Category Archives: Waste and pollution

March 17, 2019

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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 12, 2019

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Today’s Digest casts a wide net with focuses on antibiotic resistance , human gut microbiome and microbiome in extreme environments. Highlights include a review on fungi in the marine environment, a report on gut mucosal virome alterations in ulcerative colitis and finally, sleep well!

General microbiology

Review: Transcription in cyanobacteria: a distinctive machinery and putative mechanisms – Amber Riaz-Bradley – Biochemical Society Transactions

Preprint: How sample heterogeneity can obscure the signal of microbial interactions – David W. Armitage & Stuart E. Jones – bioRxiv

Behavioral heterogeneity in quorum sensing can stabilize social cooperation in microbial populations – Kelei Zhao et al. – BMC Biology

Antibiotic resistance

Antimicrobial photodynamic activity of toluidine blue encapsulated in mesoporous silica nanoparticles against Pseudomonas aeruginosa and Staphylococcus aureus – Paramanantham Parasuraman et al. – Biofouling

Metaphire guillelmi gut as hospitable micro-environment for the potential transmission of antibiotic resistance genes – Huizhen Chao et al. – Science of The Total Environment

Abundance of antibiotic resistance genes and their association with bacterial communities in activated sludge of wastewater treatment plants: Geographical distribution and network analysis – Haihan Zhang et al. – Journal of Environmental Sciences

Cationic Intrinsically Disordered Antimicrobial Peptides (CIDAMPs) Represent a New Paradigm of Innate Defense with a Potential for Novel Anti-Infectives – Ties Latendorf et al. – Scientific Reports

Preprint: Bacterial interspecies interactions modulate pH-mediated antibiotic tolerance in a model gut microbiota – Andres Aranda-Diaz et al. – bioRxiv

Human oral microbiome

** Sleep deprivation and a non–24-h working schedule lead to extensive alterations in physiology and behavior – Huan Ma et al. – FASEB J

Human gut microbiome

Review: Microbe-metabolite-host axis, two-way action in the pathogenesis and treatment of human autoimmunity – Xiang Meng et al. – Autoimmunity Reviews

Pearls: Bile salt hydrolases: Gatekeepers of bile acid metabolism and host-microbiome crosstalk in the gastrointestinal tract – Matthew H. Foley et al. – PLoS Pathogens

Review: Biomarkers for Immune Therapy in Gastrointestinal Cancers – Benjamin A. Weinberg et al. – Clinical Advances in Hematology & Oncology

Microbiota Diversity in Human Colorectal Cancer Tissues Is Associated with Clinicopathological Features – Yaxin Wu et al. – Nutrition and Cancer

Review: The microbiome, cancer, and cancer therapy – Beth A. Helmink et al. – Nature Medicine

Correlations of the Gastric and Duodenal Microbiota with Histological, Endoscopic, and Symptomatic Gastritis – Hye Seung Han et al. – Journal of Clinical Medicine

Gut-microbe-braint axis

Research Highlight: Depression linked to the microbiome – Hannah Stower – Nature Medicine

Animal experiments

Differential Sensitivity to Plasmodium yoelii Infection in C57BL/6 Mice Impacts Gut-Liver Axis Homeostasis – Joshua E. Denny et al. – Scientific Reports

Metabolic footprint and intestinal microbial changes in response to dietary proteins in a pig model – Alexandra Schutkowski et al. – Journal of Nutritional Biochemistry

Alterations of Bile Acids and Gut Microbiota in Obesity Induced by High Fat Diet in Rat Model – Hong Lin et al. – Journal of Agricultural and Food Chemistry

Effects of lifelong intake of lemon polyphenols on aging and intestinal microbiome in the senescence-accelerated mouse prone 1 (SAMP1) – Chikako Shimizu et al. – Scientific Reports

Effect of green tea and mulberry leaf powders on the gut microbiota of chicken – Yuan Chen et al. – BMC Veterinary Research

Animal microbiome

Fiddler crab bioturbation determines consistent changes in bacterial communities across contrasting environmental conditions – Jenny Marie Booth & Marco Fusi et al. – Scientific Reports

Plant, root and soil microbiome

Hypotheses: Application of filamentous phages in environment: A tectonic shift in the science and practice of ecorestoration – Radhey Shyam Sharma et al. – Ecology and Evolution

Native and Invading Yellow Starthistle (Centaurea solstitialis) Microbiomes Differ in Composition and Diversity of Bacteria – Patricia Lu-Irving et al. – mSphere

Small molecule reaction networks that model the ROS dynamics of the rhizosphere – Olga Taran et al. – Chemical Communications

Soil HONO emissions at high moisture content are driven by microbial nitrate reduction to nitrite: tackling the HONO puzzle – Dianming Wu et al. – The ISME Journal

Evidence of within-species specialization by soil microbes and the implications for plant community diversity – Jenalle L. Eck et al. – PNAS

Effects of four years of elevated ozone on microbial biomass and extracellular enzyme activities in a semi-natural grassland – Jinyang Wang et al. – Science of The Total Environment

Water and extremophile microbiome

Surveying of acid-tolerant thermophilic lignocellulolytic fungi in Vietnam reveals surprisingly high genetic diversity – Vu Nguyen Thanh et al. – Scientific Reports

Radioactive environment adapted bacterial communities constituting the biofilms of hydrothermal spring caves (Budapest, Hungary) – Nóra Tünde Enyedi et al. – Journal of Environmental Radioactivity

COD/sulfate ratio does not affect the methane yield and microbial diversity in anaerobic digesters – Zeynep Cetecioglu et al. – Water Research

** Review: Fungi in the Marine Environment: Open Questions and Unsolved Problems – Anthony Amend et al. – mBio

Holocene paleodepositional changes reflected in the sedimentary microbiome of the Black Sea – Kuldeep D. More et al. – Geobiology

Fluid geochemistry, local hydrology, and metabolic activity define methanogen community size and composition in deep-sea hydrothermal vents – Lucy C. Stewart et al. – The ISME Journal

Prebiotics, probiotics and synbiotics

Review: Potential prebiotics and their transmission mechanisms: Recent approaches – Ishu Khangwal & Pratyoosh Shukla – Journal of Food and Drug Analysis

A Preventive Prebiotic Supplementation Improves the Sweet Taste Perception in Diet-Induced Obese Mice – Arnaud Bernard et al. – Nutrients

Phages and viruses

Pancreas of coxsackie virus infected dams and their challenged pups: A complex issue – Sona Sarmirova et al. – Virulence

Preprint: Clades of huge phage from across Earth’s ecosystems – Basem Al-Shayeb et al. – bioRxiv

** Gut mucosal virome alterations in ulcerative colitis – Tao Zuo et al. – Gut

Bioinformatics

MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches – Weizhi Song et al. – Microbiome

Scientific Communication and Education

Preprint: The life of P.I. – Transitions to Independence in Academia – Sophie E Acton et al. – bioRxiv

March 11, 2019

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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 8, 2019

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Happy Friday! Read on for insights into the relationship between the oral microbiome and taste perception, how earthworms interact with pathogens during vermicomposting, the use of phages against drug resistant bacterial pathogens, and how microbiota depletion affects brown adipose tissue thermogenesis. Plus, two new techniques for shotgun metagenomes.

General microbiome
Quorum Sensing Signal Selectivity and the Potential for Interspecies Cross Talk – Samantha Wellington – mBio

Streptomyces Volatile Compounds Influence Exploration and Microbial Community Dynamics by Altering Iron Availability – Stephanie E. Jones – mBio

Microbiome Imbalances: An Overlooked Potential Mechanism in Chronic Nonhealing Wounds – Mengru Pang – The International Journal of Lower Extremity Wounds

Human oral microbiome
New insights into the relationship between taste perception and oral microbiota composition – Camilla Cattaneo – Scientific Reports

The Supragingival Biofilm in Early Childhood Caries: Clinical and Laboratory Protocols and Bioinformatics Pipelines Supporting Metagenomics, Metatranscriptomics, and Metabolomics Studies of the Oral Microbiome – Kimon Divaris – Odontogenesis

Human vaginal microbiome
Comparison of the Vaginal Microbiomes of Premenopausal and Postmenopausal Women – Karol Gliniewicz – Frontiers in Microbiology

Pregnancy and early life
Dose-interval study of a dual probiotic in preterm infants – Claire Watkins – Archives of Disease in Childhood – Fetal and Neonatal Edition

Review: The Relationship Between Perinatal Mental Health and Stress: a Review of the Microbiome – Nusiebeh Redpath – Current Psychiatry Reports

Multi-site human microbiome
Preprint: Functional metagenomics-guided discovery of potent Cas9 inhibitors in the human microbiome – Kevin J Forsberg – bioRxiv

Human gut microbiome
Infectious Complications Are Associated With Alterations in the Gut Microbiome in Pediatric Patients With Acute Lymphoblastic Leukemia – Jacob T Nearing – Frontiers in Cellular and Infection Microbiology

Preprint: HLA alleles associated with risk of ankylosing spondylitis and rheumatoid arthritis influence the gut microbiome – Mark Asquith – bioRxiv

Preprint: Gut feelings begin in childhood: how the gut metagenome links to early environment, caregiving, and behavior – Jessica Flannery – bioRxiv

Review: From gut microbiota dysfunction to obesity: could short-chain fatty acids stop this dangerous course? – Luigi Barrea – Hormones

Animal microbiome
Microbial communities in hummingbird feeders are distinct from floral nectar and influenced by bird visitation – Casie Lee – Proceedings of the Royal Society B

High individual variability in the transcriptomic response of Mediterranean mussels to Vibrio reveals the involvement of myticins in tissue injury – Magalí Rey-Campos – Scientific Reports

The Bos taurus maternal microbiome: Role in determining the progeny early-life upper respiratory tract microbiome and health – Svetlana Ferreira Lima – PLoS One

Contact with adult hen affects development of caecal microbiota in newly hatched chicks – Tereza Kubasova – PLoS One

Examination of the temporal and spatial dynamics of the gut microbiome in newborn piglets reveals distinct microbial communities in six intestinal segments – Ying Liu – Scientific Reports

Microbial diversity in the tick Argas japonicus (Acari: Argasidae) with a focus on Rickettsia pathogens – P. Yan – Medical and Veterinary Entomology

Mutual interactions of E. andrei earthworm and pathogens during the process of vermicomposting – Radka Roubalová – Environmental Science and Pollution Research

Animal experiments
Microbiota Depletion Impairs Thermogenesis of Brown Adipose Tissue and Browning of White Adipose Tissue – Baoguo Li – Cell Reports

Fasting-Mimicking Diet Modulates Microbiota and Promotes Intestinal Regeneration to Reduce Inflammatory Bowel Disease Pathology – Priya Rangan – Cell Reports

Linseed oil and heated linseed grain supplements have different effects on rumen bacterial community structures and fatty acid profiles in cashmere kids – Xue Wang – Journal of Animal Science

Sodium butyrate supplementation in high-soybean meal diets for turbot (Scophthalmus maximus L.): Effects on inflammatory status, mucosal barriers and microbiota in the intestine – Yang Liu – Fish and Shellfish Immunology

The gut microbiota composition affects dietary polyphenols-mediated cognitive resilience in mice by modulating the bioavailability of phenolic acids – Tal Frolinger – Scientific Reports

Dietary lysozyme supplementation contributes to enhanced intestinal functions and gut microflora of piglets – Xia Xiong – Food and Function

Plant, root, and soil microbiome
Potential role of weather, soil and plant microbial communities in rapid decline of apple trees – Jugpreet Singh – PLoS One

The structure of denitrifying microbial communities in constructed mangrove wetlands in response to fluctuating salinities – Guiping Fu – Journal of Environmental Management

Exploring the links between bacterial communities and magnetic susceptibility in bulk soil and rhizosphere of beech (Fagus sylvatica L.) – Carolina Chiellini – Applied Soil Ecology

Impact of Fabricated Nanoparticles on the Rhizospheric Microorganisms and Soil Environment – Mokula Mohammed Raffi – Nanomaterials and Plant Potential

Variation in soil fungal community structure during successive rotations of Casuarina equisetifolia plantations as determined by high-throughput sequencing analysis – Zhou Liuting – Plant Growth Regulation

Water and extremophile microbiome
Microbial responses to anthropogenic dissolved organic carbon in Arctic and Antarctic coastal seawaters – Elena Cerro‐Gálvez – Environmental Microbiology

Microbes in Space
A Low-Diversity Microbiota Inhabits Extreme Terrestrial Basaltic Terrains and Their Fumaroles: Implications for the Exploration of Mars – Charles S. Cockell – Astrobiolgy

Phages and Viruses
Targeting antibiotic resistant bacteria with phage reduces bacterial density in an insect host – Lauri Mikonranta – Biology Letters

Bioinformatics
Autometa: automated extraction of microbial genomes from individual shotgun metagenomes – Ian J Miller – Nucleic Acids Research

Preprint: Toward perfect reads: short reads correction via mapping on compacted de Bruijn graphs – Antoine Limasset – bioRxiv

 

February 12, 2019

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Today’s Digest features a major effect to tackle the dark matter in the human gut microbiome, comparison of 8 methods to extract DNA from the oral cavity that yielded an unexpected result, and the investigation on whether we can predict sex/age by our gut microbiota. Enjoy!

General microbiology

Perspective: Bridging the Holistic-Reductionist Divide in Microbial Ecology – Robin Tecon et al. – mSystems

Microbioime sister journal: Welcome to Animal Microbiome – Sharon A. Huws

Engineering microbial consortia by division of labor – Garrett W. Roell et al. – Microbial Cell Factories

Preprint: Revisiting the evolution and taxonomy of Clostridia, a phylogenomic update – Pablo Cruz-Morales et al. – bioRxiv

Human skin microbiome

Skin Microbiota in Contact Sports Athletes and Selection of Antiseptics for Professional Hygiene – Dilyara S. Martykanova et al. – BioMed Research International

Human oral microbiome

Qualitative and quantitative differences in the subgingival microbiome of the restored and unrestored teeth – Steven W. H. Rademacher et al. – Journal of Periodontal Research

Human respiratory microbiome

Comparison of Subtyping Approaches and the Underlying Drivers of Microbial Signatures for Chronic Rhinosinusitis – Kristi Biswas et al. – mSphere

Human gut microbiome

** 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses – Yuanqiang Zou et al. – Nature Biotechnology

Genomic insights from Monoglobus pectinilyticus: a pectin-degrading specialist bacterium in the human colon – Caroline C. Kim et al. – The ISME Journal

Pinning down the role of common luminal intestinal parasitic protists in human health and disease – status and challenges – Christen Rune Stensvold – Parasitology

Dynamics of the Gut Microbiota in Children Receiving Selective or Total Gut Decontamination Treatment During Hematopoietic Stem Cell Transplantation – Vincent Bekker & Romy D. Zwittink et al. – Biology of Blood and Marrow Transplantation

Fecal Microbiota Transplantation in Patients With Primary Sclerosing Cholangitis: A Pilot Clinical Trial – Jessica Allegretti et al. – The American Journal of Gastroenterology

** Preprint: Age and sex-dependent patterns of gut microbial diversity in human adults – Jacobo de la Cuesta-Zuluaga et al. – bioRxiv

Human reproductive tract microbiome

Cervical microbiota in women with cervical intra-epithelial neoplasia, prior to and after local excisional treatment, a Norwegian cohort study – Johanna Wiik – BMC Women’s Health

Built environment microbiome

Spatial and seasonal variation of the airborne microbiome in a rapidly developing city of China – Hu Li et al. – Science of the Total Environment

Animal experiments

Synbiotic-driven improvement of metabolic disturbances is associated with changes in the gut microbiome in diet-induced obese mice – Xinxin Ke et al. – Molecular Metabolism

The gut microbiota is largely independent of host genetics in regulating fat deposition in chickens – Chaoliang Wen et al. – The ISME Journal

The Glucoamylase Inhibitor Acarbose Has a Diet-Dependent and Reversible Effect on the Murine Gut Microbiome – Nielsen T. Baxter et al. – mSphere

Animal microbiome

Effects of polyethylene microplastics on the gut microbial community, reproduction and avoidance behaviors of the soil springtail, Folsomia candida – Hui Ju et al. – Environmental Pollution

Effects of host blood meal source on reproductive output, nutrient reserves and gut microbiome of West Nile virus vector Culex quinquefasciatus – Aparna Telang & Jessica Skinner – Journal of Insect Physiology

Plant, root and soil microbiome

Soil microbes alter plant fitness under competition and drought – Connor R. Fitzpatrick et al. – Journal of Evolutionary Biology

Multi-resistant plant growth-promoting actinobacteria and plant root exudates influence Cr(VI) and lindane dissipation – María ZoleicaSimón Solá et al. – Chemosphere

Interactions between Pseudomonas spp. and their role in improving the red pepper plant growth under salinity stress – Sandipan Samaddar et al. – Microbiological Research

Plant Defense by VOC-Induced Microbial Priming – Hongwei Liu & Laura E. Brettell – Trends in Plant Science

Water and extremophile microbiome

Microbial ecology of the cryosphere (glacial and permafrost habitats): current knowledge – Rosa Margesin & Tony Collins – Applied Microbiology and Biotechnology

Unique Patterns and Biogeochemical Relevance of Two-Component Sensing in Marine Bacteria – Noelle A. Held et al. – mSystems

Oil-Spill Triggered Shift in Indigenous Microbial Structure and Functional Dynamics in Different Marine Environmental Matrices – C. S. Neethu et al. – Scientific Reports

An integrated meta-omics approach reveals substrates involved in synergistic interactions in a bisphenol A (BPA)-degrading microbial community – Ke Yu et al. – Microbiome

Effects of biomass pyrolysis derived wood vinegar on microbial activity and communities of activated sludge – Fang Zhang et al. – Bioresource Technology

Anti-seasonal submergence dominates the structure and composition of prokaryotic communities in the riparian zone of the Three Gorges Reservoir, China – Yan Fang et al. – Science of The Total Environment

Phages and viruses

Cobaviruses – a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems – Vera Bischoff et al. – The ISME Journal

In plaque-mass spectrometry imaging of a bloom-forming alga during viral infection reveals a metabolic shift towards odd-chain fatty acid lipids – Guy Schleyer et al. – Nature Microbiology

Technology

The mucosal–luminal interface: an ideal sample to study the mucosa-associated microbiota and the intestinal microbial biogeography – Walid Mottawea et al. – Pediatric Research

Development and application of a HILIC UHPLC-MS method for polar fecal metabolome profiling – Nina Sillner et al. – Journal of Chromatography B

** Evaluation of Oral Cavity DNA Extraction Methods on Bacterial and Fungal Microbiota – Jennifer Rosenbaum et al. – Scientific Reports

Xin’s Non-microbiology pick

Preprint: Where do our graduates go? A toolkit for retrospective and ongoing career outcomes data collection for biomedical PhD students and postdoctoral scholars – Elizabeth A. Silva et al. – bioRxiv

February 8, 2019

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Happy Friday! Today’s digest includes the sea cucumber gut microbiome, bacterial diversity of volcano steam vents, and the impacts of arsenic and antimony on microbes in river sediment. Enjoy!

Human gut microbiome

Use of shotgun metagenomics for the identification of protozoa in the gut microbiota of healthy individuals from worldwide populations with various industrialization levels – Lokmer – PLoS ONE

Age-associated Impairment of the Mucus Barrier Function is Associated with Profound Changes in Microbiota and Immunity – Sovran – Scientific Reports

A single alcohol binge impacts on neutrophil function without changes in gut barrier function and gut microbiome composition in healthy volunteers – Stadlbauer – PLoS ONE

Animal experiments

TGFβ/BMP immune signaling affects abundance and function of C. elegans gut commensals – Berg – Nature Communications

Animal microbiome

Distinct microbiotas of anatomical gut regions display idiosyncratic seasonal variation in an avian folivore – Drovetski – Animal Microbiome

Characterization of the intestinal microbiota of the sea cucumber Holothuria glaberrima – Pagán-Jiménez – PLoS ONE

Dynamic distribution of gallbladder microbiota in rabbit at different ages and health states – Xing – PLoS ONE

Dietary-induced modulation of the hindgut microbiota is related to behavioral responses during stressful events in horses – Destrez – Physiology & Behavior

Review: Host-Microbe Coevolution: Applying Evidence from Model Systems to Complex Marine Invertebrate Holobionts – O’Brien – mBio

Plant, root, and soil microbiome

Environmental filtering drives distinct continental atlases of soil archaea between dryland and wetland agricultural ecosystems – Jiao – Microbiome

The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome – Shi -Microbiome

Enterobacteriaceae dominate the core microbiome and contribute to the resistome of arugula (Eruca sativa Mill.) – Cernava – Microbiome

Unlocking a high bacterial diversity in the coralloid root microbiome from the cycad genus Dioon – Suárez-Moo – PLoS ONE

Characterization of iron-metabolizing communities in soils contaminated by acid mine drainage from an abandoned coal mine in Southwest China – Gao – Environmental Science and Pollution Research

Water and extremophile microbiome

Impacts of Arsenic and Antimony Co-Contamination on Sedimentary Microbial Communities in Rivers with Different Pollution Gradients – Sun – Microbial Ecology

The bacterial diversity on steam vents from Paricutín and Sapichu volcanoes – Souza Brito – Extremophiles

Food microbiology

Spent coffee grounds extract rich in manooligosaccharides promote a healthier gut microbial community in a dose dependent manner – Pérez-Burillo – Journal of Agricultural and Food Chemistry

Impact of routine sanitation on the microbiomes in a fresh produce processing facility – Gu – International Journal of Food Microbiology

January 29, 2019

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Today’s Digest features a defined gut consortium providing protection against pathogen and cancer, a primer on parasitic modulation of host behavior, and an international collaboration all about crAssphage. Enjoy reading and stay warm!

General microbiology

Low molecular weight organic acids enhance the high molecular weight polycyclic aromatic hydrocarbons degradation by bacteria – Anithadevi Kenday Sivaram et al. – Chemosphere

Review: Function of Biohydrogen Metabolism and Related Microbial Communities in Environmental Bioremediation – Ying Teng et al. – Frontiers in Microbiology

Rare Taxa Exhibit Disproportionate Cell-Level Metabolic Activity in Enriched Anaerobic Digestion Microbial Communities – Yangyang Jia et al. – mSystems

Antimicrobial resistance

Rationally designing antisense therapy to keep up with evolving bacterial resistance – Seyfullah Kotil & Eric Jakobsson – PLoS One

Preprint: Bacteriophage resistance alters antibiotic mediated intestinal expansion of enterococci – Anushila Chatterjee et al. – bioRxiv

Preprint: Selection for antibiotic resistance is reduced when embedded in a natural microbial community – Uli Klümper et al. – bioRxiv

Higher Temperatures Do Not Always Achieve Better Antibiotic Resistance Genes Removal in Anaerobic Digestion of Swine Manure – Xu Huang et al. – Applied and Environmental Microbiology

Human respiratory microbiome

Metagenome – Inferred bacterial replication rates in cystic fibrosis airways – Katarzyna Pienkowska et al. – Journal of Cystic Fibrosis

Review: The respiratory microbiota: new insights into pulmonary tuberculosis – Setegn Eshetie & Dick van Soolingen – BMC Infectious Diseases

Human gut microbiome

Taxonomic profiling and populational patterns of bacterial bile salt hydrolase (BSH) genes based on worldwide human gut microbiome – Ziwei Song et al. – Microbiome

** A defined commensal consortium elicits CD8 T cells and anti-cancer immunity – Takeshi Tanoue et al. – Nature

Press: A gut punch fights cancer and infection – Nathan E. Reticker-Flynn & Edgar G. Engleman – Nature

Faecal microbiota transplant for eradication of multidrug-resistant Enterobacteriaceae: a lesson in applying best practice? – Benjamin H. Mullish et al. – Clinical Microbiology and Infection

Screening-level microbial risk assessment of acute gastrointestinal illness attributable to wastewater treatment systems in Nunavut, Canada – Kiley Daley et al. – Science of The Total Environment

Review: Probiotics: How Effective Are They in the Fight against Obesity? – Kiran Mazloom et al. – Nutrients

The gut microbiota heterogeneity and assembly changes associated with the IBD – Yang Sun et al. – Scientific Reports

Human gut-microbiome-brain axis

Exploration of microbiota targets for major depressive disorder and mood related traits – Yu-Chu Ella Chung et al. – Journal of Psychiatric Research

Food microbiology

Role of Intestinal Microbiota in the Bioavailability and Physiological Functions of Dietary Polyphenols – K Kawabata et al. – Molecules

Review: Dietary Advanced Glycation End Products: Digestion, Metabolism and Modulation of Gut Microbial Ecology – Matthew Snelson & Melinda T. Coughlan

Animal experiments

Intestinal bacteria modulate the foraging behavior of the oriental fruit fly Bactrocera dorsalis (Diptera: Tephritidae) – Mazarin Akami et al. – PLoS One

Effect of ZFN-edited myostatin loss-of-function mutation on gut microbiota in Meishan pigs – Wen-Tao Cui et al. – PLoS One

Oral Candida administration in a Clostridium difficile mouse model worsens disease severity but is attenuated by Bifidobacterium – Wimonrat Panpetch et al. – PLoS One

Gut microbiota affects development and olfactory behavior in Drosophila melanogaster – Huili Qiao et al. – Journal Experimental Biology

Animal microbiome

** Primer: Parasite manipulation of host behavior -David P. Hughes & Frederic Libersat – Current Biology

Effects of the captive and wild environment on diversity of the gut microbiome of deer mice (Peromyscus maniculatus) – Elliott Schmidt et al. – The ISME Journal

A longitudinal assessment of host-microbe-parasite interactions resolves the zebrafish gut microbiome’s link to Pseudocapillaria tomentosa infection and pathology – Christopher A. Gaulke et al. – Microbiome

Microbiota comparison of Pacific white shrimp intestine and sediment at freshwater and marine cultured environment – Lanfen Fan et al. – Science of The Total Environment
https://www.sciencedirect.com/science/article/pii/S004896971834909X

T6SS contributes to gut microbiome invasion and killing of an herbivorous pest insect by plant-beneficial Pseudomonas protegens – Jordan Vacheron et al. – The ISME Journal

Genomic diversity landscape of the honey bee gut microbiota – Kirsten M. Ellegaard & Philipp Engel

Dynamics of the gut microbiota in developmental stages of Litopenaeus vannamei reveal its association with body weight – Jiqiang Fan et al. – Scientific Reports

Plant, root and soil microbiome

Forum: Microbiome Applications from Lab to Field: Facing Complexity – Angela Sessitsch, Nikolaus Pfaffenbichler & Birgit Mitter – Trends in Plant Science

Review: Plant growth promoting rhizobacteria in sustainable agriculture: from theoretical to pragmatic approach – Samar Mustafa et al. – Symbiosis

Plant evenness modulates the effect of plant richness on soil bacterial diversity – Yao-Qin Sun et al. – Science of The Total Environment

Water and extremophile microbiome

Taurine Is a Major Carbon and Energy Source for Marine Prokaryotes in the North Atlantic Ocean off the Iberian Peninsula – Elisabeth L. Clifford et al. – Microbial Ecology

Organic matter from Arctic sea-ice loss alters bacterial community structure and function – Graham J. C. Underwood et al. – Nature Climate Change

Review: The unexpected habitat in sewer pipes for the propagation of microbial communities and their imprint on urban waters – Sandra L McLellan & Adélaïde Roguet – Current Opinion in Biotechnology

In situ enrichment of microbial communities on polarized electrodes deployed in alkaline hot springs – Abdelrhman Mohamed et al. – Journal of Power Sources

Genomic and metagenomic insights into the microbial community of a thermal spring – Renato Pedron et al. – Microbiome

Changes in the Active, Dead, and Dormant Microbial Community Structure Across a Pleistocene Permafrost Chronosequence – Alexander Burkert et al. – Applied and Environmental Microbiology

Phages and viruses

Adjunct phage treatment enhances the effectiveness of low antibiotic concentration against Staphylococcus aureus biofilms in vitro – James Dickey & Véronique Perrot – PLoS One

** Preprint: Global phylogeography and ancient evolution of the widespread human gut virus crAssphage – Robert Edwards et al. – bioRxiv

Technology

Metabolomics and Microbiomes as Potential Tools to Evaluate the Effects of the Mediterranean Diet – Qi Jin et al. – Nutrients

Effects of sample preservation on marine microbial diversity analysis – Athenia L.Oldham et al. – Journal of Microbiological Methods

January 25, 2019

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General microbiome

A Comparison of Homogenization vs. Enzymatic Lysis for Microbiome Profiling in Clinical Endoscopic Biopsy Tissue Samples – A Comparison of Homogenization vs. Enzymatic Lysis for Microbiome Profiling in Clinical Endoscopic Biopsy Tissue Samples – Chao Zhang – Frontiers in Microbiology

Review: Exploring the Human Microbiome: The Potential Future Role of Next-Generation Sequencing in Disease Diagnosis and Treatment – Muneer Ahmad Malla – Frontiers in Immunology

The microbiome and its relevance in complex wounds – Francesco Drago – European Journal of Dermatology

Commentary: A Link between the Gut and Bone: Bone Health Impacted by Changes in Gut Microbiota – Larry J.Suva – The American Journal of Pathology

Pregnancy and early life

Feeding intolerance alters the gut microbiota of preterm infants – Zhenya Yuan – PLOS ONE

Multi-site human microbiome

Review: A correlation between intestinal microbiota dysbiosis and osteoarthritis – Marta AnnaSzychlinska – Heliyon

Human respiratory microbiome

A survey of fungal microbiota in airways of healthy volunteer subjects from Puglia (Apulia), Italy – Giovanna Elisiana Carpagnano – BMC Infectious Diseases

The Association Between Disease Severity and Microbiome in Chronic Rhinosinusitis – Darren Rom – The Laryngoscope

Review: Microbiota and asthma: Clinical implications – Konstantinos Katsoulis – Respiratory Medicine

Human oral microbiology

Metagenome sequencing-based strain-level and functional characterization of supragingival microbiome associated with dental caries in children – Nezar Noor Al-Hebshi – Journal of Oral Microbiology

Periodontal pathogens are a risk factor of oral cavity squamous cell carcinoma, independent of tobacco and alcohol and human papillomavirus – Ian Ganly – International Journal of Cancer

Human gut microbiome

Review: Role of diet and gut microbiota on colorectal cancer immunomodulation – Carolina Vieira De Almeida – World Journal of Gastroenterology

Review: Targeting obesity management through gut microbiota modulation by herbal products: A systematic review – Hanieh-SadatEjtahed – Complementary Therapies in Medicine

Identification of Specific Oral and Gut Pathogens in Full Thickness Colon of Colitis Patients: Implications for Colon Motility – Vasudevan Dinakaran – Frontiers in Microbiology

Animal experiments

Fecal microbiota changes associated with dehorning and castration stress primarily affects light-weight dairy calves – Raies A. Mir – PLOS ONE

Advanced Age Impairs Intestinal Antimicrobial Peptide Response and Worsens Fecal Microbiome Dysbiosis Following Burn Injury in Mice – Elizabeth G Wheatley – Shock

Effects of drought‐stressed temperate forage legumes on the degradation and the rumen microbial community in vitro – Susanne Riede – Journal of Animal Physiology and Animal Nutrition

Bacillus amyloliquefaciens ameliorates Dextran Sulfate Sodium-Induced Colitis by Improving Gut Microbial Dysbiosis in Mice Model – Guangtian Cao – Frontiers in Microbiology

Bacillus subtilis 29784 induces a shift in broiler gut microbiome toward butyrate-producing bacteria and improves intestinal histomorphology and animal performance – Vincent Jacquier – Poultry Science

Green Tea Polyphenols Modify the Gut Microbiome in db/db Mice as Co‐abundance Groups Correlating with the Blood Glucose Lowering Effect – Tingting Chen – Molecular Nutrition and Food Research

Influence of Porphyromonas gingivalis in gut microbiota of streptozotocin‐induced diabetic mice – Anri Ohtsu – Oral diseases

Plant, root, and soil microbiome

Nanopore Sequencing as a Surveillance Tool for Plant Pathogens in Plant and Insect Tissues – Aline Bronzato Badial – Plant Disease

Rhizosphere Microbiomes from Root Knot Nematode Non-infested Plants Suppress Nematode Infection – Dongmei Zhou – Microbial Ecology

Water and extremophile microbiome

Copper Affects Composition and Functioning of Microbial Communities in Marine Biofilms at Environmentally Relevant Concentrations – Natàlia Corcoll – Frontiers in Microbiology

Bark and Grape Microbiome of Vitis vinifera: Influence of Geographic Patterns and Agronomic Management on Bacterial Diversity – Nicola Vitulo – Frontiers in Microbiology

Bacterial diversity in typical abandoned multi-contaminated nonferrous metal(loid) tailings during natural attenuation – Jian-liLiu – Environmental Pollution

Long- and short-chain AHLs affect AOA and AOB microbial community composition and ammonia oxidation rate in activated sludge – Jie Gao – Journal of Environmental Sciences

Food microbiology

Dominance of wine Saccharomyces cerevisiae strains over S. kudriavzevii in industrial fermentation competitions is related to an acceleration of nutrient uptake and utilization – Javier Alonso‐del‐Real – Environmental Microbiology

Phages and viruses

Commentary : Going Viral: a Novel Role for Bacteriophage in Colorectal Cancer – Scott A. Handley – mBio

January 22, 2019

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Today’s digest is packed with interesting reviews from Gut to Rhizosphere microbiomes.

General Microbiome

Short-term consumption of a high-fat diet increases host susceptibility to Listeria monocytogenes infection.Heras VL. Microbiome.

Dietary Fructose and Microbiota-Derived Short-Chain Fatty Acids Promote Bacteriophage Production in the Gut Symbiont Lactobacillus reuteri. Oh JH. Cell Host snd Microbe.

Gut Microbiome

REVIEW: The Gut Microbiome as a Target for IBD Treatment: Are We There Yet?Knox NC. Current Treatment Options in Gastroenterology

Interactions between gut microbiota and non-alcoholic liver disease: the role of microbiota-derived metabolites.Ding Y. Pharmacological Research

Gut bacterial tyrosine decarboxylases restrict levels of levodopa in the treatment of Parkinson’s disease.van Kessel SP. Nature Communications

Lung Microbiome

Multiple respiratory microbiota profiles are associated with lower airway inflammation in children with protracted bacterial bronchitis. Marsh RL. Chest.

Plant, Soil, and Air Microbiome

Resilience and Assemblage of Soil Microbiome in Response to Chemical Contamination Combined with Plant Growth. Jiao S. Applied Environmental Microbiology

Effect of plant growth promoting bacterium; Pseudomonas putida UW4 inoculation on phytoremediation efficacy of monoculture and mixed culture of selected plant species for PAH and lead spiked soils.Afegbua SL. International Journal of Phytoremediation.

REVIEW: Synergistic plant-microbes interactions in the rhizosphere: a potential headway for the remediation of hydrocarbon polluted soils.Asemoloye MD. International Journal of Phytoremediation

Spatial and temporal variation of fungal endophytic richness and diversity associated to the phyllosphere of olive cultivars.Materatski P. Fungal Biology

Rhizosphere fungal community structure succession of Xinjiang continuously cropped cotton.Wei Z. Fungal Biology.

REVIEW: To Fix or Not To Fix: Controls on Free-Living Nitrogen-Fixation in the Rhizosphere.Smercina DN. Applied Environmental Microbiology

An active β-lactamase is a part of an orchestrated cell wall stress resistance network of Bacillus subtilis and related rhizosphere species.Bucher T. Environmental Microbiology

Diversity analysis of the rhizospheric and endophytic bacterial communities of <i>Senecio vulgaris</i> L. (Asteraceae) in an invasive range. Cheng D. PeerJ

Genotype and rhizobium inoculation modulate the assembly of soybean rhizobacterial communities.Zhong Y. Plant, Cell, and Environment

Animal Experiments and Microbiome

Dose-dependent impact of oxytetracycline on the veal calf microbiome and resistome.Keijser BJF. BMC Genomics

Earthworms and cadmium – Heavy metal resistant gut bacteria as indicators for heavy metal pollution in soils?  Šrut M. Ecotoxicology and Environmental

Taxonomic and functional composition of the small intestinal microbiome in neonatal calves provide a framework for understanding early life gut health. Malmuthuge N. Applied Environmental Microbiology

Inland Waters and Marine Microbiomes

High-Throughput Sequencing of the 16S rRNA Gene as a Survey to Analyze the Microbiomes of Free-Living Ciliates Paramecium.Plotnikov AO. Microbial Ecology

Action of oxytetracycline (OTC) degrading bacterium and its application in Moving Bed Biofilm Reactor (MBBR) for aquaculture wastewater pre-treatment.Shao S. Ecotoxicology and Environmental

Metabarcoding and machine learning analysis of environmental DNA in ballast water arriving to hub ports. Gerhard WA. Environment International

January 15, 2019

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Highlights today include the organisms in the healthy infant intestinal microbiome that protect against food allergy, an algorithm to predict aging based on the gut microbiome, and how bacteria adapt to life on the International Space Station. Enjoy!

Pregnancy and early life
Healthy infants harbor intestinal bacteria that protect against food allergy – Taylor Feehley – Nature Medicine

Human gut microbiome
Preprint: Human microbiome aging clocks based on deep learning and tandem of permutation feature importance and accumulated local effects – Fedor Galkin – bioRxiv
(Covered in popular press as Your Gut Microbiome Could Actually Reveal Your Age, Study Shows)

Preprint: The virome in adult monozygotic twins with concordant or discordant gut microbiomes – J. Leonardo Moreno-Gallego – bioRxiv

Human nearly-sterile sites
Review: Microbiome–metabolome reveals the contribution of gut–kidney axis on kidney disease – Yuan-Yuan Chen – Journal of Translational Medicine

Animal experiments
Lactobacillus sakei Alleviates High-fat Diet-induced Obesity and Anxiety in Mice by Inducing AMPK Activation and SIRT1 Expression and Inhibiting Gut Microbiota-mediated NF-κB Activation – Hyo-Min Jang – Molecular Nutrition and Food Research

Aqueous raw and ripe Pu-erh tea extracts alleviate obesity and alter cecal microbiota composition and function in diet-induced obese rats – Yun Xia – Applied Microbiology and Biotechnology

Impact of intramammary inoculation of inactivated Lactobacillus rhamnosus and antibiotics on the milk microbiota of water buffalo with subclinical mastitis – Carlotta Catozzi – PLOS One

Plant, root, and soil microbiome
Superior dispersal ability can lead to persistent ecological dominance throughout succession – Primrose J. Boynton – Applied and Environmental Microbiology

Plant growth-promoting rhizobacterium Pseudomonas PS01 induces salt tolerance in Arabidopsis thaliana – Thanh Nguyen Chu – BMC Research Notes

Diversity analysis of the rhizospheric and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range – Dandan Cheng – PeerJ\

Antifungal potential of bacterial rhizosphere isolates associated with three ethno-medicinal plants (poppy, chamomile, and nettle) – Marija Mojicevic – International Microbiology

Analysis of uranium removal capacity of anaerobic granular sludge bacterial communities under different initial pH conditions – Taotao Zeng – Environmental Science and Pollution Research

Water and extremophile microbiomes
An interspecies malate–pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community – Po-Hsiang Wang – The ISME Journal

Bacterial community assembly in a typical estuarine marsh with multiple environmental gradients – Zhiyuan Yao – Applied and Environmental Microbiology

Effects of salinity on microbialite-associated production in Great Salt Lake, Utah – Melody R. Lindsay – Ecology

Preprint: Capturing the Diversity of Subsurface Microbiota – Choice of Carbon Source for Microcosm Enrichment and Isolation of Groundwater Bacteria – Xiaoqin Wu – bioRxiv

Genetic Evidence for Two Carbon Fixation Pathways (the Calvin-Benson-Bassham Cycle and the Reverse Tricarboxylic Acid Cycle) in Symbiotic and Free-Living Bacteria – Maxim Rubin-Blum – mSphere

Techniques
Generation of 13C-labeled MUC5AC mucin oligosaccharides for stable isotope probing of host-associated microbial communities – Clayton Evert – ACS Infectious Diseases

Transomics data-driven, ensemble kinetic modeling for system-level understanding and engineering of the cyanobacteria central metabolism – Hiroki Nishiguchi – Metabolic Engineering

Built environment/Microbes in Space
Pangenomic Approach To Understanding Microbial Adaptations within a Model Built Environment, the International Space Station, Relative to Human Hosts and Soil – Ryan A. Blaustein – mSystems
(Covered in the popular press as Good news: space bacteria (probably) aren’t evolving to destroy us)

Science, publishing, and career
Preprint: Tracking the popularity and outcomes of all bioRxiv preprints – Richard J. Abdill – bioRxiv