October 24, 2020

Greetings from Santiago, Chile! Today, in this Digest we have several reviews about microbiota and different conditions or interventions. We have also papers about the microbial evolution and its relationship with the host, the role of O-glycosylated mucus, the microbiome of neonates and the influence of probiotics, and more…    

Human and General Microbiome

Review: The gut microbiota-brain axis in behaviour and brain disorders – Livia H. Morais – Nature Reviews Microbiology

Review: Gut microbiota in pancreatic diseases: possible new therapeutic strategies – Li-long Pan – Acta Pharmacologica Sinica 

Review: The Gut Microbiome and the Triple Environmental Hit Concept of Inflammatory Bowel Disease Pathogenesis – Richard Kellermayer – Journal of Pediatric Gastroenterology and Nutrition

Review: Allogenic stem cell transplant-associated acute graft versus host disease: a computational drug discovery text mining approach using oral and gut microbiome signatures – M. F. Beckman – Supportive Care in Cancer 

Experimental evolution makes microbes more cooperative with their local host genotype – Rebecca T. Batstone – Science

Proximal colon-derived O-glycosylated mucus encapsulates and modulates the microbiota – Kirk Bergstrom – Science

The Microbiota Profile in Inflamed and Non-Inflamed Ileal Pouch-Anal Anastomosis – Sabrina Just Kousgaard – Microorganisms (MDPI)

Altered Gut Microbiome and Environmental Factors Associated with Development of Eczema in Hong Kong Infants: A 4-Month Pilot Study – Carmen Wing Han Chan – International Journal of Environmental Research and Public Health

Beneficial microbes and Compounds

Systematic Review: The role of pro-, pre- and symbiotics in cancer: A systematic review – Miarons Marta – Journal of Clinical Pharmacy and Therapeutics

Review: Fiber and Prebiotic Interventions in Pediatric Inflammatory Bowel Disease: What Role Does the Gut Microbiome Play? – Genelle R. Healey – Nutrients (MDPI)

Influence of probiotic supplementation on the developing microbiota in human preterm neonates – Niels van Best – Gut Microbes

Anti-Inflammatory and Intestinal Microbiota Modulation Properties of Jinxiang Garlic ( Allium sativum L.) Polysaccharides toward Dextran Sodium Sulfate-Induced Colitis – Xin Shao – Journal of Agricultural and Food Chemistry

Food Microbiome

Metagenomic characterization of bacterial community and antibiotic resistance genes in representative ready-to-eat food in southern China – YiMing Li – Scientific Reports

Animal Microbiome

Review: Toxin Degradation by Rumen Microorganisms: A Review – Zhi Hung Loh – Toxins (MDPI)

Gut dysbiosis associated with the rats’ responses in methamphetamine-induced conditioned place preference – Cheng Yang – Addiction Biology

A High-Fat Diet Increases Gut Microbiota Biodiversity and Energy Expenditure Due to Nutrient Difference – Botao Wang – Nutrients (MDPI)

Plant Microbiome

Microbiome-wide association studies reveal correlations between the structure and metabolism of the rhizosphere microbiome and disease resistance in cassava – Lin Zhang – Plant Biotechnology Journal

Daring to be differential: metabarcoding analysis of soil and plant-related microbial communities using amplicon sequence variants and operational taxonomical units – Lisa Joos – BMC Genomics

Bioinformatics

Clustering on Human Microbiome Sequencing Data: A Distance-Based Unsupervised Learning Model – Dongyang Yang – Microorganisms (MDPI)

A generalized machine-learning aided method for targeted identification of industrial enzymes from metagenome: a xylanase temperature dependence case study – Mehdi Foroozandeh Shahraki – Biotechnology and Bioengeenering

October 20,2020

Good morning! Today’s post features several articles relating to the development of the gut microbiome as it pertains to c-section and immune development as well as how dietary nutrients shape gut microbes and intestinal mucosa via epigenetic modifications. There is also an in-depth article on the impact of microbiota in evolving herd immunity against viral diseases which is especially relevant in the covid-19 pandemic. Enjoy reading and have a great day!

COVID-19

Preprint: The effect of temperature and humidity on the stability of SARS-CoV-2 and other enveloped viruses – Dylan H. Morris, et al. bioRxiv

[PDF] Impact of Microbiota: A Paradigm for Evolving Herd Immunity against Viral Diseases – A Shelly, et al. – Viruses

ORAL MICROBIOME

Preprint: Impact of Commiphora myrrha on bacteria (Streptococcus mutans and Lactobacillus species) related to dental caries – REEM IZZELDIEN, et al. – bioRxiv

[HTML] Human oral microbiome dysbiosis as a novel non-invasive biomarker in detection of colorectal cancer – S Zhang, et al. – Theranostics

GENERAL MICROBIOME

Microbiota Effects on Carcinogenesis: Initiation, Promotion and Progression -LR Lopez, et al. – Annual Review of Medicine

[HTML] Emerging role of bacterial extracellular vesicles in cancer – A Chronopoulos, R Kalluri – Oncogene

HUMAN GUT MICROBIOME

News Article: Microbiome drug reduces recurrent CDI – Healio

[PDF] Immune development of children born from Caesarean section – Z Munasir, LC Khoe – World Nutrition Journal

[PDF] Caesarean section and gut microbiota in children – AD Widodo, M Juffrie – World Nutrition Journal

Gut microbiome stability and resilience: elucidating the response to perturbations in order to modulate gut health -M Fassarella, et al. – Gut

Dietary nutrients shape gut microbes and intestinal mucosa via epigenetic modifications – J Wu, et al. – Critical Reviews in Food

HUMAN RESPIRATORY MICROBIOME

Preprint: Cystic Fibrosis Acidic Microenvironment Determines Antibiotic Susceptibility and Biofilm Formation of Pseudomonas aeruginosa – Qiao Lin, et al. – bioRxiv

ANIMAL EXPERIMENTS

Integrated phosphoproteomic and metabolomic profiling reveals perturbed pathways in the hippocampus of gut microbiota dysbiosis mice – H Wang, et al.- Translational Psychiatry

ANIMAL MICROBIOME

[HTML] Microbial communities associated with the camel tick, Hyalomma dromedarii: 16S rRNA gene-based analysis -N Perveen, et al. – Scientific Reports

PLANT, ROOT AND SOIL MICROBIOME

Preprint: Soil disturbance affects plant growth via soil microbial community shifts – Taylor J Seitz, et al. – bioRxiv

Pinewood Nematode Alters the Endophytic and Rhizospheric Microbial Communities of Pinus massoniana – W Zhang, et al. – Microbial Ecology

WATER AND EXTREMOPHILE MICROBIOME

Role of Extremophiles and Extremophilic Proteins in Industrial Waste Treatment – S Tapadar, et al. – Removal of Emerging …

PHAGES AND VIRUSES

Preprint: The structure of enteric human adenovirus 41 – a leading cause of diarrhoea in children – Karim Rafie, et al. -bioRxiv

Preprint: Clustered Rapid Induction of Apoptosis Limits ZIKV and DENV-2 Proliferation in the Midguts of Aedes aegypti -Jasmine B Ayers, et al. -bioRxiv

BIOINFORMATICS

[PDF] Multi-omics for Biomedical Applications – MS Khan, et al – J Appl Bioanal

October 17, 2020

Have a nice weekend! Today, in this brief Digest, several papers about microbiome studies in animal models. Additionally, some highlighted studies in humans: the vaginal microbiota in a Swedish cohort, and the microbiota from the urinary tract, by the use of culturomics.

Human and General Microbiome

Using data science for medical decision making case: role of gut microbiome in multiple sclerosis – Jasminka Hasic Telalovic- BMC Medical Informatics and Decision Making

Deciphering the Urinary Microbiota Repertoire by Culturomics Reveals Mostly Anaerobic Bacteria From the Gut – Grégory Dubourg – Frontiers in Microbiology

Vaginal microbiota and human papillomavirus infection among young Swedish women – Liqin Cheng – npj Biofilms and Microbiomes

Review: Engineering the Microbiome to Prevent Adverse Events: Challenges and Opportunities – Saad Khan – Annual Review of Pharmacology and Toxicology 

Animal Microbiome

Developmental stages in microbiota, bile acids, and clostridial species in healthy puppies – Amanda B. Blake – Journal of Veterinary Internal Medicine

Screening of Microbes Associated With Swine Growth and Fat Deposition Traits Across the Intestinal Tract – Shi Tang – Frontiers in Microbiology

Differential Responses to Dietary Protein and Carbohydrate Ratio on Gut Microbiome in Obese vs. Lean Cats – Qinghong Li – Frontiers in Microbiology

Inulin alleviates adverse metabolic syndrome and regulates intestinal microbiota composition in Nile Tilapia ( Oreochromis niloticus) fed with high-carbohydrate diet – Tong Wang – British Journal of Nutrition

Minireview: Transmission of the sponge microbiome: moving towards a unified model – Bruno Francesco Rodrigues de Oliveira  – Environmental Microbiology Reports 

Co-selection of antibiotic resistance genes, and mobile genetic elements in the presence of heavy metals in poultry farm environments – Sohaib H.Mazhar – Science of The Total Environment

Friend or foe? Effects of host immune activation on the gut microbiome in the caterpillar Manduca sexta – Laura E. McMillan – Journal of Experimental Biology

Environmental Microbiome

Correspondence: Towards meaningful scales in ecosystem microbiome research – Francisco Dini‐Andreote – Environmental Microbiology

Preprint: Genomics-accelerated discovery of diverse fungicidal bacteria – Matthew B Biggs – BioXriv

Preprint: Functional repertoire convergence of distantly related eukaryotic plankton lineages revealed by genome-resolved metagenomics – Tom O. Delmont – BioXriv

Beneficial Microbes and Compounds

The chemopreventive effects of Huangqin-tea against AOM-induced preneoplastic colonic aberrant crypt foci in rats and omics analysis – Jie Shen – Food & Function

Prophylactic effects of oral administration of Lactobacillus casei on house dust mite-induced asthma in mice – Lingzhi Li – Food & Function

Lactobacillus plantarum Shinshu N-07 isolated from fermented Brassica rapa L. attenuates visceral fat accumulation induced by high-fat diet in mice – T. Yin – Beneficial Microbes

October 15, 2020

Hi all! We’ve got a pretty short post for you today. Most notably, there are a few new articles out evaluating microbiome x diet interactions and feed efficiency in livestock.

Animal experiments
Metagenomic analysis reveals linkages between caecal microbiota and feed efficiency in Xiayan chicken – Du et al. – Poultry Science

Oat bran and wheat bran impact net energy by shaping microbial communities and fermentation products in pigs fed diets with or without xylanase – Lyu et al. – Journal of Animal Science and Biotechnology

Comparison of the microbial communities of alpacas and sheep fed diets with three different ratios of corn stalk to concentrate – Chao et al. – Journal of Animal Physiology and Animal Nutrition

Plant, root, and soil (and lichen) microbiome
Metaproteomics reveals the structural and functional diversity of Dermatocarpon miniatum (L.) W. Mann. microbiota – Ullah et al. – Fungal Biology

Water and extremophile microbiome

16S rRNA gene diversity in ancient gray and pink salt from San Simón Salt Mines in Tarija, Bolivia – Pecher et al. – Microbiology Resource Announcement

Seagrass vegetation affect the vertical organization of microbial communities in sediment – Sun et al. – Marine Environmental Research

October 13, 2020

Today’s mid-week digest is about – meta analysis of metabolic benefits of probiotics, probiotics and synbiotics, microbiome association with narcolepsy type 1, design of microbial consortium for reduced C. difficle colonization, new sequencing technique for pathogen identification in cerebrospinal fluid and many more… Happy reading!

Human microbiome

The effect of probiotics, prebiotics or synbiotics on metabolic outcomes in individuals with diabetes: a systematic review and meta-analysis – Patricia M. Bock – Diabetologia

Effect of a Nonoptimal Cervicovaginal Microbiota and Psychosocial Stress on Recurrent Spontaneous Preterm Birth – Kristin D. Gerson – American Journal of Perinatology

Targeting the microbiome-gut-brain axis for improving cognition in schizophrenia and major mood disorders: A narrative review – Miquel Bioque – Progress in Neuro-Psychopharmacology and Biological Psychiatry

Inflammatory Bowel Disease Environmental Risk Factors: Diet and Gut Microbiota – Sarah Altajar – Current Gastroenterology Reports

Co‐ and polymicrobial infections in the gut mucosa: the host‐microbiota‐pathogen perspective – Teresa Frisan – Cellular Microbiology

Gut microbiota composition is associated with narcolepsy type 1 – Alexandre Lecomte – Neurology

A parental transcriptional response to microsporidia infection induces inherited immunity in offspring – Alexandra R. Willis – BioRxiv

Melamine contamination and associated health risks: Gut microbiota does make a difference – Meenakshi Rajpoot – Biotechnology and Applied Biochemistry

Animal microbiome

Rational design of a microbial consortium of mucosal sugar utilizers reduces Clostridiodes difficile colonization – Fátima C. Pereira – Nature Communications

Effects of seasonality and previous logging on faecal helminth-microbiota associations in wild lemurs – I. I. de Winter – Scientific Reports

Bacterial community analysis on the different mucosal immune inductive sites of gastrointestinal tract in Bactrian camels – Wang-Dong Zhang – PlosOne

Sows affect their piglets’ faecal microbiota until fattening but not their Salmonella enterica shedding status – Guillaume Larivière‐Gauthier – Letters in Applied Microbiology

Plant, root and soil microbiome

Comparison of soil microbial community between reseeding grassland and natural grassland in Songnen Meadow – Ruifen Zhu – Scientific Reports

Evidence for signatures of ancient microbial life in paleosols – Katharina Frindte – Scientific Reports

Techniques

Pathogen identification in culture-negative cerebrospinal fluid specimens of patients with purulent meningitis using next-generation sequencing technology – Xin Men – International Journal of Clinical Experimental Pathology

October 10, 2020

Good morning everyone! 

Highlights of today’s microbiome digest include: 

  • A genome-wide association study showed an association between host genetic variants and the gut microbiome in the Chinese population.
  • Association of sugar intake with the gut microbiome composition in the Malmö Offspring Study.
  • Gut microbial changes in Holstein cows from birth to adulthood.
  •  Fecal microbiome and antimicrobial resistance profiles in healthy Australian foals.
  • A new method for the detection of functional potential from metagenomic sequences.

Enjoy reading!

General microbiome

Review: Interactions among microbes, the immune system, and the circadian clock – John F. Brooks – Seminars in Immunopathology

https://link.springer.com/article/10.1007%2Fs00281-020-00820-1

Comment: Know Your Model: Microbiota & phenotypes – Michelle N. Perry – Lab Animal

https://www.nature.com/articles/s41684-020-00660-4

The wasted chewing gum bacteriome – Leila Satari – Scientific Reports

https://www.nature.com/articles/s41598-020-73913-4

A realism-based approach to an ontological representation of symbiotic interactions – Matthew Diller – BMC Medical Informatics and Decision Making

https://bmcmedinformdecismak.biomedcentral.com/articles/10.1186/s12911-020-01273-0

Review: Multi-omics tools for studying microbial biofilms: current perspectives and future directions – Chaminda J. Seneviratne – Critical Reviews in Microbiology

https://www.tandfonline.com/doi/abs/10.1080/1040841X.2020.1828817?journalCode=imby20

Review: Challenges & opportunities for phage-based in situ microbiome engineering in the gut – Peter J Voorhees

https://www.sciencedirect.com/science/article/abs/pii/S0168365920303503?via%3Dihub

Human gut microbiome

Review: Modulation of the Microbiome in Parkinson’s Disease: Diet, Drug, Stool Transplant, and Beyond – Ethan G. Brown – Neurotherapeutics

https://link.springer.com/article/10.1007%2Fs13311-020-00942-2

Review: Gut microbiome and anorexia nervosa: The relationship between microbiome and gut-brain interaction in the context of anorexia nervosa – J. Seitz – Nervenarzt

https://link.springer.com/article/10.1007%2Fs00115-020-01003-x

The interplay between host genetics and the gut microbiome reveals common and distinct microbiome features for complex human diseases – Fengzhe Xu – Microbiome

https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-020-00923-9

Gut microbiota composition in relation to intake of added sugar, sugar-sweetened beverages and artificially sweetened beverages in the Malmö Offspring Study – Stina Ramne – European Journal of Nutrition

https://link.springer.com/article/10.1007%2Fs00394-020-02392-0

Gut microbiome mediated epigenetic regulation of brain disorder and application of machine learning for multi-omics data analysis – Harpreet Kaur – Genome

https://cdnsciencepub.com/doi/10.1139/gen-2020-0136

Review: The Gut Microbiome and Bone Strength – Macy Castaneda – Current Osteoporosis Reports

https://link.springer.com/article/10.1007%2Fs11914-020-00627-x

Review: Effects of Antibiotic Treatment on Gut Microbiota and How to Overcome Its Negative Impacts on Human Health – Camila Fontoura Acosta Ribeiro

https://pubs.acs.org/doi/10.1021/acsinfecdis.0c00036

Mechanisms linking the human gut microbiome to prophylactic and treatment strategies for COVID-19 – Gemma E Walton- British Journal of Nutrition

https://www.cambridge.org/core/journals/british-journal-of-nutrition/article/mechanisms-linking-the-human-gut-microbiome-to-prophylactic-and-treatment-strategies-for-covid19/A3E1ADF2053768F34BCA72BF620AC86F

Oral and respiratory microbiome

Toll like Receptor signalling by Prevotella histicola activates alternative NF-κB signalling in Cystic Fibrosis bronchial epithelial cells compared to P. aeruginosa – Anne Bertelsen – PloS One

https://pubmed.ncbi.nlm.nih.gov/33031374/

Vaginal microbiome

Effect of a Nonoptimal Cervicovaginal Microbiota and Psychosocial Stress on Recurrent Spontaneous Preterm Birth – Kristin D Gerson – American Journal of Perinatology

https://www.thieme-connect.de/products/ejournals/abstract/10.1055/s-0040-1717098

Animal microbiome / Animal experiments

Enteromorpha prolifera Diet Drives Intestinal Microbiome Composition in Siganus oramin – Yan Xu – Current Microbiology

https://link.springer.com/article/10.1007%2Fs00284-020-02218-6

High-Fat Proteins Drive Dynamic Changes in Gut Microbiota, Hepatic Metabolome, and Endotoxemia-TLR-4-NFκB-Mediated Inflammation in Mice – Muhammad Ijaz Ahmad – J. Agric. Food Chem

https://pubs.acs.org/doi/10.1021/acs.jafc.0c02570

Dynamic change of the gastrointestinal bacterial ecology in cows from birth to adulthood – Chun Y. Guo – Microbiology Open

https://onlinelibrary.wiley.com/doi/10.1002/mbo3.1119

Effects of seasonality and previous logging on faecal helminth-microbiota associations in wild lemurs – I. I. de Winter – Scientific Reports

https://www.nature.com/articles/s41598-020-73827-1

Effects of inulin and isomalto-oligosaccharide on diphenoxylate-induced constipation, gastrointestinal motility-related hormones, short-chain fatty acids, and the intestinal flora in rats – Junhong Lan – Food & Function

https://pubs.rsc.org/en/content/articlelanding/2020/FO/D0FO00865F

Probiotic-fermented blueberry juice prevents obesity and hyperglycemia in high fat diet-fed mice in association with modulating the gut microbiota – Hao Zhong – Food & Function

https://pubs.rsc.org/en/content/articlelanding/2020/FO/D0FO00334D

Faecal microbiota and antimicrobial resistance gene profiles of healthy foals – Yuhong Liu – Equine Veterinary Journal

https://beva.onlinelibrary.wiley.com/doi/10.1111/evj.13366

Sows affect their piglets’ faecal microbiota until fattening but not their Salmonella enterica shedding status – Guillaume Lariviere-Gauthier – Letters in Applied Microbiology

https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/lam.13406

Probiotics / prebiotics

Review: Current status of probiotics for prevention and management of gastrointestinal cancers – Abdul Arif Khan – Expert Opinion on Biological Therapy

https://www.tandfonline.com/doi/abs/10.1080/14712598.2021.1828858?journalCode=iebt20

Plant, root, and soil microbiome

Characterization of the Leaf Microbiome from Whole-Genome Sequencing Data of the 3000 Rice Genomes Project – Veronica Roman-Reyna – Rice

https://thericejournal.springeropen.com/articles/10.1186/s12284-020-00432-1

Air, water and extremophile microbiome

Review: Urbanisation reduces the abundance and diversity of airborne microbes – but what does that mean for our health? A systematic review – Emily J. Flies – Science of The Total Environment

https://www.sciencedirect.com/science/article/abs/pii/S0048969720338596

Impact of a synthetic fungicide (fosetyl-Al and propamocarb-hydrochloride) and a biopesticide (Clonostachys rosea) on soil bacterial, fungal, and protist communities – BertrandFournier – Science of The Total Environment

https://www.sciencedirect.com/science/article/abs/pii/S0048969720331557

Methods

RBUD: A New Functional Potential Analysis Approach for Whole Microbial Genome Shotgun Sequencing – Zhikai Xing – Microorganisms

https://www.mdpi.com/2076-2607/8/10/1563

October 5th, 2020


God morgon!

Good morning from Sweden.

Today’s digest starts with a super interesting preprint on COVID-19 where the researchers have shown that anti-COVID-19 drugs induce lytic reactivation of an oncogenic virus. As if COVID-19 wasn’t dangerous enough, its treatment is now even more dangerous!

New research has revealed numerous genera of bacteria associated with Amoebozoa, which haven’t been looked into; polyamines as new substrates for a previously known efflux pump in Acinetobacter; genomic differences between the influenza viruses causing infections of different severity; and novel interactions between mycorrhizal fungi and plants.

Hope you’ll enjoy today’s digest!

COVID-19

Preprint: SARS-CoV-2 proteins and anti-COVID-19 drugs induce lytic reactivation of an oncogenic virus – Jungang Chen, et al.

Bacteria Hysteria

Preprint: Characterization of the antimicrobial activity of the cell-penetrating peptide TAT-RasGAP317-326 – Maria Georgieva, et al.

Preprint: Bacteriophage Resistance Affects Flavobacterium columnare Virulence Partly via Mutations in Genes Related to Gliding Motility and Type IX Secretion System – Heidi MT Kunttu, et al.

Preprint: ROS-dependent innate immune mechanisms control Staphylococcus aureus MRSA virulence in the Drosophila larval model – Elodie Ramond, et al.

Preprint: Transposon-insertion sequencing in a clinical isolate of Legionella pneumophila identifies essential genes and determinants of natural transformation – Léo Hardy, et al.

Preprint: Spermidine and spermine are the natural substrates of the Acinetobacter baumannii AmvA multidrug efflux pump – Francesca L. Short, et al.

Gut Microbiome

Preprint: Comparing Fecal, Saliva, and Chicha Microbiomes Between Mothers and Children in an Indigenous Ecuadorian Cohort – Eric Daniel Adams, et al.

Preprint: Spatial analysis of gut microbiome reveals a distinct ecological niche associated with the mucus layer – Kellyanne Duncan, et al.

Preprint: Comprehensive Comparative Genomics Reveals Over 50 Phyla of Free-living and Pathogenic Bacteria are Associated with Diverse Members of the Amoebozoa – Yonas I. Tekle, et al.

β-glucan attenuates cognitive impairment via the gut-brain axis in diet-induced obese mice – Hongli Shi, et al., Microbiome

Faecal microbiota transplant from aged donor mice affects spatial learning and memory via modulating hippocampal synaptic plasticity- and neurotransmission-related proteins in young recipients – Alfonsina D’Amato, et al., Microbiome

Plants

Preprint: Comparative analysis of temporal transcriptome reveals the relationship between pectin degradation and pathogenicity of defoliating Verticillium dahliae to Upland cotton (Gossypium hirsutum) – Fan Zhang, et al.

Preprint: Silencing of ATP synthase β reduces phytoplasma multiplication in the leafhopper vector Euscelidius variegatus – Luciana Galetto, et al.

Trophic interactions as determinants of the arbuscular mycorrhizal fungal community with cascading plant-promoting consequences – Yuji Jiang, et al., Microbiome

Preprint: Characterization of Met25 as a Color Associated Genetic Marker in Yarrowia lipolytica – Harley Edwards, et al.

General Microbiome

Preprint: Fine scale sampling unveils diazotroph patchiness in the South Pacific Ocean – Mar Benavides, et al.

Preprint: Sedimentation rate and organic matter dynamics shape microbiomes across a continental margin – Sabyasachi Bhattacharya, et al.

Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula – Shawn P. Brown, et al., Microbiome

Viruses

Preprint: A potent neutralizing mouse monoclonal antibody specific to dengue virus type 1 Mochizuki strain recognized a novel epitope around the N-67 glycan on the E protein: a possible explanation of dengue virus evolution regarding the acquisition of N-67 glycan – Tomohiro Kotaki, et al.

Preprint: Differential Disease Severity and Whole Genome Sequence Analysis for Human Influenza A/H1N1pdm Virus in 2015-2016 Influenza Season – Hsuan Liu, et al.

Viral ecogenomics across the Porifera – Cecília Pascelli, et al., Microbiome

Infections

Preprint: A Universal Stress Protein upregulated by hypoxia may contribute to chronic lung colonisation and intramacrophage survival in cystic fibrosis – Andrew O’Connor, et al.

Preprint: Modulation of early host innate immune response by a Fowlpox virus (FWPV) lateral body protein – Efstathios S Giotis, et al.

Techniques

Preprint: Accurate Microbiome Sequencing with Synthetic Long Read Sequencing – Nico Chung, et al.

Investigating host-microbiome interactions by droplet based microfluidics – Alexandra S. Tauzin, et al., Microbiome

October 3, 2020

Shalom and good morning from Israel!

Today’s digest is highly diverse, with papers about naming microbes (bottom line- be creative and interesting!), human hair microbiome, the role of one single bacteria in plant growth, how phages weaponizes host bacteria and much more.

Lastly, a bit of ‘self promotion’- the lockdown in Isrel encouraged me to finally create AgrimicroPapers, a twitter-bot (using this great manual) for agriculture- and plant microbiome-realted papers. Feel free to follow and DM papers if they were missed by the bot. Enjoy!

General microbiology

Prokaryotic names: the bold and the beautiful, Aharon Oren, FEMS Micro. Letters

Human and animal microbiome

**Understanding the impact of antibiotic perturbation on the human microbiome, D.J. Schwartz, Genome Medicine

Salivary microbiome in patients undergoing hemodialysis and its associations with the duration of the dialysis, Xiaobo Duan, BMC Nephrology

Phytochemicals as modifiers of gut microbial communities, Giulia Dingedo, Food & Function

Relationship between the bacterial community structures on human hair and scalp, Kota Watanabe, Biosc. Biotech. Bioche

Pangenome sequence evolution within human gut microbiomes is explained by gene-specific rather than host-specific selective pressures, Arnaud N’Guessan, bioRxiv

Changes in dietary fiber intake in mice reveal
associations between colonic mucin Oglycosylation and specific gut bacteria
, Hasinika Gamage, Gut Microbes

Gut metabolites are more predictive of disease- and cohoused- states than gut bacterial features in a mouse model of polycystic ovary syndrome, Bryan Ho, bioRxiv

Environmental microbiome

**A single bacterial genus maintains root growth in a complex microbiome, Omri Finkel, Nature

The Soil-Borne Identity and Microbiome-Assisted Agriculture: Looking Back to the Future, Peter H.A.M Bakker, Molecular Plant (Cell)

Quantification of Extracellular Proteases and Chitinases from Marine Bacteria, Yang Zou, Current Micro.

Characterization of microbial communities in commercial bee pollen used for mass rearing of Bombus impatiens,Vicente D. Moreno Andrade, J. Apicultural Research

Phages

Phages weaponize their bacteria with biosynthetic gene clusters, Anna Dragos, bioRxiv

Microbiome news

Biotechs have big ambitions for the microbiome, SFBT

Core metagenomic functions of the poultry microbiome, Poultry World

October 2, 2020

Today’s exciting updates – FMT method to restore normal microbial development in caesarean-born infants, mechanism unveiled how dietary tryptophan improves alcohol induced liver injury, advance in droplet based microfluidics to study host-microbiome interactions, prebiotics encapsulation of probiotic to suppress colon cancer and new hope to curb plastic waste by discovery of plastic-eating enzyme cocktail. Happy weekend, stay safe!

General microbiome

Eligible blood donors’ decisions about donating stool for fecal microbiota transplantation: Does ambivalence play a role? – Melissa K. Hyde – Transfusion

Microbiota-Dependent Effects of IL-22 – Morsal Sabihi – Cells

Human microbiome

Maternal Fecal Microbiota Transplantation in Cesarean-Born Infants Rapidly Restores Normal Gut Microbial Development: A Proof-of-Concept Study – Katri Korpela – Cell

Comparative analysis of the tonsillar microbiota in IgA nephropathy and other glomerular diseases – Ji In Park – Scientific Reports

Dysbiosis in the oral microbiomes of anti-CCP positive individuals at risk of developing rheumatoid arthritis – Zijian Cheng – Annals of the Rheumatic Diseases

Animal microbiome

Microbiota tryptophan metabolism induces aryl hydrocarbon receptor activation and improves alcohol-induced liver injury – Laura Wrzosek – Gut

Faecal microbiota transplant from aged donor mice affects spatial learning and memory via modulating hippocampal synaptic plasticity- and neurotransmission-related proteins in young recipients – Alfonsina D’Amato – Microbiome

Competitive reduction of poultry-borne enteric bacterial pathogens in chicken gut with bioactive Lactobacillus casei – Zajeba Tabashsum – Scientific Reports

Offspring susceptibility to metabolic alterations due to maternal high-fat diet and the impact of inhaled ozone used as a stressor – Samantha J. Snow – Scientific Reports

Beneficial effects of mung bean seed coat on the prevention of high-fat diet-induced obesity and the modulation of gut microbiota in mice – Dianzhi Hou – European Journal of Nutrition

Prebiotics‐Encapsulated Probiotic Spores Regulate Gut Microbiota and Suppress Colon Cancer – Di‐Wei Zheng – Advanced Materials

Multi-Omic Analysis Reveals Different Effects of Sulforaphane on the Microbiome and Metabolome in Old Compared to Young Mice – Se-Ran Jun – Microorganisms

Plant microbiome

Protists as catalyzers of microbial litter breakdown and carbon cycling at different temperature regimes – Stefan Geisen – Isme Journal

Techniques

Investigating host-microbiome interactions by droplet based microfluidics – Alexandra S. Tauzin – Microbiome

Non-specific amplification of human DNA is a major challenge for 16S rRNA gene sequence analysis – Sidney P. Walker – Scientific Reports

Non-microbiology picks

Plastic-eating enzyme ‘cocktail’ heralds new hope for plastic waste – Science Daily

October 1, 2020

Greetings, friends!

Today’s digest contains a wealth of microbiology articles focused on everything from the dog ear canal microbiome to estuarine methanogen communities. Rather than highlight a specific research article, today I’d like to encourage you to check out this week’s New York Times article profiling the organizers of Black in Micro Week and this commentary published by one of the organizers in mSphere. Black in Micro week began this Monday and programming is scheduled to continue through October 4th. If you missed earlier events, you’re in luck! The organizers have already uploaded videos of all completed events at the Black in Micro youtube channel.

Enjoy!


Events

Black in Micro Week is this week (September 28 – October 4th, 2020) on your favorite social media platforms! Check out the Black in Microbiology website for additional information, including a full programming schedule, and follow @BlackinMicro and #BlackinMicro on Twitter and Instagram.

Human respiratory microbiome

Airway microbiota is associated with the severity of non‐CF bronchiectasis – Li et al. – The Clinical Respiratory Journal

Human gut microbiome

Systematic analysis of gut microbiota in pregnant women and its correlations with individual heterogeneity – Yang et al. – npj Biofilms and Microbiomes

Review: Implication of gut microbiota in cardiovascular diseases – Zhou et al. – Oxidative Medicine and Cellular Longevity

Animal experiments

Changes in the ear canal microbiota of dogs with otitis externa – Kasai et al. – Journal of Applied Microbiology

Plant, root, and soil microbiome

Soil borne Fusarium solani exhibited pathogenic effect on tomato cultivars in Nigeria – Abiala et al. – Archives of Phytopatholgy and Plant Protection

A symbiotic nutrient exchange within the cyanosphere microbiome of the biocrust cyanobacterium, Microcoleus vaginatus – Nelson et al. – The ISME Journal

Successional change of the fungal microbiome pine seedling roots inoculated with Tricholoma matsutake – Park et al. – Frontiers in Microbiology

Review: Arbuscular mycorrhizal fungi: an ecological accelerator of phytoremediation of metal contaminated soils – Tiwari et al. – Archives of Agronomy and Soil Science

Co‐occurrence history increases ecosystem stability and resilience in experimental plant communities – van Moorsel et al. – Ecology

Quantitative estimation of stochastic and deterministic processes for soil prokaryotic community assembly in the Yellow River floodplain – Yu et al. – European Journal of Soil Science

Water and extremophile microbiome

Homogeneous environmental selection dominates microbial community assembly in the oligotrophic South Pacific Gyre – Allen et al. – Molecular Ecology

An unexpectedly broad thermal and salinity-tolerant estuarine methanogen community – Blake et al. – Microorganisms

Microbial communities responded to tetracyclines and Cu(II) in constructed wetlands microcosms with Myriophyllum aquaticum – Guo et al. – Ecotoxicology and Environmental Safety

Built environment

Microbial community and function in nitrogen transformation of ectopic fermentation bed system for pig manure composting – Chen et al. – Bioresource Technology

Effect of hydrothermal hot-compression method on the antimicrobial performance of green building materials from heterogeneous cellulose wastes – Echeverria et al. – Journal of Cleaner Production

Nitrous oxide emission and microbial community of full-scale anoxic/aerobic membrane bioreactors at low dissolved oxygen setpoints – Wen et al. – Journal of Water Process Engineering

Response of Cyperus involucratus to sulfamethoxazole and ofloxacin-contaminated environments: Growth physiology, transportation, and microbial community – Xu et al. – Ecotoxicology and Environmental Safety

Microbes in the news

Black microbiologists push for visibility amid a pandemic – Wu – New York Times

Science, publishing, and career

Commentary: mSphere of influence: That’s racist—COVID-19, biological determinism, and the limits of hypotheses – Taylor – mSphere