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

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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.

March 21, 2019

Happy Spring! Today’s Digest features a megaphylogeny of mushrooms, new papers about the respiratory microbiome, fecal microbiome and metatranscriptomic analysis from nonhuman primates, and the microbial ecology of snow. Bonus: a pick about the first woman to win the Abel Prize.

General Microbiome
Megaphylogeny resolves global patterns of mushroom evolution – Torda Varga – Nature Ecology and Evolution

Fate of CMY-2-encoding plasmids introduced into the human fecal microbiota by exogenous Escherichia coli – Mehreen Anjum – Antimicrobial Agents and Chemotherapy

Review: The impact of indigenous microbes on Parkinson’s disease – Timothy Sampson – Neurobiology of Disease

Pregnancy and Early Life
Michigan cohorts to determine associations of maternal pre-pregnancy body mass index with pregnancy and infant gastrointestinal microbial communities: Late pregnancy and early infancy – Kameron Y. Sugino – PLOS One

Human Respiratory Microbiome
Bacterial and viral respiratory tract microbiota and host characteristics in children with lower respiratory tract infections: a matched case-control study – Wing Ho Man – The Lancet Respiratory Medicine

The Yin and Yang of Streptococcus Lung Infections in Cystic Fibrosis: A Model for Studying Polymicrobial Interactions – Jessie E. Scott – Journal of Bacteriology

The nasal and oropharyngeal microbiomes of healthy livestock workers – Ashley E. Kates – PLOS One

Human Gut Microbiome
Review: Role of SCFAs in gut microbiome and glycolysis for colorectal cancer therapy – Gang Wang – Journal of Cellular Physiology

Review: Obesity, Motility, Diet, and Intestinal Microbiota—Connecting the Dots – Maya Fayfman – Current Gastroenterology Reports

Review: The gut microbiome and response to immune checkpoint inhibitors: preclinical and clinical strategies – Jun Gong – Clinical and Translational Medicine

The exosome secretion inhibitor neticonazole suppresses intestinal dysbacteriosis-induced tumorigenesis of colorectal cancer – Lei Gu – Investigational New Drugs

Glutamate interactions with obesity, insulin resistance, cognition and gut microbiota composition – María Encarnación Palomo-Buitrago – Acta Diabetologica

Understanding the gut–kidney axis among biopsy-proven diabetic nephropathy, type 2 diabetes mellitus and healthy controls: an analysis of the gut microbiota composition – Sibei Tao – Acta Diabetologica

Identification of the microbial diversity after fecal microbiota transplantation therapy for chronic intractable constipation using 16s rRNA amplicon sequencing – Tadashi Ohara – PLOS One

Animal Experiments
Gut microbiota from infant with Cow’s Milk Allergy promotes clinical and immune features of atopy in a murine model – A. Mauras – Allergy

N-(1-carbamoyl-2-phenylethyl) butyramide reduces antibiotic-induced intestinal injury, innate immune activation and modulates microbiota composition – Adriano Lama – Scientific Reports

Immunosuppression-induced alterations in fish gut microbiota may increase the susceptibility to pathogens – Xiao-Zhou Qi – Fish & Shellfish Immunology

Rifaximin Alters Intestinal Microbiota and Prevents Progression of Ankylosing Spondylitis in Mice – Lianjun Yang – Frontiers in Cellular and Infection Microbiology

Hydroxytyrosol Improves Obesity and Insulin Resistance by Modulating Gut Microbiota in High-Fat Diet-Induced Obese Mice – Zhuoqun Liu – Frontiers in Microbiology

Review: Dietary Fiber and Intestinal Health of Monogastric Animals – Rajesh Jha – Frontiers in Veterinary Science

Circadian disruption and divergent microbiota acquisition under extended photoperiod regimens in chicken – Anne-Sophie Charlotte Hieke – PeerJ

Animal Microbiome
Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization – Samuel T. Westreich – Microbiome

Microbiome Profiles of Ligature-Induced Periodontitis in Nonhuman Primates Across the Lifespan – Sreenatha Kirakodu – Infection and Immunity

Diabetic cats have decreased gut microbial diversity and a lack of butyrate producing bacteria – Ida Nordang Kieler – Scientific Reports

Exploring the bacteriome in anthropophilic ticks: To investigate the vectors for diagnosis – Aránzazu Portillo – PLOS One

Plant, Root, and Soil Microbiome
Microbiota in Non-flooded and Flooded Rice Culms – Hui-Ling Cui – FEMS Microbiology Ecology

Microbial community structure in full scale anaerobic mono-and co-digesters treating food waste and animal waste – Taewoan Koo – Bioresource Technology

Variations in pH significantly affect cadmium uptake in grafted muskmelon (Cucumis melo L.) plants and drive the diversity of bacterial communities in a seedling substrate – Jian Zhang – Plant Physiology and Biochemistry

Divergent microbial communities in groundwater and overlying soils exhibit functional redundancy for plant-polysaccharide degradation – Martin Taubert – PLOS One

Microbial diversity and soil physiochemical characteristic of higher altitude – Saurabh Kumar – PLOS One

Water and Extremophile Microbiome
Microbial Ecology of Snow Reveals Taxa-Specific Biogeographical Structure – Shawn P. Brown – Microbial Ecology

Bacterial community in cold and alkaline environments of Hoh Xil basin in Qinghai–Tibet Plateau and isolation of potential sources of microbiota – Rui Xing – Annals of Microbiology

Bacterial communities of the microbial mats of Chokrak sulfide springs – Ekaterina I. Burganskaya – Archives of Microbiology

Dynamics of microbial community in the bioreactor for bisphenol S removal – Wen-Cong Huang – Science of the Total Environment

High-throughput DNA sequencing reveals the dominance of pico- and other filamentous cyanobacteria in an urban freshwater Lake – Hanyan Li – Science of the Total Environment

A novel phenol and ammonia recovery process for coal gasification wastewater altering the bacterial community and increasing pollutants removal in anaerobic/anoxic/aerobic system – Xuefei Gui – Science of the Total Environment

Built Environment
Biodeterioration of mortar coating in historical buildings: Microclimatic characterization, material, and fungal community – Fernanda L. Guerra – Building and Environment

A different suite: The assemblage of distinct fungal communities in water-damaged units of a poorly-maintained public housing building – Iman A. Sylvain – PLOS One

Microbes in Space
Subsurface Microbial Habitats in an Extreme Desert Mars-Analog Environment – Kimberley A. Warren-Rhodes – Frontiers in Microbiology

Food Microbiology
Microbiome patterns reveal the transmission of pathogenic bacteria in hilsa fish (Tenualosa ilisha) marketed for human consumption in Bangladesh – Md Javed Foysal – Journal of Applied Microbiology

Impact of turning, pod storage and fermentation time on microbial ecology and volatile composition of cocoa beans – Yasmine Hamdouche – Food Research International

Probiotic potential of a Lactobacillus rhamnosus cheese isolate and its effect on the fecal microbiota of healthy volunteers – Joaquin Bautista-Gallego – Food Research International

Dynamics of biogenic amines and bacterial communities in a Thai fermented pork product Nham – Pannita Santiyanont – Food Research International

Probiotics/Prebiotics
16S rRNA gene profiling and genome reconstruction reveal community metabolic interactions and prebiotic potential of medicinal herbs used in neurodegenerative disease and as nootropics – Christine Tara Peterson – PLOS One

Phages and Viruses
Review: Phage therapy: What factors shape phage pharmacokinetics and bioavailability? Systematic and critical review – Krystyna Dąbrowska – Medicinal Research Reviews

Bioinformatics
MetaPheno: A Critical Evaluation of Deep Learning and Machine Learning in Metagenome-Based Disease Prediction – Nathan LaPierre – Methods

Assessing alignment-based taxonomic classification of ancient microbial DNA – Raphael Eisenhofer – PeerJ

Techniques
A comparison of storage methods for gut microbiome studies in teleosts: Insights from rainbow trout (Oncorhynchus mykiss) – Mathis Hildonen – Journal of Microbiological Methods

Alyson’s Non-Microbiology Picks
Soap-bubble pioneer is first woman to win prestigious maths prize

Girls who share a womb with boys tend to make less money than those with twin sisters

 

March 17, 2019

Have a good sunday! Today, we have a quite long digest, containing a variety of articles and studies: reviews about the microbiome and breastfeeding and Parkinson’s disease; microbiota alterations in pulmonary fibrosis, association with stress in pregnant women, and relationships between oral microbiome and pancreatic cancer. And so much more!

 

Human/General Microbiome

Review: Microbiome programming of brain development: implications for neurodevelopmental disorders – Hans Forssberg – Developmental Medicine and Child Neurology

Review: Microbiome, Parkinson’s Disease and Molecular Mimicry – Fabiana Miraglia – Cells

Review: The Use of Defined Microbial Communities To Model Host-Microbe Interactions in the Human Gut – Janneke Elzinga – Microbiology and Molecular Biology Reviews

Review: Indoles: metabolites produced by intestinal bacteria capable of controlling liver disease manifestation – T. Hendrikx – Journal of Internal Medicine

Review: Shaping the Gut Microbiota by Breastfeeding: The Gateway to Allergy Prevention? – Lieke W. J. van den Elsen – Frontiers in Pediatrics

Minireview: Nonalcoholic fatty liver disease and the gut microbiome: Are bacteria responsible for fatty liver? – Tien S Dong – Experimental Biology and Medicine

Perspectives: Is the fountain of youth in the gut microbiome?John F. Cryan – The Journal of Physiology

Bugs to debug? The exploration of gut microbiome in human health and diseases – Yen-Hsuan Ni – Journal of the Formosan Medical Association

Impact of a bathing tradition on shared gut microbe among Japanese families – Toshitaka Odamaki – Scientific Reports

Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome – Promi Das – BMC Genomics

Fecal and blood microbiota profiles and presence of nonalcoholic fatty liver disease in obese versus lean subjects – Yeojun Yun – PLoS One

H. pylori eradication with antibiotic treatment causes changes in glucose homeostasis related to modifications in the gut microbiota – Gracia Mª Martín-Núñez – PLoS One

Oral microbial dysbiosis in patients with Kostmann syndrome – Nursen Topcuoglu – Journal of Medical Microbiology

Alterations in the gut microbiota of patients with silica-induced pulmonary fibrosis – Yao Zhou – Journal of Occupational Medicine and Toxicology

Association between Psychosocial Stress and Fecal Microbiota in Pregnant Women – C. Hechler – Scientific Reports

Differential composition of gut microbiota among healthy volunteers, morbidly obese patients and post-bariatric surgery patients – Fu‑Gang Wang – Experimental and Therapeutic Medicine

Role of Fecal Microbiota Transplantation for Maintenance of Remission in Patients with Ulcerative Colitis: A Pilot Study – Ajit Sood – Journal of Crohn’s and Colitis

Differential effects of depot medroxyprogesterone acetate administration on vaginal microbiome in Hispanic White and Black women – Liying Yang – Emerging Microbes & Infections

Spatial and Temporal Analysis of the Stomach and Small-Intestinal Microbiota in Fasted Healthy Humans – Anna M. Seekatz – mSphere

Persistence of Candida albicans in the Oral Mucosa Induces a Curbed Inflammatory Host Response That Is Independent of Immunosuppression – Florian R. Kirchner – Frontiers in Immunology

Enrichment of oral microbiota in early cystic precursors to invasive pancreatic cancer – Rogier Aäron Gaiser – Gut

Disordered intestinal microbes are associated with the activity of Systemic Lupus Erythematosus – Yao Li – Clinical Science

Long-Term Azithromycin Reduces Haemophilus influenzae and Increases Antibiotic Resistance in Severe Asthma – Steven L Taylor – American Journal of Respiratory and Critical Care Medicine

Dietary Nutrients Involved in One-Carbon Metabolism and Colonic Mucosa-Associated Gut Microbiome in Individuals with an Endoscopically Normal Colon – Shawn Gurwara – Nutrients

Analysis of the Effects of Dietary Pattern on the Oral Microbiome of Elite Endurance Athletes – Nida Murtaza – Nutrients

 

Animal Microbiome / Animal Experiments

TLR4 May Be Involved in the Regulation of Colonic Mucosal Microbiota by Vitamin A – Lu Xiao – Frontiers in Microbiology

Tunicate-associated bacteria show a great potential for the discovery of antimicrobial compounds – Diah Ayuningrum – PLoS One

Effects of Arsenic on Gut Microbiota and Its Biotransformation Genes in Earthworm Metaphire sieboldi – Hong-Tao Wang – Environmental Science and Technology

A metagenomics investigation of carbohydrate-active enzymes along the goat and camel intestinal tract – Saad Al-Masaudi – International Microbiology

Species identity dominates over environment in shaping the microbiota of small mammals – S. C. L. Knowles – Ecology Letters

Three types of gut bacteria collaborating to improve Kui Jie’an enema treat DSS-induced colitis in mice – Wei Yu – Biomedicine & Pharmacotherapy

The Skin Commensal Yeast Malassezia Triggers a Type 17 Response that Coordinates Anti-fungal Immunity and Exacerbates Skin Inflammation – Florian Sparber – Cell Host Microbe

Dietary inulin alleviates diverse stages of type 2 diabetes mellitus via anti-inflammation and modulating gut microbiota in db/db mice – Ke Li – Food & Function

Apple consumption is associated with a distinctive microbiota, proteomics and metabolomics profile in the gut of Dawley Sprague rats fed a high-fat diet – Jose F. Garcia-Mazcorro – PLoS One

Sema3A – mediated modulation of NR1D1 expression may be involved in the regulation of axonal guidance signaling by the microbiota – Xunzhong Qia – Life Sciences

Multi-hit early life adversity affects gut microbiota, brain and behavior in a sex-dependent manner – Marion Rincel – Brain, Behavior, and Immunity

Letrozole treatment of adult female mice results in a similar reproductive phenotype but distinct changes in metabolism and the gut microbiome compared to pubertal mice – Pedro J. Torres – BMC Microbiology

Supplementation of dietary non-digestible oligosaccharides from birth onwards improve social and reduce anxiety-like behaviour in male BALB/c mice – Kirsten Szklany – Nutritional Neuroscience

Potential Functions of the Gastrointestinal Microbiome Inhabiting the Length of the Rat Digest Tract – Dongyao Li – International Journal of Molecular Sciences

Alteration of GLP-1/GPR43 expression and gastrointestinal motility in dysbiotic mice treated with vancomycin – Xin Xu – Scientific Reports

Subchronic low-dose 2,4-D exposure changed plasma acylcarnitine levels and induced gut microbiome perturbations in mice – Pengcheng Tu – Scientific Reports

The influence of the host microbiome on 3,4-methylenedioxymethamphetamine (MDMA)-induced hyperthermia and vice versa – Emily A. Ridge – Scientific Reports

Effects of Dietary Supplementation With Enterococcus faecium and Clostridium butyricum, Either Alone or in Combination, on Growth and Fecal Microbiota Composition of Post-weaning Pigs at a Commercial Farm – Yoshiaki Sato – Frontiers in Veterinary Science

Saponin-Induced Shifts in the Rumen Microbiome and Metabolome of Young Cattle – Bing Wang – Frontiers in Microbiology

Intestinal dysbiosis augments liver disease progression via NLRP3 in a murine model of primary sclerosing cholangitis – Lijun Liao – Gut

 

Plant Microbiome

Long-Term Organic Farming Manipulated Rhizospheric Microbiome and Bacillus Antagonism Against Pepper Blight (Phytophthora capsici) – Huixiu Li – Frontiers in Microbiology

 

Other Microbes

Preview: Strain-Level Diversity in the Gut: The P. copri Case  – Amira Metwaly – Cell Host Microbe

 

Bioinformatics and ‘-Omics’

Novel insights from uncultivated genomes of the global human gut microbiome – Stephen Nayfach – Nature

Complex Microbiome in Brain Abscess Revealed by Whole-Genome Culture-Independent and Culture-Based Sequencing – Jyun-Hong Lin – Journal of Clinical Medicine

Detection of critical antibiotic resistance genes through routine microbiome surveillance – Zachary M. Burcham – PLoS One

MNEMONIC: MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations – Aleksandra I. Perz – BMC Bioinformatics

Rarity of microbial species: In search of reliable associations – Arnaud Cougoul – PLoS One

Stoplight: De novo Assembly Vastly Expands the Known Microbial Universe – Samuel S. Minot – Trends in Microbiology

 

Beneficial Microbes and Compounds

Guarana supplementation attenuated obesity, insulin resistance, and adipokines dysregulation induced by a standardized human Western diet via brown adipose tissue activation Rafael Calixto Bortolin – Phytotherapy Research

Prebiotic supplementation in frail older people affects specific gut microbiota taxa but not global diversity – Tam T. T. Tran – Microbiome

 

Water Microbiome

Composition and Dynamics of the Activated Sludge Microbiome during Seasonal Nitrification Failure – Juliet Johnston – Scientific Reports

 

March 14, 2019

Today’s digest covers interesting reviews on microbiota for immunotherapies, non-digestible carbohydrates for infant microbiota and contribution of marine microbiota in reactive oxygen species; research articles on how gluten sensitivity is affected by duodenal microbiota and how ginger intake affects mouse microbiota.

General microbiome

Review: Mining the microbiota for microbial and metabolite-based immunotherapies – Ashwin N. Skelly – Nature Reviews Immunology

Pregnancy and early life microbiome

Relationship between vitamin D status and the vaginal microbiome during pregnancy – Kimberly K. Jefferson – Journal of Perinatology

Review: Shaping the Infant Microbiome With Non-Digestible Carbohydrates – Stella A. Verkhnyatskaya – Frontiers in Microbiology

Variations in early gut microbiome are associated with childhood eczema – Yu Zhang – FEMS Microbiology Letters

Human gut microbiome

Gut microbiota in HIV–pneumonia patients is related to peripheral CD4 counts, lung microbiota, and in vitro macrophage dysfunction – Meera K. Shenoy – Microbiome

Effects of bowel preparation on the human gut microbiome and metabolome – Naoyoshi Nagata – Scientific Reports

Human colon mucosal biofilms from healthy or colon cancer hosts are carcinogenic – Sarah Tomkovich – The Journal of Clinical Investigation

Animal experiments

Host NLRP6 exacerbates graft-versus-host disease independent of gut microbial composition – Tomomi Toubai – Nature Microbiology

Duodenal bacterial proteolytic activity determines sensitivity to dietary antigen through protease-activated receptor-2 – Alberto Caminero – Nature Communications

The dynamics of the antibiotic resistome in the feces of freshly weaned pigs following therapeutic administration of oxytetracycline – Mahdi Ghanbari – Scientific Reports

Beneficial effects of ginger on prevention of obesity through modulation of gut microbiota in mice – Jing Wang – European Journal of Nutrition

Six‐Week High‐Fat Diet Alters the Gut Microbiome and Promotes Cecal Inflammation, Endotoxin Production, and Simple Steatosis without Obesity in Male Rats – Melisa Crawford – Lipids

Gut microbiome structure and adrenocortical activity in dogs with aggressive and phobic behavioral disorders – Elisabetta Mondo – BioRxiv

The gut microbiota regulates mouse biliary regenerative responses – Wenli Liu – BioRxiv

Plant, root, soil microbiome

Consistent bacterial selection by date palm root system across heterogeneous desert oasis agroecosystems – Maria J. Mosqueira – Scientific Reports

Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments – Adam J. Kessler – Nature Microbiology

Effects of graphene oxide and graphite on soil bacterial and fungal diversity – Christian Forstner – BioRxiv

Water microbiome and extremophiles

Review: The microbial contribution to reactive oxygen species dynamics in marine ecosystems – Erik R. Zinser – Environmental Microbiology Reports

Non-microbiology picks

Nano-bot can probe inside human cells – Science Daily

March 11, 2019

To start off the week, here’s a rundown of new papers, including how symbiotic Vibrio signals drive squid gene expression, the intergenerational fur seal microbiome, and a few food microbiology studies on kimchi and pasta. Happy reading!

Pregnancy and Early Life
Review: Neonatal microbiome – a brief review – Anchala Singh – The Journal of Maternal-Fetal & Neonatal Medicine

Feeding practice influences gut microbiome composition in very low birth weight preterm infants and the association with oxidative stress: A prospective cohort study – Chenxi Cai – Free Radical Biology and Medicine

Human Skin Microbiome
Commensal Staphylococci Influence Staphylococcus aureus Skin Colonization and Disease – Corey P. Parlet – Trends in Microbiology

Human Oral Microbiome
No differences in microbiome changes between anti-adhesive and antibacterial ingredients in toothpastes during periodontal therapy – Daniel Hagenfeld – Journal of Periodontal Research

Human Gut Microbiome
Endocytosis of commensal antigens by intestinal epithelial cells regulates mucosal T cell homeostasis – Mark S. Ladinsky – Science

Review: Mendelian randomization reveals causal effects of the gut microbiota – Hugh Thomas – Nature Reviews Gastroenterology & Hepatology

Association Between Antibiotics in the First Year of Life and Celiac Disease – Stine Dydensborg Sander – Gastroenterology

Daiokanzoto (Da-Huang-Gan-Cao-Tang) is an effective laxative in gut microbiota associated with constipation – Kento Takayama – Scientific Reports

Dietary raisin intake has limited effect on gut microbiota composition in adult volunteers – Akemi T. Wijayabahu – Nutrition Journal

Early gut microbiota signature of aGvHD in children given allogeneic hematopoietic cell transplantation for hematological disorders – Elena Biagi – BMC Medical Genomics

Fecal Calprotectin and Fecal Indole Predicts Outcome of Fecal Microbiota Transplantation in Subjects with Recurrent Clostridium difficile Infection – J. Hibbard – Anaerobe

Gut microbiota-stimulated cathepsin K secretion mediates TLR4-dependent M2 macrophage polarization and promotes tumor metastasis in colorectal cancer – Rui Li – Cell Death & Differentiation

Alterations in bacterial communities, SCFA and biomarkers in an elderly HIV-positive and HIV-negative population in western Mexico – Luz A. González-Hernández – BMC Infectious Diseases

RA and the microbiome: do host genetic factors provide the link? – Philippa M. Wells – Journal of Autoimmunity

The Gut Microbiota in Causation, Detection, and Treatment of Cancer – Clodagh Murphy – The American Journal of Gastroenterology

Gut-Brain Axis
From Infection to the Microbiome: An Evolving Role of Microbes in Schizophrenia – Emily G. Severance – Current Topics in Behavioral Neurosciences

Animal Experiments
Critical symbiont signals drive both local and systemic changes in diel and developmental host gene expression – Silvia Moriano-Gutierrez – PNAS

Different host-specific responses in thyroid function and gut microbiota modulation between diet-induced obese and normal mice given the same dose of iodine – Huiting Shen – Applied Microbiology and Biotechnology

Antibiotic treatment affects the expression levels of copper transporters and the isotopic composition of copper in the colon of mice – Kerri A. Miller – PNAS

Protective effect of prebiotic and exercise intervention on knee health in a rat model of diet-induced obesity – Jaqueline Lourdes Rios – Scientific Reports

Chlorogenic acid alleviates obesity and modulates gut microbiota in high-fat-fed mice – Zhengyu Wang – Food Science & Nutrition

Crucial Role of Microbiota in Experimental Psoriasis Revealed by a Gnotobiotic Mouse Model – Zuzana Stehlikova – Frontiers in Microbiology

Parasitoid envenomation alters the Galleria mellonella midgut microbiota and immunity, thereby promoting fungal infection – Olga V. Polenogova – Scientific Reports

Nutritional Interventions Improved Rumen Functions and Promoted Compensatory Growth of Growth-Retarded Yaks as Revealed by Integrated Transcripts and Microbiome Analyses – Rui Hu – Frontiers in Microbiology

Animal Microbiome
Fur seal microbiota are shaped by the social and physical environment, show mother-offspring similarities and are associated with host genetic quality – Stefanie Grosser – Molecular Ecology

Intensity of Nosema ceranae infection is associated with specific honey bee gut bacteria and weakly associated with gut microbiome structure – Andrey Rubanov – Scientific Reports

Characterizing the microbiota in gastrointestinal tract segments of Rhabdophis subminiatus: Dynamic changes and functional predictions – Wenjiao Tang – MicrobiologyOpen

Studying the microbiota of bats: Accuracy of direct and indirect samplings – Muriel Dietrich – Ecology and Evolution

A cellulolytic fungal biofilm enhances the consolidated bioconversion of cellulose to short chain fatty acids by the rumen microbiome – Charilaos Xiros – Applied Microbiology and Biotechnology

Plant, Root, and Soil Microbiome
Changes in the soil microbial community are associated with the occurrence of Panax quinquefolius L. root rot diseases – Jinglong Jiang – Plant and Soil

Metagenomic analysis reveals distinct patterns of denitrification gene abundance across soil moisture, nitrate gradients – Sarah A. Nadeau – Environmental Microbiology

Divergent national-scale trends of microbial and animal biodiversity revealed across diverse temperate soil ecosystems – Paul B. L. George – Nature Communications

Impact of Wuyiencin Application on the Soil Microbial Community and Fate of Typical Antibiotic Resistance Genes – Liming Shi – Scientific Reports

Airborne microbial transport limitation to isolated Antarctic soil habitats – Stephen D. J. Archer – Nature Microbiology

Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots – Samiran Banerjee – ISMEJ

Biochars reduced the bioaccessibility and (bio)uptake of organochlorine pesticides and changed the microbial community dynamics in agricultural soils -Neelum Ali – Chemosphere

Molecular identification and biocontrol activity of sugarcane rhizosphere bacteria against red rot pathogen Colletotrichum falcatum – Prittesh Patel – Biotechnology Reports

Natural and assisted dissipation of polycyclic aromatic hydrocarbons in a long-term co-contaminated soil with creosote and potentially toxic elements
F.Madrid – Science of The Total Environment

Horizontal gene transfer and shifts in linked bacterial community composition are associated with maintenance of antibiotic resistance genes during food waste composting – Hanpeng Liao – Science of The Total Environment

Sedimentary Marl mudstone as a substrate in a xeric environment revealed by microbiome analysis – Oksana Koryachenko – Extremophiles

Water and Extremophile Microbiome
Drivers of Regional Bacterial Community Structure and Diversity in the Northwest Atlantic Ocean – Jackie Zorz – Frontiers in Microbiology

Microbial community composition in alpine lake sediments from the Hengduan Mountains – Binqiang Liao – MicrobiologyOpen

Stepwise pH control to promote synergy of chemical and biological processes for augmenting short-chain fatty acid production from anaerobic sludge fermentation – Xu Wang – Water Research

Food Microbiology
Effects of the supplementation of plant-based formulations on microbial fermentation and predicted metabolic function in vitro – Renée Maxine Petri – Anaerobe

Effects of functional pasta ingredients on different gut microbiota as revealed by TIM-2 in vitro model of the proximal colon – A. Martina – Beneficial Microbes

Effect of pasteurization on delayed kimchi ripening and regression analysis for shelf life estimation of kimchi – Hyun‐Gyu Lee – Food Science & Nutrition

Optimization on production of konjac oligo‐glucomannan and their effect on the gut microbiota – Catarina Aprilia Ariestanti – Food Science & Nutrition

Probiotics
Mechanisms and immunomodulatory properties of pre- and probiotics – V.B.M. Peters – Beneficial Microbes

Wild bacterial probiotics fed to larvae of mass-reared Queensland fruit fly [Bactrocera tryoni (Froggatt)] do not impact long-term survival, mate selection or locomotor activity – Lucas A. Shuttleworth – Insect Science

Bioinformatics
Web-gLV: A Web Based Platform for Lotka-Volterra Based Modeling and Simulation of Microbial Populations – Bhusan K. Kuntal – Frontiers in Microbiology

Techniques
PCR effects of melting temperature adjustment of individual primers in degenerate primer pools – Ankur Naqib -PeerJ

Review: Combinatory biotechnological intervention for gut microbiota – Ishu Khangwal – Applied Microbiology and Biotechnology

March 4, 2019

Human Microbiome

Polyamines and microbiota in bicuspid and tricuspid aortic valve aortopathy – Amalia Forte – Journal of Molecular and Cellular Cardiology

Targeting the Gut Microbiota to Investigate the Mechanism of Lactulose in Negating the Effects of a High-Salt Diet on Hypertension – Zheng Zhang – Molecular Nutrition and Food Research

Food allergy: could the gut microbiota hold the key? – Supinda Bunyavanich – Nature Reviews Gastroenterology & Hepatology

The gut mycobiota: insights into analysis, environmental interactions and role in gastrointestinal diseases – Mathias L. Richard – Nature Reviews Gastroenterology & Hepatology

Type VI Secretion Systems and the Gut Microbiota –  Michael J. Coyne – Microbiology Spectrum

Autism Spectrum Disorders and the Gut Microbiota – Antonella Fattorusso – Nutrients

New Approaches to Detect Biosynthetic Gene Clusters in the Environment – Ray Chen – Medicines

Impact of microbiota on central nervous system and neurological diseases: the gut-brain axis – Qianquan Ma – Journal of Neuroinflammation

Dysregulated Lung Commensal Bacteria Drive Interleukin-17B Production to Promote Pulmonary Fibrosis through Their Outer Membrane Vesicles – Daping Yang – Immunity

Altered gut microbiome after bariatric surgery and its association with metabolic benefits: A systematic review – Naomi K. Davies – Surgery for Obesity and Related Diseases

Trimethylamine N-oxide, Mediterranean diet, and nutrition in healthy, normal-weight adults: also a matter of sex? – Luigi Barrea – Nutrition

The composition of the pulmonary microbiota in sarcoidosis – an observational study – André Becker – Respiratory Research

Emerging trends and research foci in gastrointestinal microbiome – Xiaoquan Huang – Journal of Translational Medicine

Updates on Clostridioides (Clostridium) difficile Infection With Emphasis on Long-Term Care – Eddie Grace –  The Senior Care Pharmacist

 

Animal Microbiome

Host genetics and diet composition interact to modulate gut microbiota and predisposition to metabolic syndrome in spontaneously hypertensive stroke-prone rats – Arashdeep Singh – The FASEB Journal

Comparative effects of n-hexane and methanol extracts of elecampane (Inula helenium L.) rhizome on growth performance, carcass traits, feed digestibility, intestinal antioxidant status and ileal microbiota in broiler chickens – Mirza-Ebrahim Abolfathi – Archives of Animal Nutrition

Comparison of the Gut Microbiota Composition between the Wild and Captive Tibetan Wild Ass (Equus kiang) – Hongmei Gao – Journal of Applied Microbiology

Consumption of drinking water N-Nitrosamines mixture alters gut microbiome and increases the obesity risk in young male rats – Jianqiang Zhu – Environmental Pollution

Modularity and predicted functions of the global sponge-microbiome network – Miguel Lurgi – Nature Communications

Relative abundance of Akkermansia spp. and other bacterial phylotypes correlates with anxiety- and depressive-like behavior following social defeat in mice – Kara D. McGaughey – Scientific Report

Loading ceftriaxone, vancomycin, and Bifidobacteria bifidum TMC3115 to neonatal mice could differently and consequently affect intestinal microbiota and immunity in adulthood – RuYue Cheng – Scientific Report

Dietary Protein Intake Level Modulates Mucosal Healing and Mucosa-Adherent Microbiota in Mouse Model of Colitis – Sandra Vidal-Lletjós – Nutrients

Farm stage, bird age and body site dominantly affect the quantity, taxonomic composition, and dynamics of respiratory and gut microbiota of commercial layer chickens – John M. Ngunjiri – Applied and Environmental Microbiology

Development and Function of the Intestinal Microbiome and Potential Implications for Pig Production – Tanya L. Nowland – Animals

Green Coffee Extract Improves Cardiometabolic Parameters and Modulates Gut Microbiota in High-Fat-Diet-Fed ApoE-/- Mice – Erika Caro-Gómez – Nutrients

Dysbiosis of the Gut Microbiota on the Inflammatory Background due to Lack of Suppressor of Cytokine Signalling-1 in Mice – Y. Gendo – Inflammatory Intestinal Diseases

 

Beneficial Microbes and Compounds

Prebiotic supplementation of in vitro faecal fermentations inhibits proteolysis by gut bacteria and host diet shapes gut bacterial metabolism and response to intervention – Xuedan Wang – Applied and Environmental Microbiology

Probiotics and Colon Cancer – Lorenzo Drago – Microorganisms

The Therapeutic Implications of the Gut Microbiome and Probiotics in Patients with NAFLD – Brandon J. Perumpail – Diseases

Cranberry Polyphenols: Natural Weapons against Dental Caries – Nebu Philip – Dentistry Journal

Dietary Components That May Influence the Disturbed Gut Microbiota in Chronic Kidney Disease – Denise Mafra – Nutrients

Liposomal Irinotecan for Treatment of Colorectal Cancer in a Preclinical Model – Jiao-Ren Huang – Cancers

Effects of acupuncture in treating insomnia due to spleen-stomach disharmony syndrome and its influence on intestinal microbiome: Study protocol for a randomized controlled trial –  Ya-ru Huangfu – Journal of Integrative Medicine

Patient perception and approval of faecal microbiota transplantation (FMT) as an alternative treatment option for obesity – F. Gundling – Obesity Science and Practice

 

Water Microbiome

Bacterial release from pipe biofilm in a full-scale drinking water distribution system – Sandy Chan – npj Biofilms and Microbiomes

 

Plant Microbiome

The tea leaf microbiome shows specific responses to chemical pesticides and biocontrol applications – Tomislav Cernava – Science of The Total Environment

Algae bacteria interactions that balance the planktonic microbiome – Emilio Cirri – New Phytologist

 

Bioinformatics

VERA: agent-based modeling transmission of antibiotic resistance between human pathogens and gut microbiota – Oksana E Glushchenko – Bioinformatics

CRISPRs for Strain Tracking and Their Application to Microbiota Transplantation Data Analysis – Tony J. Lam – The CRISPR Journal

 

Other

Impact of primary carbon sources on microbiome shaping and biotransformation of pharmaceuticals and personal care products – Karen Rossmassler – Biodegradation

GrgA as a potential target of selective antichlamydials – Huirong Zhang – PLoS ONE

Quenching by sodium thiosulfate does not influence 16S rRNA gene sequencing profiles of reclaimed water from three sites in the Mid-Atlantic, United States – Sarah M.Allard – Environmental Research