Category Archives: Uncategorized

November 6, 2020

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Shalom from Israel!

While the eyes of the world are looking at the US elections results, it’s good to know that the world of microbiome research is stable and produces great scientific discoveries. So stop refreshing the news websites, grab yourself a cup of cofee and enjoy your Saturday.

Today’s digest has some great papers about memory in microboimes, factors that shapes bacterial growth, infant skin microbial communities, degraded soils restoration using self-assembly communities, songbirds microbiome, antiSMASH3 is out (!), useful youtube video for metagenome ML analysis in MATLAB and more. Reminding those of you who are intrested in agriculture-related microbioe studies to stop by and follow my bot agmicroPapers

General microbiology

Memory shapes microbial populations, Chaitanya S Gokhale , bioRxiv

Bacterial–fungal interactions revealed by genome-wide analysis of bacterial mutant fitness, Emily C. Pierce, Nature Microbiology

Environmental and Physiological Factors Affecting High-Throughput Measurements of Bacterial Growth, Esha Atolia , mBio

Human microbiome

Host variables confound gut microbiota studies of human disease, Ivan Vujkovic-Cvijin, Nature

Infant Skin Bacterial Communities Vary by Skin Site and Infant
Age across Populations in Mexico and the United States, Melissa B. Manus, mSystems

Plant and soil microbiome

Microbiome manipulation by a soil-borne fungal plant pathogen using effector proteins, Nick C. Snelders, Nature Plants

Assembly and variation of root-associated microbiota of rice during their vegetative growth phase with and without lindane pollutant, Jiayin Feng, Soil Ecology Letters

Restoring degraded microbiome function with self-assembled communities, Carlos Fernando Gutierrez Landazuri , FEMS Micro. Eco.

Multi-species relationships in legume roots: From pairwise legume-symbiont interactions to the plant – microbiome – soil continuum, Myrto Tsiknia, FEMS Micro. Eco.

Animal microbiome

Evidence supporting the microbiota–gut–brain axis in a songbird, Morgan C. Slevin, Biology Letters

Comparative Analysis of the Fecal Microbiota of Wild and Captive Beal’s Eyed Turtle (Sacalia bealei) by 16S rRNA Gene Sequencing, Jonathan J. Fong , Front. Micro.

High-Throughput Cultivation for the Selective Isolation of Acidobacteria From Termite Nests, Markus Oberpaul , Front. Micro.

Bioinformatics

EUKulele: Taxonomic annotation of the unsung
eukaryotic microbes, Arianna I. Krinos, JOSS

The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes, Kai Blin, Nucleic Acids Research

**Youtube Video- Microbiome: How to Navigate Through Matlab to Perform Machine Learning Analysis on Metagenomics Data

**Help questionnaire! Natural Products – Data Repositories Questionnaire

November 5, 2020

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Hello, friends!

I’m an American who grew up in North Carolina, lived in Georgia for many years, and now counts Pennsylvania as home. All of this is to say, I’ve been especially consumed by the US election this morning and so today’s digest is tailor made to distract me for a few hours. It contains a heavy dose of general microbiome, environmental microbiology, and microbial ecology articles. If you need a bigger distraction than usual, I’ve highlighted a few articles that I am particularly looking forward to reading and am using this space as an opportunity to reintroduce myself and share why these articles have peaked my interest.

I completed my PhD research on the cockroach gut microbiome and through this work, I realized how complex microbiome-host-environmental interactions can be. Because of this, my first highlighted article is a review about cockroach-associated microbes. Currently, I work in a national lab studying environmental-associated microbes (and their functional capacity!) in a variety of different energy-associated environments. It’s no wonder I’m excited to read the second highlighted article focused on novel soil microbes found in an abandoned coal mine! I’m also very hungry at the moment, so as soon I read the phrase “smoked cow cheese” I was motivated to explore my cheese drawer as well as think more about microbial food safety and the microbial production of favor compounds. Finally, I love musical theater and science outreach, so I’m delighted to share a mouldy article that combines both passions.

Happy reading, everyone!

General microbiome

Review: The pneumococcal social network – Aggarawal et al. – PLOS Pathogens

Expanding magnetic organelle biogenesis in the domain Bacteria – Lin et al. – Microbiome

Gene duplication drives genome expansion in a major lineage of Thaumarchaeota – Sheridan et al. – Nature Communications

Metatranscriptomic analysis reveals active microbes and genes responded to short-term Cr(VI) stress – Yu et al. – Ecotoxicology

Effects of heavy ion particle irradiation on spore germination of Bacillus spp. from extremely hot and cold environments – Zammuto et al. – Life
Human gut microbiome

Gut microbiome

Gut microbiota ecology: Biodiversity estimated from hybrid neutral-niche model increases with health status and aging – Sala et al. – PLOS ONE

Implication of gut microbiota in the physiology of rats intermittently exposed to cold and hypobaric hypoxia – Ramos-Romero et al. – PLOS ONE

Animal microbiome

Exploring the resident gut microbiota of stranded odontocetes: high similarities between two dolphin species Tursiops truncatus and Stenella coeruleoalba – Abdelrhman et al. – Journal of the Marine Biological Association of the UK

**Review: Bacteria associated with cockroaches: health risk or biotechnological opportunity? – Guzman & Vilcinskas – Applied Microbiology and Biotechnology

Water and extremophile microbiome

Impact of land uses, drought, flood, wildfire, and cascading events on water quality and microbial communities: A review and analysis – Mishra et al. – Journal of Hydrology

Dams shift microbial community assembly and imprint nitrogen transformation along the Yangtze River – Gao et al. – Water Research

Built environment

**Isolation and characterization of soil bacteria from an abandoned coal mine in southeast Kansas – Bechtold et al. – BioOne Complete

Review: Understanding building-occupant-microbiome interactions toward healthy built environments – Li et al. – Frontiers of Environmental Science & Engineering

Food microbiology

**Microbial quality of smoked cow cheese “Parencia” – Kačániová et al. – Scientific Papers: Animal Science and Biotechnologies

Phages and viruses

Virome of bat guano from nine northern California roosts – Li et al. – Journal of Virology

Bioinformatics

The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities – Chen et al. – Nucleic Acids Research

PhANNs, a fast and accurate tool and web server to classify phage structural proteins – Cantu et al. – PLOS Computational Biology

Techniques

Low-cost biofuel-powered autoclaving machine for use in rural health care centres – Ahmed et al. – Journal of Medical Engineering & Technology

**‘The Mould that Changed the World’: Quantitative and qualitative evaluation of children’s knowledge and motivation for behavioural change following participation in an antimicrobial resistance musical – Hall et al. – PLOS ONE

Harnessing the power of eDNA metabarcoding for the detection of deep-sea fishes – McClenaghan et al. – PLOS ONE

November 3, 2020

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Greetings Everyone!!

Happy reading of an interesting digest for November 3, 2020.

General microbiome
The perfect condition for the rising of superbugs: person-to-person contagion and antibiotic use are the key factors responsible for the positive correlation between antibiotic resistance gene diversity and virulence gene diversity in human metagenomes -Domingues et al – bioRxiv

Human gut microbiome
Parallel and non-parallel changes of the gut microbiota during trophic diversification in repeated young adaptive radiations of sympatric cichlid fish – Härer et al – Microbiome

Exploring the resident gut microbiota of stranded odontocetes: high similarities between two dolphin species Tursiops truncatus and Stenella coeruleoalba – Abdelrhman et al – Journal of the Marine Biological Association of the United Kingdom

Animal experiments
Investigating the cow skin and teat canal microbiomes of the bovine udder using different sampling and sequencing approaches – Dean et al – Journal of Dairy Science

Animal microbiome
Review: Defining Coral Bleaching as a Microbial Dysbiosis within the Coral Holobiont – Boilard et al – microorganisms

Plant, root, and soil microbiome
Free Iron and Iron-Reducing Microorganisms in Permafrost and Permafrost-Affected Soils of Northeastern Siberia – Rivkina et al – Eurasian

Soil Science
Behaviors of cadmium in rhizosphere soils and its interaction with microbiome communities in phytoremediation – Niu et al – Chemosphere

Water and extremophile microbiome
Uncovering the genomic potential of the Amazon River microbiome to degrade rainforest organic matter – Santos-Júnior et al – Microbiome

Microbiome variability across the native and invasive range of the ascidian Clavelina oblonga – Goddard-Dwyer et al – Applied and Environmental Biology

Microbiome of the Black Sea water column analyzed by genome centric metagenomics – Cabello-Yeves et al – bioRxiv

Built environment
Review: Understanding building-occupant-microbiome interactions toward healthy built environments: A review – Li et al – Frontiers of Environmental Science & Engineering

Microbes in space
Molecular repertoire of Deinococcus radiodurans after 1 year of exposure outside the International Space Station within the Tanpopo mission – Ott et al – Microbiome

Bioinformatics
NBZIMM: negative binomial and zero-inflated mixed models, with application to microbiome/metagenomics data analysis – Zhang and Yi – BMC Bioinformatics

Techniques
MASI: microbiota—active substance interactions database – Zeng et al – Nucleic Acids Research

October 29, 2020

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Good morning! The highlight today would be a trial detailing the use of faecal microbiota transplantation in diabetes – with some surprising findings. There is also an interesting paper on the role of iron uptake systems in intestinal virulence in the Escherichia genus to read!

COVID-19

[Preview] Identification of SARS-CoV-2 Inhibitors using Lung and Colonic Organoids. Han et al. Nature.

Human gut microbiome

Toplogical analysis reveals state transitions in human gut and marine bacterial communities. Chang et al. npj Biofilms and Microbiomes.

Faecal microbiota transplantation halts progression of human new-onset type 1 diabetes in a randomised controlled trial. Groot et al. Gut.

[Review] A review of a potential and promising probiotic candidate ‐ Akkermansia muciniphila. Cheng and Xie. Journal of Applied Microbiology.

Vaginal microbiome

Vaginal microbiota and human papillomavirus infection among young Swedish women. Cheng et al. npj Biofilms and Microbiomes.

Animal Experiments

Correlation of gut microbiota and neurotransmitters in a rat model of post-traumatic stress disorder. Zhou et al. Journal of Traditional Chinese Medical Sciences.

Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study. Galardini et al. PLOS genetics.

Campylobacter jejuni persistently colonizes gnotobiotic altered Schaedler flora C3H/HeN mice and induces mild colitis. Brand et al. FEMS Microbiology Letters.

Animal microbiome

Comparative Microbiome Analysis of Three Species of Laboratory-Reared Periplaneta Cockroaches Lee et al. Korean journal of Parasitology.

Plant, root and soil microbiome

Biological invasions alter environmental microbiomes: A meta-analysis. Malacrinó et al. PLOS one.

October 24, 2020

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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

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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

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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

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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

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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

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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