Category Archives: Food Microbiology

March 21, 2019

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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

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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 14, 2019

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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

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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 4, 2019

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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

March 1, 2019

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Human Microbiome

The human microbiome in health and disease: hype or hope – Gwen Falony – Acta Clinica Belgica

Bottom-Up Approaches to Synthetic Cooperation in Microbial Communities – Daniel Rodríguez Amor – Life

Influence of Crohn’s disease related polymorphisms in innate immune function on ileal microbiome – Ellen Li – PLoS ONE

Interactions between gut microbiota and non-alcoholic liver disease: the role of microbiota-derived metabolites – Kyongbum Lee – Pharmacological Research

Microbial bile salt hydrolases mediate the efficacy of faecal microbiota transplant in the treatment of recurrent Clostridioides difficile infection – Benjamin H Mullish – Gut

Fecal microbiota dynamics and its relation with disease course in Crohn’s disease – Gianluca Galazzo – Journal of Crohn’s and Colitis

Associations Between Gut Microbiota and Alzheimer’s Disease: Current Evidences and Future Therapeutic and Diagnostic Perspectives – Liang Shen – Journal of Alzheimer’s Disease

Western diet regulates immune status and the response to LPS-driven sepsis independent of diet-associated microbiome – Brooke A. Napier – PNAS

The Human Fecal Microbiota Metabolizes Foodborne Heterocyclic Aromatic Amines by Reuterin Conjugation and Further Transformations – Falco Beer – Molecular Nutrition and Food Research

Clinical Review on the Utility of Fecal Microbiota Transplantation in Immunocompromised Patients – Hamzah Abu-Sbeih – Current Gastroenterology Reports

Cellular and Molecular Therapeutic Targets in Inflammatory Bowel Disease-Focusing on Intestinal Barrier Function – Ida Schoultz – Cells

Can Gut Microbiota and Lifestyle Help Us in the Handling of Anorexia Nervosa Patients? – Vanessa Mendez-Figueroa – Microorganisms

Impact of the Gastro-Intestinal Bacterial Microbiome on Helicobacter-Associated Diseases – Maxime Pichon – Healthcare

Influence of short-term changes in dietary sulfur on the relative abundances of intestinal sulfate-reducing bacteria – Allison Dostal Webster – Gut Microbes

Fecal microbiota transplantation research output from 2004 to 2017: a bibliometric analysis – Yan Li – PeerJ

Conjunctival microbiome changes associated with fungal keratitis: metagenomic analysis – C. Ge – International Journal of Ophthalmology

Gut Microbiota and Chronic Constipation: A Review and Update – Toshifumi Ohkusa – Frontiers in Medicine

An altered fecal microbiota profile in patients with non-alcoholic fatty liver disease (NAFLD) associated with obesity – E. Nistal – The Spanish Journal of Gastroenterology

Paternal Programming of Liver Function and Lipid Profile Induced by a Paternal Pre-Conceptional Unhealthy Diet: Potential Association with Altered Gut Microbiome Composition – X. Zhang – Kidney and Blood Pressure Research

Tryptophan Metabolism and Related Pathways in Psychoneuroimmunology: The Impact of Nutrition and Lifestyle – J. M. Gostner – Neuropsychobiology

The Impact of Starvation on the Microbiome and Gut-Brain Interaction in Anorexia Nervosa – Jochen Seitz – Frontiers in Endocrinology

Sperm Microbiota and Its Impact on Semen Parameters – David Baud – Frontiers in Microbiology

A review of 10 years of human microbiome research activities at the US National Institutes of Health, Fiscal Years 2007-2016 – NIH Human Microbiome Portfolio Analysis Team – Microbiome

 

Microbiome and Cancer

Impact of chemotherapy on the association between fear of cancer recurrence and the gut microbiota in breast cancer survivors – Ryo Okubo – Brain, Behavior, and Immunity

Bugs, drugs, and cancer: can the microbiome be a potential therapeutic target for cancer management? – Biying Chen – Drug Discovery Today

 

Early Childhood Microbiome

Crosstalk Between the Microbiome and Gestational Immunity in Autism-Related Disorders – Matt J. Paysour – DNA and Cell Biology

Cohort profile: The LoewenKIDS Study – life-course perspective on infections, the microbiome and the development of the immune system in early childhood – Cornelia Gottschick – International Journal of Epidemiology

Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month – Nina Iszatt – Microbiome

 

Animal Microbiome

Convergence, constraint and the potential for mutualism between ants and gut microbes – Elizabeth G. Pringle – Molecular Ecology

Germ-Free Mice Exhibit Mast Cells With Impaired Functionality and Gut Homing and Do Not Develop Food Allergy – Martin Schwarzer – Frontiers in Immunology

Fto Deficiency Reduces Anxiety- and Depression-Like Behaviors in Mice via Alterations in Gut Microbiota – Lijuan Sun – Theranostics

 

Beneficial Bugs, Foods and Compounds

Re-purposing is needed for beneficial bugs, not for the drugs – Hari Ram – International Microbiology

Probiotic mixture of Lactobacillus helveticus R0052 and Bifidobacterium longum R0175 attenuates hippocampal apoptosis induced by lipopolysaccharide in rats – Ghazaleh Mohammadi – International Microbiology

The Use of Probiotic Therapy to Modulate the Gut Microbiota and Dendritic Cell Responses in Inflammatory Bowel Diseases – Pablo Alagón Fernández del Campo – Medical Sciences

Dietary fibers as emerging nutritional factors against diabetes: focus on the involvement of gut microbiota – Vemana Gowd – Critical Reviews in Biotechnology

Gut microbiota, a new frontier to understand traditional Chinese medicines – Wuwen Feng – Pharmacological Research

Fructooligosaccharides Ameliorating Cognitive Deficits and Neurodegeneration in APP/PS1 Transgenic Mice through Modulating Gut Microbiota – Jing Sun – Journal of Agricultural and Food Chemistry

Short-chain fatty acid delivery: assessing exogenous administration of the microbiome metabolite acetate in mice – Tyler B. Shubitowski – Physiological Reports

Dietary intake of whole strawberry inhibited colonic inflammation in dextran sulfate sodium-treated mice via restoring immune homeostasis and alleviating gut microbiota dysbiosis – Yanhui Han – Journal of Agricultural and Food Chemistry

Ganoderma lucidum polysaccharide improves rat DSS-induced colitis by altering cecal microbiota and gene expression of colonic epithelial cells – Jinli Xie –  Food & Nutrition Research

In Vitro Infant Faecal Fermentation of Low Viscosity Barley β-Glucan and Its Acid Hydrolyzed Derivatives: Evaluation of Their Potential as Novel Prebiotics – Ka-Lung Lam – Molecules

Role of intestinal microecology in the regulation of energy metabolism by dietary polyphenols and their metabolites – Shaoling Lin – Food & Nutrition Research

Neuroprotection of Fasting Mimicking Diet on MPTP-Induced Parkinson’s Disease Mice via Gut Microbiota and Metabolites – Zhi-Lan Zhou – Neurotherapeutics

Refined versus Extra Virgin Olive Oil High-Fat Diet Impact on Intestinal Microbiota of Mice and Its Relation to Different Physiological Variables – Nieves Martínez – Microorganisms

Engineered and wild-type L. lactis promote anti-inflammatory cytokine signalling in inflammatory bowel disease patient’s mucosa – Saša Simčič – World Journal of Microbiology and Biotechnology

Sialyllactose and Galactooligosaccharides Promote Epithelial Barrier Functioning and Distinctly Modulate Microbiota Composition and Short Chain Fatty Acid Production In Vitro – Olaf Perdijk – Frontiers in Immunology

 

Built Environments

Man-made microbial resistances in built environments – Alexander Mahnert – Nature Communications

House dust microbiome and human health risks – Yifan Shan – International Microbiology

Microbiomes of China’s Space Station During Assembly, Integration, and Test Operations – Ying Zhang – Microbial Ecology

 

Environmental and Plant Microbiome

Microbiota dispersion in the Uyuni salt flat (Bolivia) as determined by community structure analyses – Cesar A. Pérez-Fernández – International Microbiology

Protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soils – Zhi-Bo Zhao – Microbiome

The deep continental subsurface: the dark biosphere – Cristina Escudero – International Microbiology

 

Bioinformatics

Batch effects correction for microbiome data with Dirichlet-multinomial regression – Zhenwei Dai – Bioinformatics

Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and whole rrn operon – Anna Cuscó – F1000Research

 

Methods

Guanidine thiocyanate solution facilitates sample collection for plant rhizosphere microbiome analysis – Xiaoxiao Sun – PeerJ

In Vitro Methods to Study Colon Release: State of the Art and An Outlook on New Strategies for Better In-Vitro Biorelevant Release Media – Marie Wahlgren – Pharmaceutics

 

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 31, 2019

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Today’s digest covers articles describing sphingolipids in host-microbiome interaction, unique microbiome and metabolome of Indian population, selection and stabilization of soil microbiome and effect of probiotics on early sepsis in patients and immune response in children. Enjoy reading!

General microbiome

Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview – Partho Sen – Metabolites

Altered composition and function of intestinal microbiota in autism spectrum disorders: a systematic review – Feitong Liu – Translational Psychiatry

Sphingolipids in host–microbial interactions – Stacey L. Heaver – Current Opinion in Microbiology

Pregnancy and early life

Mixed Viral-Bacterial Infections and Their Effects on Gut Microbiota and Clinical Illnesses in Children – Shilu Mathew – Scientific Reports

Pathways linking caesarean delivery to early health in a dual burden context: Immune development and the gut microbiome in infants and children from Galápagos, Ecuador – Amanda L. Thompson – American Journal of Human Biology

Human gut microbiome

The vagino-cervical microbiome as a woman’s life history – Zhuye Jie – BioRxiv

Dynamics of Human Gut Microbiota and Short-Chain Fatty Acids in Response to Dietary Interventions with Three Fermentable Fibers – Nielson T. Baxter – mBio

The unique composition of Indian gut microbiome, gene catalogue and associated faecal metabolome deciphered using multi-omics approaches – D.B. Dhakan – Gigascience

Animal experiments

Oral neonatal antibiotic treatment perturbs gut microbiota and aggravates central nervous system autoimmunity in Dark Agouti rats – Suzana Stanisavljević – Scientific Reports

Intestinal epithelial N-acylphosphatidylethanolamine phospholipase D links dietary fat to metabolic adaptations in obesity and steatosis – Amandine Everard – Nature Communications

Mutual interplay between IL-17–producing γδT cells and microbiota orchestrates oral mucosal homeostasis – Anneke Wilharm – PNAS

Plant, root and soil microbiome

Selection, succession and stabilization of soil microbial consortia – Elias K. Zegeye – BioRxiv

Comparison of the bacterial and methanotrophic diversities between an Italian paddy field and its neighboring meadow – Mohammad Ghashghavi – BioRxiv

Quality of Irrigation Water Affects Soil Functionality and Bacterial Community Stability in Response to Heat Disturbance – Sammy Frenk – Applied and Environmental Microbiology

Water and extremophiles microbiome

Archaea dominate the microbial community in an ecosystem with low-to-moderate temperature and extreme acidity – Aleksei A. Korzhenkov – Microbiome

Antibiotic disturbance affects aquatic microbial community composition and foodweb interactions but not community resilience – Ester M. Eckert – Molecular Ecology

 Phages and viruses

Megaphages infect Prevotella and variants are widespread in gut microbiomes – Audra E. Devoto – Nature Microbiology

Probiotics / prebiotics

Dysbiosis in early sepsis can be modulated by a multispecies probiotic: a randomised controlled pilot trial – V. Stadlbauer – Beneficial Microbes

Lactobacillus plantarum IS-10506 supplementation increases faecal sIgA and immune response in children younger than two years – P.D. Kusumo – Beneficial Microbes

Supplementation with Lactobacillus kefiranofaciens ZW3 from Tibetan Kefir improves depression-like behavior in stressed mice by modulating the gut microbiota – Ye Sun – Food and Function

Non-microbiology picks

Identification of Enteroendocrine Regulators by Real-Time Single-Cell Differentiation Mapping – Helmuth Gehart – Cell

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 28, 2019

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Human and General Microbiome

Book Chapter: Necrotizing Enterocolitis and the Preterm Infant Microbiome. – Jillian R. Baranowski – Part of the Advances in Experimental Medicine and Biology book series

Book Chapter: Shaping Microbiota During the First 1000 Days of Life. – Marta Selma-Royo – Part of the Advances in Experimental Medicine and Biology book series

Book Chapter: Targeting Food Allergy with Probiotics. – Lorella Paparo – Part of the Advances in Experimental Medicine and Biology book series

Review: The relation of the vaginal microbiota to early pregnancy development during In Vitro Fertilization treatment-A meta-analysis. – M. Singer – Journal of Gynecology Obstetrics and Human Reproduction

Review: Neuropeptides in the microbiota-brain axis and feeding behavior in autism spectrum disorder. – Sergueï O.Fetissov – Nutrition (Elsevier)

Review: Gut microbiome and cancer immunotherapy. – Weina Li – Cancer Letters

Review: The Microbiome-Host Interaction as a Potential Driver of Anastomotic Leak. – Victoria M. Gershuni – Current Gastroenterology Reports

Review: The links between the gut microbiome and non-alcoholic fatty liver disease (NAFLD). – Zahra Safari – Cellular and Molecular Life Sciences

Review: The role of chronic kidney disease-associated dysbiosis in cardiovascular disease.  – Mark A Bryniarski – Experimental Biology and Medicine

Review: The Interplay between Immunity and Microbiota at Intestinal Immunological Niche: The Case of Cancer. – Rossella Cianci – International Journal of Molecular Sciences

Spotlight: Ethnicity-Influenced Microbiota: A Future Healthcare Perspective. – Madhusmita Dehingia – Trends in Microbiology

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

Altered fecal bacterial composition correlates with disease activity in inflammatory bowel disease and the extent of IL8 induction. – Farnaz Heidarian – Current Research in Translational Medicine

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

Among older adults, age-related changes in the stool microbiome differ by HIV-1 serostatus. – Jay Liu – EBioMedicine

Deep sequencing reveals specific bacterial signatures in the subgingival microbiota of healthy subjects. – Eri Ikeda – Clinical Oral Investigations

Close social relationships correlate with human gut microbiota composition. – Kimberly A. Dill-McFarland – Scientific Reports

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

The respiratory microbiota: new insights into pulmonary tuberculosis. – Setegn Eshetie – BMC Infectious Diseases

 

Faecal Transplants

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

Clinical characteristic and fecal microbiota responses to probiotic or antidepressant in patients with diarrhea-predominant irritable bowel syndrome with depression comorbidity: a pilot study. – Lu Zhang – Chinese Medical Journal

Multi-session fecal microbiota transplantation using colonoscopy has favorable outcomes for the treatment of steroid-dependent ulcerative colitis. – Young-Seok Cho – Intestinal Research

 

Beneficial Microbes and Compounds

Effect of Probiotic Use on Adverse Events in Adult Patients with Inflammatory Bowel Disease: a Retrospective Cohort Study. – Maria Pina Dore – Probiotics and Antimicrobial Proteins

Identification of the novel role of butyrate as AhR ligand in human intestinal epithelial cells. – Ludovica Marinelli – Scientific Reports

Bifidobacterium bifidum ATCC 15696 and Bifidobacterium breve 24b metabolic interaction based on 2′-O-fucosyl-lactose studied in steady-state cultures in a Freter-style chemostat. – Manuela Centanni – Applied and Environmental Microbiology

Oral supplements of combined fructo- and xylo-oligosaccharides during perinatal period significantly offsets acrylamide-induced oxidative impairments and neurotoxicity in rats. – Muralidhara Krishna – Journal Of Physiology And Pharmacology

Impact of Grain Sorghum Polyphenols on Microbiota of Normal Weight and Overweight/Obese Subjects during In Vitro Fecal Fermentation. – Danielle Ashley – Nutrients

Geographical location specific composition of cultured microbiota and Lactobacillus occurrence in human breast milk in China. – Mengfan Ding – Food & Function

 

Animal Microbiome

Review: The Road Not Taken: The Rumen Microbiome, Functional Groups, and Community States. – Sarah Moraïs – Trends in Microbiology

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

Genomic diversity landscape of the honey bee gut microbiota. – Kirsten M. Ellegaard – Nature Communications

Abnormal composition of gut microbiota contributes to delirium-like behaviors after abdominal surgery in mice. – Jie Zhang – Neuroscience and Therapeutics

Functional Interactions between Gut Microbiota Transplantation, Quercetin and High Fat Diet Determine Non-Alcoholic Fatty Liver Disease Development in Germ-Free Mice. – David Porras – Molecular Nutrition and Food Research

Metagenomic dissection of the canine gut microbiota: insights into taxonomic, metabolic and nutritional features. – Giulia Alessandri – Environmental Microbiology

 

Environmental Microbiome

Succession Patterns and Physical Niche Partitioning in Microbial Communities from Subsurface Coal Seams. – Silas H.W.Vick – iScience

 

Food Microbiome

Book Chapter: Microbial Ecology of Fermented Vegetables and Non-Alcoholic Drinks and Current Knowledge on Their Impact on Human Health. – Laura Lavefve – Advances in Food and Nutrition Research

 

Methodologies

Review: A crash course in sequencing for a microbiologist. – Aleksandra Kozińska – Journal of Applied Genetics

Review: The Quest for Novel Antimicrobial Compounds: Emerging Trends in Research, Development, and Technologies. – Pavan K. Mantravadi – Antibiotics

Effects of the long-term storage of human fecal microbiota samples collected in RNAlater. – Julien Tap – Scientific Reports

A sensitive GC/MS detection method for analyzing microbial metabolites short chain fatty acids in fecal and serum samples. – Shuming Zhang – Talanta