June 9, 2018

Human respiratory microbiome

Lung Dysbiosis, Inflammation, and Injury in Hematopoietic Cell Transplantation – David N O’Dwyer, American Journal of Respiratory and Critical Care Medicine

Heterogeneity of Microbiota Dysbiosis in Chronic Rhinosinusitis: Potential Clinical Implications and Microbial Community Mechanisms Contributing to Sinonasal Inflammation – Keehoon Lee, Frontiers in Cell and Infection Microbiology

Human skin microbiome

A systematic literature review of the human skin microbiome as biomarker for dermatological drug development – T. van der Kolk, British Journal of Clinical Pharmacology

Human gut microbiome

Inadequate Vitamin C Status in Prediabetes and Type 2 Diabetes Mellitus: Associations with Glycaemic Control, Obesity, and Smoking – Renée Wilson, Nutrients

Altered Stool Microbiota of Infants with Cystic Fibrosis Shows Reduction in Genera Associated with Immune Programming – Katherine Anosca, bioRxiv

Gut Microbiota Diversity across Ethnicities in the United States – Andrew W Brooks, bioRxiv

From the Mediterranean Diet to the Microbiome – Caroline E Childs, The Journal of Nutrition

Letter: improvements in mental health after faecal microbiota transplantation—an underexplored treatment‐related benefit? – B. H. Mullish, Alimentary Pharmacology and Therapeutics

Letter: improvements in mental health after faecal microbiota transplantation—an underexplored treatment‐related benefit? Authors’ reply – J. Jalanka, Alimentary Pharmacology and Therapeutics

Microbiota‐gut‐brain axis: Interaction of gut microbes and their metabolites with host epithelial barriers – Y. Bhattarai, Neurogastroenterology & Motility

Animal experiments

Bisphenol-A alters microbiota metabolites derived from aromatic amino acids and worsens disease activity during colitis – Jennifer AA DeLuca, Experimental Biology and Medicine

Fumonisin-Exposure Impairs Age-Related Ecological Succession of Bacterial Species in Weaned Pig Gut Microbiota – Ivan Mateos, Toxins

Ethanol extract of Ganoderma lucidum ameliorates lipid metabolic disorders and modulates the gut microbiota composition in high-fat diet fed rats – Wei-Ling Guo, Food & Function

Gut microbiota promotes production of aromatic metabolites through degradation of barley leaf fiber – Daotong Li, The Journal of Nutritional Biochemistry

Dietary Supplementation of Potato Peel Powders Prepared from Conventional and Organic Russet and Non-organic Gold and Red Potatoes Reduces Weight Gain in Mice on a High-Fat Diet – Salem Elkahoui, Journal of Agricultural and Food Chemistry

Microbial dysbiosis associated with impaired intestinal Na+/H+ exchange accelerates and exacerbates colitis in ex-germ free mice – Christy A. Harrison, Mucosal Immunology

Animal microbiome

Comparison of Channel Catfish and Blue Catfish Gut Microbiota Assemblages Shows Minimal Effects of Host Genetics on Microbial Structure and Inferred Function – Jacob W. Bledsoe, Frontiers in Microbiology

Inter-individual variability in copepod microbiomes reveals bacterial networks linked to host physiology – Manoshi S. Datta, The ISME Journal

Metagenomics detection and characterisation of viruses in faecal samples from Australian wild birds – Jessy Vibin, Scientific Reports

Microorganism’s adaptation of Crucian carp may closely relate to its living environments – Huanxin Zhang, Microbiology Open

Diversity, specificity, co-occurrence and hub taxa of the bacterial–fungal pollen microbiome – Binoy Ambika Manirajan, FEMS Microbiology Ecology

Differential carbohydrate utilization and organic acid production by honey bee symbionts – Fredrick J Lee, FEMS Microbiology Ecology

Plant, root, and soil microbiome

The effect of periphyton on seed germination and seedling growth of rice (Oryza sativa) in paddy area – Haiying Lu, Science of The Total Environment

Diversity of Bacteria and the Characteristics of Actinobacteria Community Structure in Badain Jaran Desert and Tengger Desert of China – Ye Sun, Frontiers in Microbiology

Vancomycin and/or Multidrug-Resistant Citrobacter Freundii Altered the Metabolic Pattern of Soil Microbial Community – Mariusz Cycoń, Frontiers in Microbiology

Degradation of dibutyl phthalate in two contrasting agricultural soils and its long-term effects on soil microbial community – Jinjin Cheng, Science of The Total Environment

Impact of Bactrocera oleae on the fungal microbiota of ripe olive drupes – Ahmed Abdelfattah, bioRxiv

Potential of Finger Millet Indigenous Rhizobacterium Pseudomonas sp. MSSRFD41 in Blast Disease Management—Growth Promotion and Compatibility With the Resident Rhizomicrobiome – Jegan Sekar, Frontiers in Microbiology

Biochars from olive mill waste have contrasting effects on plants, fungi and phytoparasitic nematodes – Roberta Marra, Plos One

Water and extremophile microbiome 

Effects of Ice-Algal Aggregate Export on the Connectivity of Bacterial Communities in the Central Arctic Ocean – Josephine Z. Rapp, Frontiers in Microbiology

Built environment

The Airplane Cabin Microbiome – Howard Weiss, Microbial Ecology

Food microbiology

Sequencing of the Cheese Microbiome and Its Relevance to Industry – Bhagya. R. Yeluri Jonnala, Frontiers in Microbiology

Comparison of Bacterial Diversity Between Two Traditional Starters and the Round-Koji-Maker Starter for Traditional Cantonese Chi-Flavor Liquor Brewing – Jie Wang, Frontiers in Microbiology

Microbial ecology

Syntrophic growth with direct interspecies electron transfer between pili-free Geobacter species – Xing Liu, The ISME Journal

Uneven distribution of cobamide biosynthesis and dependence in bacteria predicted by comparative genomics – Amanda N Shelton, bioRxiv

Microbial Diversity and Nitrogen‐metabolizing Gene Abundance in Backyard Food Waste Composting Systems – T. C. Weglarz, Journal of Applied Microbiology

Enhancement of methanogenesis by electric syntrophy with biogenic iron‐sulfide minerals – Souichiro Kato, Microbiology Open

Probiotics/Prebiotics

Probiotics Ameliorate Stool Consistency in Patients with Chronic Constipation: A Randomized, Double-Blind, Placebo-Controlled Study – Jin Young Yoon, Digestive Diseases and Sciences

Supplementation of p40, a Lactobacillus rhamnosus GG-derived protein, in early life promotes epidermal growth factor receptor-dependent intestinal development and long-term health outcomes – Xi Shen, Mucosal Immunology

Bioinformatics

Detection of Multidimensional Co-Exclusion Patterns in Microbial Communities – Levent Albayrak, Bioinformatics

 

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June 7, 2018

 

Today’s microbiology highlights: Microbiome in pregnancies, microbiome of SLE, Mycobacteria of a karst region, skin microbiome of non-human mammals. And lab diversity, potential problem in big data, Paris climate agreement of 1.5⁰C increase among the non-microbe highlights.

 

General microbiome

Biochemical, molecular and antibiotic resistance profile of multi-potential toluene metabolizing bacteria isolated from tannery effluents – F Muccee – bioRxiv

Pregnancy and early life

Review: Microbiome in normal and pathological pregnancies: A literature overview – CR Taddei – AJRI

Multi-site human microbiome

Multidrug resistant pathogens respond differently to the presence of co-pathogen, commensal, probiotic and host cells – AP Chan – Scientific Reports

 

Human gut microbiome

Proton Pump Inhibitor Initiation and Withdrawal affects Gut Microbiota and Readmission Risk in Cirrhosis – JS Bajaj – AJG

Review: Early-Life Food Nutrition, Microbiota Maturation and Immune Development Shape Life-Long Health – X Zhou – Critical Reviews in Food Science and Nutrition

Animal experiments

Intermittent Fasting Confers Protection in CNS Autoimmunity by Altering the Gut Microbiota – F Cignarella – Cell Metabolism

The Microbiome and Systemic Lupus Erythematosus – JT Rosenbaum – The New England Journal of Medicine

Review: The probiotic effectiveness in experimental colitis is correlated with gut microbiome and host genetic features – S Suwal – bioRxiv

Animal microbiome 

Comprehensive skin microbiome analysis reveals the uniqueness of human skin and evidence for phylosymbiosis within the class Mammalia – AA Ross – PNAS

Alterations in the gut (Gallus gallus) microbiota following the consumption of zinc biofortified wheat (Triticum aestivum) -based diet – S Reed – ACS

Water and extremophile microbiome 

Nontuberculous mycobacteria in the environment of Hranice Abyss, the world’s deepest flooded cave (Hranice karst, Czech Republic) – I Pavlik – Environmental Science and Pollution Research

Built environment 

Toxicity assessment of pharmaceutical compounds on mixed culture from activated sludge using respirometric technique: The role of microbial community structure – IA Vasiliadou – Science of The Total Environment

Food microbiology

Effect of herbal feed additives on performance parameters, intestinal microbiota, intestinal morphology and meat lipid oxidation of broiler chickens – I Giannenas – British Poultry Science

 

Techniques

Identifying and Overcoming Threats to Reproducibility, Replicability, Robustness, and Generalizability in Microbiome Research – PD Schloss – mBio

Next-Generation Sequencing Could be a Promising Diagnostic Approach for Pathogen Detection: Pathogenic Analysis of Pediatric Bacterial Meningitis by Next-Generation Sequencing Technology Directly from Cerebrospinal Fluid Specimens – L Guo – bioRxiv

Microbes in the news

Media Advisory: Live exhibit of dance and song on tiny world of bacteria inside us comes to Buffalo Museum of Science – UB News Center

Non-microbiology picks

These labs are remarkably diverse — here’s why they’re winning at science – Nature

Big data little help in megafauna mysteries – Nature

What does it take to make an institution more diverse? – Nature

The many possible climates from the Paris Agreement’s aim of 1.5 °C warming – Nature

 

May 26, 2018

We have a big variety of topics covered in today’s posts, from built environment to bat microbiome to biolfilms!

Biofilms

Genomic identification of microbial species adhering to maxillofacial prostheses and susceptibility to different hygiene protocols – Juliana Barchelli, The Journal of Bioadhesion and Biofilm Research

Anti-biofilm effect of a butenolide/polymer coating and metatranscriptomic analyses – Wei Ding, The Journal of Bioadhesion and Biofilm Research

Microbial ecology

Keystone taxa as drivers of microbiome structure and functioning – Samiran Banerjee, Nature Reviews Microbiology

Diversity, Stability, and Reproducibility in Stochastically Assembled Microbial Ecosystems – Akshit Goya, Physical Review Letters

Pregnancy and early life

Iron supplementation has minor effects on gut microbiota composition in overweight and obese women in early pregnancy – Marloes Dekker Nitert, British Journal of Nutrition

Human respiratory microbiome

The concordance between upper and lower respiratory microbiota in children with Mycoplasma pneumoniae pneumonia – Wenkui Dai, Emerging Microbes & Infections

The lung microbiome in children with HIV-bronchiectasis: a cross-sectional pilot study – Refiloe Masekela, BMC Pulmonary Medicine

Human skin microbiome

Does Lindioil (Indirubin) treatment affect the composition of Malassezia species on psoriatic skin? – Y. K. Lin, British Journal of Dermatology

Shift in skin microbiota of Western European women across aging – Romain Jugé, Journal of Applied Microbiology

Human vaginal microbiome

Understanding mucosal and microbial functionality of the female reproductive tract by metaproteomics: Implications for HIV transmission – Alicia R. Berard, American Journal of Reproductive Immunology

Vaginal microbiome studies in pregnancy must also analyse host factors – S.S. Witkin, BJOG: An International Journal of Obstetrics & Gynaecology

Vaginal microbiome in early pregnancy and subsequent risk of spontaneous preterm birth: a case‐control study – Negar Tabatabaei, BJOG: An International Journal of Obstetrics & Gynaecology

Human gut microbiome

Structural Alteration of Gut Microbiota during the Amelioration of Human Type 2 Diabetes with Hyperlipidemia by Metformin and a Traditional Chinese Herbal Formula: a Multicenter, Randomized, Open Label Clinical Trial – Xiaolin Tong, mBio

The role of diet in the aetiopathogenesis of inflammatory bowel disease – Hamed Khalili, Nature Reviews Gastroenterology & Hepatology

Animal experiments

Ethanolamine enhances intestinal functions by altering gut microbiome and mucosal anti-stress capacity in weaned rats – Jian Zhou, British Journal of Nutrition

Helicobacter pylori-infected C57BL/6 mice with different gastrointestinal microbiota have contrasting gastric pathology, microbial and host immune responses – Zhongming Ge, Scientific Reports

Evaluation of the impact of glyphosate and its residues in feed on animal health – European Food Safety Authority (EFSA), EFSA Journal

Risks for animal health related to the presence of fumonisins, their modified forms and hidden forms in feed – EFSA Panel on Contaminants in the Food Chain (CONTAM), EFSA Journal

Plateau hypoxia attenuates the metabolic activity of intestinal flora to enhance the bioavailability of nifedipine – Juanhong Zhang, Drug Delivery

Animal microbiome

Fecal Microbiota Composition Changes after a Body Weight Loss Diet in Beagle Dogs – A Salas, Journal of Animal Sciences

The fecal bacterial microbiota of bats; Slovenia – Modest Vengust, PLOS One

Plant, root, and soil microbiome

Fertilization shapes a well-organized community of bacterial decomposers for accelerated paddy straw degradation – Yushan Zhan, Scientific Reports

Paddy-upland rotation for sustainable agriculture with regards to diverse soil microbial community – Ping-Fu Hou, Scientific Reports

Annual post‐market environmental monitoring report on the cultivation of genetically modified maize MON 810 in 2016 – European Food Safety Authority (EFSA), EFSA Journal

Conserved Responses in a War of Small Molecules between a Plant-Pathogenic Bacterium and Fungi – Joseph E. Spraker, mBio

Pseudomonads contribute to regulation of Pratylenchus penetrans (Nematoda) populations on apple – Tristan T. Watson, Canadian Journal of Microbiology

Water and extremophile microbiome

Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm – Jennifer M. Michaud, Nature Communications

Combined genotyping, microbial diversity and metabolite profiling studies on farmed Mytilus spp. from Kiel Fjord – Caroline Utermann, Scientific Reports

Bathyarchaeota: globally distributed metabolic generalists in anoxic environments – Zhichao Zhou, FEMS Microbiology Reviews

Probiotics / prebiotics

Dietary fibers, prebiotics, and exopolysaccharides produced by lactic acid bacteria: potential health benefits with special regard to cholesterol-lowering effects – E. Korcz, Food and Function

Pharmacomicrobiomics: exploiting the drug-microbiota interactions in anticancer therapies – Concetta Panebianco, Microbiome

Built environment

City-scale distribution and dispersal routes of mycobiome in residences – Xinzhao Tong, Microbiome

Unraveling bacterial fingerprints of city subways from microbiome 16S gene profiles – Alejandro R. Walker, Biology Direct

Bioinformatics

ASaiM: a Galaxy-based framework to analyze microbiota data – Bérénice Batut, GigaScience

Comprehensive benchmarking and ensemble approaches for metagenomic classifiers – Alexa B. R. McIntyre, Genome Biology

Techniques

The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain – Elena A. Oniciuc, Genes

A microbial endocrinology-based simulated small intestinal medium for the evaluation of neurochemical production by gut microbiota – Daniel N Villageliú, FEMS Microbiology Ecology

May 23, 2018

Today’s digest is packed full of awesome gut microbiome studies, a bunch of plant/soil studies, new features to QIIME and other bioinformatics, as well as a good serving of interesting pre-prints, editorials, and doctoral theses. Enjoy!

General microbiome

Microbial micropatches within microbial hotspots – Lisa M. Dann – PLOS ONE

Pregnancy and early life

The matter of the reproductive microbiome – Sam Schoenmakers – Obstetric Medicine

Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum – Mie Korslund Wiinblad Crusell – Microbiome

The importance of appropriate initial bacterial colonization of the intestine in newborn, child, and adult health – W Allan Walker – Pediatric Research

Human oral microbiome

Oral health status in historic population: Macroscopic and metagenomic evidence – Claire Willmann – PLOS ONE

The Subgingival Microbiome of Periodontal Pockets With Different Probing Depths in Chronic and Aggressive Periodontitis: A Pilot Study – Meng Shi – Frontiers in Cellular and Infection Microbiology

Human gut microbiome

[Pre-print] Gut microbiota markers in obese adolescent and adult patients: age-dependent differential patterns – Federica Del Chierico – Frontiers in Microbiology

Clinical applications of gut microbiota in cancer biology – Sunny H. Wong – Seminars in Cancer Biology

* Microbiome-Mediated Effects of the Mediterranean Diet on Inflammation – Melisa A Bailey – Advances in Nutrition

** Characterizing the gut microbiome in trauma: significant changes in microbial diversity occur early after severe injury – Benjamin M Howard – Trauma Surgery & Acute Care Open

Hypoxia induces senescence of bone marrow mesenchymal stem cells via altered gut microbiota – Junyue Xing – Nature Communications

Animal experiments

The bacterial and archaeal community structures and methanogenic potential of the cecal microbiota of goats fed with hay and high-grain diets – Wei Jin – Antonie van Leeuwenhoek

Effects of whole-grain rice and wheat on composition of gut microbiota and short-chain fatty acids in rats – Fei Han – Journal of Agriculture and Food Chemistry

Animal microbiome

Diet breadth and exploitation of exotic plants shift the core microbiome of Cephaloleia, a group of tropical herbivorous beetles – Chelsea L. Blankenchip – PeerJ

Altered gut microbiota associated with intestinal disease in grass carp (Ctenopharyngodon idellus) – Ngoc Tuan Tran – World Journal of Microbiology and Biotechnology

The gut microbiome is associated with behavioural task in honey bees – J. C. Jones – Insectes Sociaux

The role of the gut microbiome in health and disease of adult honey bee workers – Kasie Raymann – Current Opinion in Insect Science

Plant, root, and soil microbiome

Microbial communities in soil profile are more responsive to legacy effects of wheat-cover crop rotations than tillage systems – Anil Somenahally – Soil Biology and Biochemistry

New insights into the effects of support matrix on the removal of organic micro-pollutants and the microbial community in constructed wetlands – Liang Zhang – Environmental Pollution

[Doctoral thesis] Imprint of management on microbial communities in arable soil – Putz, Martina

Study of microbial diversity in plant–microbe interaction system with oil sludge contamination – Dhote, Monika – International Journal of Phytoremediation

Effect of different potassium levels on nitrogen metabolism, nitrogen bacteria and nitrogen archaea bacteria communities in rhizosphere of tobacco plant – WENG Zebin – Acta Tabacaria Sinica

Canola Root–Associated Microbiomes in the Canadian Prairies – Chih-Ying Lay – Frontiers in Microbiology

Leaf-associated bacterial microbiota of coffee and its correlation with manganese and calcium levels on leaves – Leandro Pio de Sousa – Genetics and Molecular Biology

[Review] Organic Amendments, Beneficial Microbes, and Soil Microbiota: Toward a Unified Framework for Disease Suppression – Giuliano Bonanomi – Annual Review of Phytopathology

[Pre-print] Metagenomic sequencing provides insights into the location of microbial detoxification in the gut of a small mammalian herbivore – Kevin D. Kohl – bioRxiv

[Pre-print] Archaeal, bacterial, and eukaryal microbial community structure of sediment and seawater in a coastal region near Puerto Nuevo, Baja California – Sabah Ul-Hasan – bioRxiv

Water and extremophile microbiome 

Deterministic mechanisms define the long-term anaerobic digestion microbiome and its functionality regardless of the initial microbial community – M.Peces – Water Research

Built environment

[Editorial] Microbiome Yarns: microbiome of the built environment, paranormal microbiology, and the power of single cell genomics – Kenneth Timmis – microbial biotechnology

New Techniques for the Generation and Analysis of Tailored Microbial Systems on Surfaces – Ariel L. Furst – Biochemistry

* [Pre-print] Strain­level overlap between infant and hospital fungal microbiomes revealed through de novo assembly of eukaryotic genomes from metagenomes – Matthew R. Olm – bioRxiv

Probiotics / prebiotics

The effects of probiotics supplementation on metabolic health in pregnant women: An evidence based meta-analysis – Jia Zheng – PLOS ONE

Bioinformatics

[Pre-print / doctoral thesis] Recovering 2,032 Baltic Sea microbial genomes by optimized metagenomic binning – Alneberg, Johannes – DiVA

** Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin – Nicholas A. Bokulich – Microbiome

Techniques

Functional Genomics Approaches to Studying Symbioses between Legumes and Nitrogen-Fixing Rhizobia – Martina Lardi – High-Throughput

VSITA, an Improved Approach of Target Amplification in the Identification of Viral Pathogens – Yi Zhang – Europe PMC

Making and Sequencing Heavily Multiplexed, High-Throughput 16S Ribosomal RNA Gene Amplicon Libraries Using a Flexible, Two-Stage PCR Protocol – Ankur Naqib – Gene Expression Analysis

Ed’s non-microbiology picks 

The Environmental Protection Agency in the Early Trump Administration: Prelude to Regulatory Capture

Perspectives on the Great Amazon Reef: Extension, Biodiversity, and Threats

Fasting boosts stem cells’ regenerative capacity

Eggs not linked to cardiovascular risk, despite conflicting advice

Noninvasive spinal stimulation method enables paralyzed people to regain use of hands, study finds

Cannabidiol significantly reduces seizures in patients with severe form of epilepsy

May 16, 2018

Today we have a interesting set of reviews. In addtion: research about virome in infants, microbiome changes in Alzheimer’s disease and changes in neonate and maternal microbiome under gestational diabetes. We have also the report of the Oral Microbiome Bank of China and some papers about invertebrate microbiome.  

 

Human/General Microbiome

Review: Microbiome-Immune Interactions and Liver Disease – James H. Tabibian –  Clinical Liver Disease

Review: Microbial Metabolism in the Mammalian Gut: Molecular Mechanisms and Clinical Implications – Anne Hall – Journal of Pediatric Gastroenterology and Nutrition

Review: Starch Tolerance and the Short Bowel – Jan de Laffolie – Journal of Pediatric Gastroenterology and Nutrition

Review: Microbial Fermentation of Starch: Its Impact on the Range of Acceptable Carbohydrate Intake – Satish C. Kalhan – Journal of Pediatric Gastroenterology and Nutrition

Review: Pathways and mechanisms linking dietary components to cardiometabolic disease: thinking beyond calories – K. L. Stanhope – Obesity Reviews

Review: On the potential role of intestinal microbial community in hepatocarcinogenesis in chronic hepatitis B – Ashraf Mohamadkhani – Cancer Medicine

Review: The gut microbiota and the brain-gut-kidney axis in hypertension and chronic kidney disease – Tao Yang – Nature Reviews Nephrology

Review: Epithelial Barrier Dysfunctions in Atopic Dermatitis: A Skin-Gut-Lung Model Linking Microbiome Alteration and Immune Dysregulation – T.H. Zhu – British Journal of Dermatology

Review: Association between Fusobacterium nucleatum and colorectal cancer: Progress and future directions – Sheng Zhang – Journal of Cancer

Viromes of one year old infants reveal the impact of birth mode on microbiome diversity – Angela McCann​ – PeerJ

Dysbiosis of maternal and neonatal microbiota associated with gestational diabetes mellitus – Jinfeng Wang – Gut

Analysis of Gut Microbiome and Diet Modification in Patients with Crohn’s Disease – Sumathi Sankaran Walters – SOJ Microbiology & Infectious Diseases

Gut Microbiome is Altered in Patients with Alzheimer’s Disease – Zhuang, Zhen-Qian – Journal of Alzheimer’s Disease

The Oral Microbiome Bank of China – Peng Xian – International Journal of Oral Science

 

Animal Microbiome

Microbiota modification by probiotic supplementation reduces colitis associated colon cancer in mice – Maria Carolina S Mendes – World Journal of Gastroenterology

A cytokine network involving IL-36γ, IL-23, and IL-22 promotes antimicrobial defense and recovery from intestinal barrier damage – Vu L. Ngo – PNAS

Biodegradation of polyethylene and plastic mixtures in mealworms (larvae of Tenebrio molitor) and effects on the gut microbiome – Anja Malawi Brandon – Environmental Science and Technology

Supplementation with organic acids showing different effects on growth performance, gut morphology and microbiota of weaned pigs fed with highly or less digestible diets – S. Li – Journal of Animal Science

Metagenomics Analysis of Gut Microbiota in a High Fat Diet-Induced Obesity Mouse Model Fed with (-)-Epigallocatechin 3-O-(3-O-Methyl) Gallate (EGCG3”Me) – Xin Zhang – Molecular Nutrition and Food Research

Low bacterial community diversity in two introduced aphid pests revealed with 16S rRNA amplicon sequencing – Francisca Zepeda-Paulo​ – PeerJ

Uncovering the hidden players in Lepidoptera biology: the heritable microbial endosymbionts – Anne Duplouy – PeerJ

The influence of diet and environment on the gut microbial community of field crickets – Soon Hwee Ng – Ecology and Evolution

Changes in intestinal microbiota across an altitudinal gradient in the lizard Phrynocephalus vlangalii – Wenya Zhang – Ecology and Evolution

 

Food Microbiome

The changes of dominant lactic acid bacteria and their metabolites during corn stover ensiling – Zhenshang Xu – Journal of Applied Microbiology

Characterization of the Microbiota in Air- or Vacuum-Packed Crisp Grass Carp ( Ctenopharyngodon idella C. et V.) Fillets by 16S rRNA PCR-Denaturing Gradient Gel Electrophoresis and High-Throughput Sequencing – Ziqiang Pan – Journal of Food Protection

Succession of bacterial microbiota in tilapia fillets at 4 °C and in situ investigation of spoilers – Shan Duan – World Journal of Microbiology and Biotechnology

 

Bioinformatics/Genomics

Preprint: Measures of reproducibility in sampling and laboratory processing methods in high-throughput microbiome analysisPatricia Vera-Wolf (and featuring our Microbiome Digest founder, Elisabeth Bik)BioRxiv

Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments – Alexandre Almeida – GigaScience

Uncovering the drivers of host-associated microbiota with joint species distribution modeling – Johannes R. Björk – Molecular Ecology

 

Beneficial Microbes and Compounds

Review: Vitamin D in inflammatory bowel disease: more than just a supplement – John Gubatan – Current Opinion in Gastroenterology

Review: Bleach for Atopic Dermatitis – Melody Maarouf – Dermatitis

Simultaneous Amelioratation of Colitis and Liver Injury in Mice by Bifidobacterium longum LC67 and Lactobacillus plantarum LC27 – Se-Eun Jang – Scientific Reports

 

Pathogens

Cross-specificity of protective human antibodies against Klebsiella pneumoniae LPS O-antigen – Tim Rollenske – Nature Immunology

 

Environmental Microbiome (including Built environments)

Responses of stream microbes to multiple anthropogenic stressors in a mesocosm study – Julia K.Nuy – Science of The Total Environment

Fine grained compositional analysis of Port Everglades Inlet microbiome using high throughput DNA sequencing – Lauren O’Connell​​ – PeerJ

 

Antimicrobial Resistance

Emerging Infectious Diseases, Antimicrobial Resistance and Millennium Development Goals: Resolving the Challenges through One Health – G. V. Asokan – Central Asian Journal of Global Health

 

Other

Discovery and characterization of a prevalent human gut bacterial enzyme sufficient for the inactivation of a family of plant toxins – Nitzan Koppel – eLife

The Interaction of Anti-diabetic α-Glucosidase Inhibitors and Gut Bacteria α-Glucosidase – Kemin Tan – Protein Science

 

May 12, 2018

Today’s highlights in our Microbiology picks: Antibacterial activity of nested concentric patterns, relationship between the microbiota epitopes and antigenic epitopes, a book chapter on N-Acetyl transferase microbes, core microbiota for de novo IBD, soil microbes and disease suppression, fungi of office dust, microbes of potable  water from the Himalayan region, articles from ‘Techniques’ section.

Today’s highlights in our non-microbes picks: Epidemiology is important, recent on-goings on harassment, mental health awareness in academia, mimicking the prebiotic chemistry using flow chemistry, step taken by Wellcome Trust against misconduct in academia including harassment, Horizon 2020 budget for 2021-27.

 

Events and jobs

Laboratory Manager : New York, NY, United States – Albert Einstein College of Medicine – Deadline: 18 May 2018

General microbiome

Supramolecular Kandinsky circles with high antibacterial activity – H Wang – Nature Communications

Microbiota epitope similarity either dampens or enhances the immunogenicity of disease-associated antigenic epitopes – SC Pro – PLoS One

Genomic evolution of Staphylococcus aureus isolates colonizing the nares and progressing to bacteremia – JB Benoit – PLoS One

Book chapter: N-Acetyltransferases Microorganisms – S Boukouvala – Arylamine N-acetyltransferases in Health and Disease:From Pharmacogenetics to Drug Discovery and Diagnostics

 

Human vaginal microbiome

Preprint: Metatranscriptome analysis of the vaginal microbiota reveals potential mechanisms for protection against metronidazole in bacterial vaginosis – Z-L Deng – bioRxiv

Human gut microbiome

Preprint: Variability of core microbiota in newly diagnosed treatment-naïve paediatric Inflammatory Bowel Disease patients – TGJ de Meij – bioRxiv

Compositional and Functional Differences in the Human Gut Microbiome Correlate with Clinical Outcome following Infection with Wild-Type Salmonella enterica Serovar Typhi – Y Zhang – mBio

Animal experiments 

Preprint: Bottlenecks in the transmission of Porcine reproductive and respiratory syndrome virus (PRRSV1) to naïve pigs and quasi-species variation during infection in partially immune pigs – M Cortey – bioRxiv

Lactobacillus gasseri PA-3 utilizes the purines GMP and guanosine and decreases their absorption in rats – N Yamada – Nucleosides, Nucleotides & Nucleic Acids

An exclusive metabolic niche enables strain engraftment in the gut microbiota – ES Sheperd – Nature

Interleukin 1α-Deficient Mice Have an Altered Gut Microbiota Leading to Protection from Dextran Sodium Sulfate-Induced Colitis – M Nunberg – mSystems

Animal microbiome 

Low bacterial community diversity in two introduced aphid pests revealed with 16S rRNA amplicon sequencing – F Zepeda-Paulo – PeerJ

Plant, root, and soil microbiome

Effect of land use and soil organic matter quality on the structure and function of microbial communities in pastoral soils: Implications for disease suppression – BEA Dignam – PLoS One

Relations between bacterial communities and enzyme functions of two paddy soils – X Luo – European Journal of Soil Science

Nematophagus fungi increasing phosphorus uptake and promoting plant growth – TSA Monteiro – Biological Control

Water and extremophile microbiome 

Effect of elevated pressure on ferric iron reduction coupled to sulfur oxidation by biomining microorganisms – R Zhang – Hydrometallurgy

Halophilic & halotolerant prokaryotes in humans – EH Seck – Future Medicine

Preprint: Structural variability and functional association in the epiphytic bacteria assemblies of freshwater macrophytes (Myriophyllum spicatum) – L Xian – bioRxiv

Investigation of nutrients and faecal coliforms removal in wastewater using a hydroponic system – SF Ndulini – Physics and Chemistry of the Earth, Parts A/B/C

Built environment 

Characterization of fungi in office dust: comparing results of microbial secondary metabolites, fungal ITS region sequencing, viable culture, and other microbial indices – J-H Park – Indoor Air

 

Phages and viruses

Preprint: First report on Bacterial Diversity of Potable Spring water of Indian Himalayan Region – AK Singh – bioRxiv

Preprint: “In plaque-mass spectrometry imaging” reveals a major metabolic shift towards odd-chain fatty acid lipids induced by host-virus interactions – G Schleyer – bioRxiv

Preprint: Adventitious viruses persistently infect three commonly used mosquito cell lines – J Weger-Lucarelli – bioRxiv

Techniques

Preprint: High-resolution ISR amplicon sequencing reveals personalized oral microbiome – C Mukherjee – bioRxiv

Preprint: Transcriptome Analysis of Neisseria gonorrhoeae During Natural Infection Reveals Differential Expression of Antibiotic Resistance Determinants Between Men and Women – K Nudel – bioRxiv

Designer cells programming quorum-sensing interference with microbes – F Sedlmeyer – Nature Communications

A comprehensive model for assessment of liver stage therapies targeting Plasmodium vivax and Plasmodium falciparum – A Roth – Nature Communications

Preprint: Detection and quantification of the heterogeneity of S. aureus bacterial populations to identify antibiotic-induced persistence – MH Hasan – bioRxiv

Rapid isolation of fast-growing methanotrophs from environmental samples using continuous cultivation with gradually increased dilution rates – J Kim – Applied Microbiology and Biotechnology

Microbes in the news

Stanley Falkow, Who Saw How Bacteria Cause Disease, Dies at 84 – NY Times

How the Bugs In Your Gut Could Affect Your Blood Vessels – Live Science

Faeces transplant: The best cure for severe diarrhoea may be more faeces – Times Live

Cancer-killing viruses show promise — and draw billion-dollar investment – Nature

Does where we live affect our skin microbiome? – Medical News Bulletin

Non-Microbiology Picks

Editorial: Epidemiology is a science of high importance – Nature Communications

Mimicking the surface and prebiotic chemistry of early Earth using flow chemistry – DJ Ritson – Nature Communications

I’d whisper to my student self: you are not alone – D Reay – Nature

Harassment should count as scientific misconduct – E Marín-Spiotta – Nature

€100-billion budget proposed for Europe’s next big research programme – I Vesper – Nature

Editorial: The #MeToo campaign is gaining ground in China – Nature

Editorial: What to do to improve postgraduate mental health – Nature

Report harassment or risk losing funding, says top UK science funder – H Else – Nature

78,000-year-old record of Middle and Later stone age innovation in an East African tropical forest – C Shipton – Nature Communications

KACST Impact – Nature Communications

 

May 10, 2018

Today we have quite a few interesting papers in “Water microbiome”, there you can read about: drift in the community structuring of bacteria and microbial eukaryotes by R.Logares; phylogeny‐based database “EukRef–Ciliophora” by V. Boscaro;  diverse bacterial and viral populations in agricultural freshwater pond by J. Chopyk. In a “Bioinformatics” section you can read about “MIMOSA: Algorithms for Microbial Profiling” (by O. U. Nalbantoglu) and about use of SplinectomeR package in longitudinal microbiome studies by R.R. Shields- Cutler. Enjoy!

Jobs

PhD position for anaerobic microbiology of the Black Sea, Netherlands

General microbiome

Cargo Transport Shapes the Spatial Organization of a Microbial Community – Abhishek Shrivastava – bioRxiv

The Effect of Berberine on the Transcriptome and Proteome of E. coli – Zhang Shilei – bioRxiv

Predator-by-Environment Interactions Mediate Bacterial Competition in the Dictyostelium discoideum Microbiome – R. Fredrik Inglis – Frontiers in Microbiology / Evolutionary and Genomic Microbiology

Diversity time-period and diversity-time-area relationships exemplified by the human microbiome – Zhanshan (Sam) Ma – Scientific Reports

Pregnancy and early life

Microbial Biomarkers of Intestinal Barrier Maturation in Preterm Infants – Bing Ma – bioRxiv

Influence of human milk oligosaccharides on adherence of bifidobacteria and clostridia to cell lines – Musilova Sarka  – Acta Microbiologica et Immunologica Hungarica

 

Oral microbiome

Research on oral microbiota of monozygotic twins with discordant caries experience – in vitro and in vivo study – Hongle Wu – Scientific Reports

Glycemic Status Affects the Subgingival Microbiome of Diabetic Patients – Priscila Larcher Longo – Journal of Clinical Periodontology

Research on oral microbiota of monozygotic twins with discordant caries experience – in vitro and in vivo study – Hongle Wu – Scientific Reports

Human gut microbiome

Fecal microbiota transplantation in experimental ulcerative colitis reveals associated gut microbial and host metabolic reprogramming – Zhixiang Yan – Applied and Environmental Microbiology

Fecal microbiota transplantation treatment for refractory ulcerative colitis with allergy to 5-aminosalicylic acid: A case report – Hong-Gang Wang – Medicine

Review: Influence of Commensal Microbiota on the Enteric Nervous System and Its Role in Neurodegenerative Diseases – Endres K. – Journal of Innate Immunology

Loss of Ethanolamine Utilization in Enterococcus faecalis Increases Gastrointestinal Tract Colonization – Karan Gautam Kavala – mBio

Compositional and Functional Differences in the Human Gut Microbiome Correlate with Clinical Outcome following Infection with Wild-Type Salmonella enterica Serovar Typhi – Yan Zhang – mBio

Animal experiments

Effects of gut microbiota and time of treatment on tissue levels of green tea polyphenols in mice – Anna B. Liu – BioFactors

Gastrointestinal microbiota and mucosal immune gene expression in neonatal pigs reared in a cross-fostering model – Nidia Maradiaga – Microbial Pathogenesis

Prolonged restraint stressor exposure in outbred CD-1 mice impacts microbiota, colonic inflammation, and short chain fatty acids – Ross M. Maltz – PLOS One

Review: Biomarkers for monitoring intestinal health in poultry: present status and future perspective – Richard Ducatelle – Veterinary Research

Animal microbiome 

Near full-length 16S rRNA gene next-generation sequencing revealed Asaia as a common midgut bacterium of wild and domesticated Queensland fruit fly larvae – Ania T. Deutscher – Microbiome

Crown-of-thorns sea star, Acanthaster cf. solaris, have tissue-characteristic microbiomes with potential roles in health and reproduction – Lone Høja – Applied and Environmental Microbiology

Multilevel social structure and diet shape the gut microbiota of the gelada monkey, the only grazing primate – Pål Trosvik – Microbiome

Antimicrobial activity in culturable gut microbial communities of springtails – Valeria Agamennone  – Journal of Applied Microbiology

Diversity and antimicrobial potential in sea anemone and holothurian microbiomes – Elizabeth León-Palmero  – PLOS One

Plant, root, and soil microbiome

Niche partition of phenanthrene-degrading bacteria along a Phragmites australis rhizosphere gradient – Xiaofei Lv – Biology and Fertility of Soils

Core microbiomes for sustainable agroecosystems – Toju H -Nature Plants

Determination of agricultural impact on soil microbial activity using δ18OP HCl and respiration experiments – Katherine Polain – ACS Earth and Space Chemistry

Seasonal dynamics of bacterial communities in a Betula albosinensis forest – C. Du – European Journal of Soil Science

Niche partition of phenanthrene-degrading bacteria along a Phragmites australis rhizosphere gradient – Xiaofei Lv – Biology and Fertility of Soils

Water and extremophile microbiome

Effects of Xiantao sewage treatment on microbial community structure of shallow groundwater in wetland – Shu-Fen Song – bioRxiv

Unexpected versatility in the metabolism and ecophysiology of globally relevant nitrite-oxidizing Nitrotoga bacteria – Andrew Boddicker – bioRxiv

Long-term seasonality of marine photoheterotrophic bacteria reveals low cohesiveness within the different phylogroups – Adrià Auladell – bioRxiv

Molecular cloning of glutathione peroxidase gene of Antarctic ice microalga Chlamydomonas sp. ICE‐L and its expression changes under temperature and salinity stress – Jin Hui Wang – Phycological Research

Contrasting prevalence of selection and drift in the community structuring of bacteria and microbial eukaryotes – Ramiro Logares – Environmental Microbiology

EukRef–Ciliophora: A manually curated, phylogeny‐based database of small subunit rRNA gene sequences of ciliates – Vittorio Boscaro – Environmental Microbiology

Novel human-associated Lachnospiraceae genetic markers improve detection of fecal pollution sources in urban waters – Shuchen Feng – Applied and Environmental Microbiology

Municipal wastewater treatment potential and metal accumulation strategies of Colocasia esculenta (L.) Schott and Typha latifolia L. in a constructed wetland – Vivek Rana – Environmental Monitoring and Assessment

Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations – Jessica Chopyk – Frontiers in Microbiology / Aquatic Microbiology

Characterization of a Highly Enriched Microbial Consortium Reductively Dechlorinating 2,3-Dichlorophenol and 2,4,6-Trichlorophenol and the Corresponding cprA Genes from River Sediment – Wael S. El-Sayed – Polish Journal of Microbiology

Built environment

Characterization of fungi in office dust: comparing results of microbial secondary metabolites, fungal ITS region sequencing, viable culture, and other microbial indices – Ju Hyeong Park – Indoor Air

Investigation of the Active Biofilm Communities on Polypropylene Filter Media in a Fixed Biofilm Reactor for Wastewater Treatment – Iffat Naz – Journal of Chemical Technology and Biotechnology

Food microbiology

Characterization of the contaminant bacterial communities in sugarcane first-generation industrial ethanol production – Maria L. Bonatelli – FEMS Microbiology Letters

Probiotics / prebiotics

Phylotype-level profiling of lactobacilli in highly complex environments by means of an ITS-based metagenomic approach – Christian Milani – Applied and Environmental Microbiology

Comparative Genomics Reveals the Regulatory Complexity of Bifidobacterial Arabinose and Arabino-Oligosaccharide Utilization – Aleksandr A. Arzamasov – Frontiers in Microbiology /Evolutionary and Genomic Microbiology

 

Bioinformatics

MIMOSA: Algorithms for Microbial Profiling – Ozkan Ufuk Nalbantoglu – IEEE/ACM Transactions on Computational Biology and Bioinformatics

SplinectomeR Enables Group Comparisons in Longitudinal Microbiome Studies – Robin R. Shields-Cutler – Frontiers in Microbiology / Systems Microbiology

Metagenome enrichment approach used for selection of oil-degrading bacteria consortia for drill cutting residue bioremediation – Alaine B.Guerra – Environmental Pollution

Biotechnology

Microbial co-culturing systems: butanol production from organic wastes through consolidated bioprocessing – Yujia Jiang – Applied Microbiology and Biotechnology

Techniques

Sensitive detection of Live Escherichia coli by bacteriophage amplification-coupled immunoassay on the Luminex® MAGPIX instrument – Tomotaka Mido – bioRxiv

Microbes in the news

Scientists use dietary seaweed to manipulate gut bacteria in mice

Microbes are savvy investors when contributing to the common good