkaline Lakes in the Nebraska Sandhills Based on 16S rRNA Gene Amplicon Sequence Data – Nicole A. Fiore – Microbiology Resource Announcements

Methods

A Customized At-Home Stool Collection Protocol for Use in Microbiome Studies Conducted in Cancer Patient Populations – Stephanie R. Hogue – Microbial Ecology

Effect of storage and DNA extraction method on 16S rRNA-profiled fecal microbiota in Japanese adults – Yuki Kawada – Journal of Clinical Biochemistry and Nutrition

Bioinformatics

𝑊∗𝑑Wd∗-test: robust distance-based multivariate analysis of variance – Bashir Hamidi – Microbiome

Identification and reconstruction of novel antibiotic resistance genes from metagenomes – Fanny Berglund – Microbiome