October 22, 2020

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Good morning! A relatively short collection of articles to share with you today—highlights include a human microbiome study that evaluated disease markers in more than 3,000 subjects, a study of emerging antibiotic resistance in melting Alaskan permafrost, and a preprint that found multiple immune responses typically associated with the microbiome may actually be more closely linked to viruses.

Human gut microbiome

Health and disease markers correlate with gut microbiome composition across thousands of people, Ohad Manor et al., Nature Communications

Newly Explored Faecalibacterium Diversity Is Connected to Age, Lifestyle, Geography, and Disease, Francesca De Filippis et al., Current Biology

Preprint: Extraintestinal pathogenic (ExPEC) lineages explain prolonged faecal carriage of travel-acquired extended-spectrum β-lactamase-producing Escherichia coli, Boas CL van der Putten et al., bioRxiv

Intestinal microbiology shapes population health impacts of diet and lifestyle risk exposures in Torres Strait Islander communities, Fredrick M Mobegi et al., eLife

Animal experiments

A longitudinal study reveals the alterations of the Microtus fortis colonic microbiota during the natural resistance to Schistosoma japonicum infection, Du Zhang et al., Experimental Parasitology

Animal microbiome

Seasonal variation in the gut microbiota of rhesus macaques inhabiting limestone forests of southwest Guangxi, China, Yuhui Li et al., Archives of Microbiology

Preprint: Persistence of the ground beetle (Coleoptera: Carabidae) microbiome to diet manipulation, Anita Silver et al., bioRxiv

Plant, root, and soil microbiome

Preprint: Unearthing the Boreal Soil Resistome Associated with Permafrost Thaw, Haan and Drown, bioRxiv

Phages and viruses

Preprint: Enteric viruses evoke broad host immune responses resembling bacterial microbiome, Simone Dallari et al., bioRxiv

October 21, 2020

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Good morning from Northern Germany,

Today’s selection comprises among others new research about intestinal microbiome and breast cancer (by Koren lab), a perspective about the human microbiome in the 21st century and the diversity in marine sediments. Additionally, we selected a study about linking genetics, microbiome and autoimmunity (multiple sclerosis) in a mouse model and a study about postmortomics.

Conferences

The 3rd Microbiome Movement – Skin Health & Dermatology Summit unites leaders from academia and industry to address the unique challenges that working within the skin microbiome possesses, with the goal to accelerate microbiome-targeted therapeutics and cosmetics.
View the event website for more details.

General microbiome

[Review] Metabolomics Signatures of Aging: Recent Advances – Sunil and Yulan – Aging and Disease

The human microbiome in the 21st century – Rackaityte & Lynch – Nature Communications

Human gut microbiome

The intestinal microbiome, weight, and metabolic changes in women treated by adjuvant chemotherapy for breast and gynecological malignancies – Uzan-Yulzari et al. BMC Medicine

[Review] The Role of the Gut Microbiota in Coronary Heart Disease – Liu et al. – Coronary Heart Disease

[Review] Gut microbial molecules in behavioural and neurodegenerative conditions – Needham, Kaddurah & Mazmanian – Nature Reviews Neuroscience

Animal experiments

Interactions between host genetics and gut microbiota determine susceptibility to CNS autoimmunity – Montgomery et al. – PNAS

Bifidobacterium alters the gut microbiota and modulates the functional metabolism of T regulatory cells in the context of immune checkpoint blockade – Sun et al. – PNAS

Bugs and drugs: a systems biology approach to characterising the effect of moxidectin on the horse’s faecal microbiome – Daniels, Swann & Proudman – Animal Microbiome

A pioneer calf foetus microbiome – Guzman et al. – Scientific Reports

Water and extremophile microbiome

Global diversity of microbial communities in marine sediment – Hoshino et al. – PNAS

Bioinformatics

[Review] Statistical and Machine-Learning Analyses in Nutritional Genomics Studies – Khorraminezhad et al. – nutrients
[Review] A need to consider the evolutionary genetics of host‐symbiont mutualisms – Stoy et al. – Journal of Evolutionary Biology

Techniques

Postmortomics: The Potential of Untargeted Metabolomics to Highlight Markers for Time Since Death – Pesko et al. – OMICS: A Journal of Integrative Biology

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 16, 2020

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In today’s digest read about how food additives affect the intestinal microbiota and induce intestinal inflammation, the role of the gut microbiome in honey bee nestmate recognition, how to use gene-level analysis to identify microbial “genome islands” associated with human health, and more. Check out the list of audiobooks about microbes. Happy Friday!

General microbiome

Time as a microbial resource – Karen G. Lloyd – Environmental Microbiology Reports

Review: The Central Role of Interbacterial Antagonism in Bacterial Life – S. Brook Peterson – Current Biology

Gut microbiome

*Dietary Emulsifiers Directly Impact Adherent-Invasive E. coli Gene Expression to Drive Chronic Intestinal Inflammation – Emilie Viennois – Cell Reports

Microbial Strain Engraftment, Persistence and Replacement after Fecal Microbiota Transplantation – Daniel Podlesny – medRxiv

Characterization of presumptive vancomycin-resistant enterococci recovered during infection control surveillance in Dallas, Texas – Sara Ping – bioRxiv

Metabolic dissimilarity determines the establishment of cross-feeding interactions in bacteria – Samir Giri – bioRxiv

Metabolic Response of Faecalibacterium prausnitzii to Cell-Free Supernatants from Lactic Acid Bacteria – Mathilde Lebas – Microorganisms

A combination of metagenomic and cultivation approaches reveals hypermutator phenotypes within Vibrio cholerae infected patients – Inès Levade – bioRxiv

Safety and functional enrichment of gut microbiome in healthy subjects consuming a multi-strain fermented milk product: a randomised controlled trial – Anne-Sophie Alvarez – Scientific Reports

Skin microbiome

Microbial and transcriptional differences elucidate atopic dermatitis heterogeneity across skin sites – Noora Ottman – Allergy

Respiratory microbiome

Multicenter analysis of sputum microbiota in tuberculosis patients – Claudia Sala – PlosOne

Lacticaseibacillus casei AMBR2 modulates the epithelial barrier function and immune response in a donor-derived nasal microbiota manner – Charlotte De Rudder – Scientific Reports

Animal microbiome

*The gut microbiome defines social group membership in honey bee colonies – Cassondra L. Vernier – Science Advances

Early-life gut dysbiosis linked to juvenile mortality in ostriches – Elin Videvall – Microbiome

Animal experiment

The Immune System Fails to Mount a Protective Response to Gram-Positive or Gram-Negative Bacterial Prostatitis – Federico Lupo – Journal of Immunology

The aging mouse microbiome has obesogenic characteristics – Dana Binyamin – Genome Medicine

Tetracycline Antibiotics Induce Host-Dependent Disease Tolerance to Infection – Henrique G. Colaço – Immunity

Water microbiome

Impact of phosphate dosing on the microbial ecology of drinking water distribution systems: Fieldwork studies in chlorinated networks – Isabel Douterelo – Water Research

Sustained nitrogen loss in a symbiotic association of Comammox Nitrospira and Anammox bacteria – Ekaterina Y. Gottshall – bioRxiv

Viruses and phages

Culturing novel and abundant pelagiphages in the ocean – Zefeng Zhang – Environmental Microbiology

High-throughput mapping of the phage resistance landscape in E. coli – Vivek K. Mutalik – PlosBiology

Fungi

Minireview: Fun(gi)omics: Advanced and Diverse Technologies to Explore Emerging Fungal Pathogens and Define Mechanisms of Antifungal Resistance – Brianna Ball – mBio

Technique

Bac-PULCE: Bacterial Strain and AMR Profiling Using Long Reads via CRISPR Enrichment – Andrea Sajuthi – bioRxiv

Bioinformatics

*Gene-level metagenomics identifies genome islands associated with immunotherapy response – Samuel S Minot – bioRxiv

PUMAA: A Platform for Accessible Microbiome Analysis in the Undergraduate Classroom – Keith Mitchell – Frontiers in Microbiology

Raman2imzML converts Raman imaging data into the standard mass spectrometry imaging format – Stefania Alexandra Iakab – BMC Bioinformatics

Scientific writing

Eight problems with literature reviews and how to fix them – Neal R. Haddaway – Nature Ecology & Evolution

Scientific art

Inktober2020 #PathogenPortraits by Dr Eliza Wolfson

Citizen science

The Human Diets & Microbiome Initiative in the US (THDMI): A unique opportunity to become a citizen scientist. Join for FREE to uncover the secret of the gut microbiome.

Books

11 Audiobooks About Microbes – Justine Dees – Joyful Microbe

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 14, 2020

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Good morning from sunny San Francisco, California! Today’s digest shares some fascinating in vivo studies including a paper from Ou et al. examining the role of host antimicrobial proteins α-definsins in bacterial colonization and epithelial cell adherence in the gut and a proof-of-concept paper from Hsu et al. in which the authors orally delivered an engineered phage to the gut of mice that was capable of specifically repressing gene expression in bacteria. Additionally, there are some great plant, root, and soil microbiome papers (Kusstatscher et al. show that treating maize seeds with a plant growth-promoting rhizobacteria improves plant health) and water microbiome papers (León-Zayas et al. published a super collaborative paper looking at microbiome sharing between sediments, seagrasses, and reef fish at multiple sites). Finally, I wanted to highlight a paper by Zelaya et al. outlining a course-based undergraduate research experience for teaching microbiology that focuses on the bean beetle microbiome. Happy reading!

Pregnancy and Early Life
Review: The early life education of the immune system: Moms, microbes and (missed) opportunities. – Nitya, J. et al., Gut Microbes

Delayed Establishment of Gut Microbiota in Infants Delivered by Cesarean Section. – Kim, G. et al., Frontiers in Microbiology

Human Respiratory Microbiome
Proteins produced by Streptococcus species in the lower respiratory tract can modify antiviral responses against influenza virus in respiratory epithelial cells. – Nishioka, K. et al., Microbes and Infection

Human Vaginal Microbiome
Vaginal host immune-microbiome interactions in a cohort of primarily African-American women who ultimately underwent spontaneous preterm birth or delivered at term. – Florova, V. et al., Cytokine

Human Oral Microbiome
Isolation and Characterization of Nitrate-Reducing Bacteria as Potential Probiotics for Oral and Systemic Health. – Rosier, B.T. et al., Frontiers in Microbiology

Human Gut Microbiome
Translocation of Viable Gut Microbiota to Mesenteric Adipose Drives Formation of Creeping Fat in Humans. – Ha, C.W.Y. et al., Cell

Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity. – Fang, X. et al., Inflammatory Bowel Diseases

Animal Experiments
α-Defensins Promote Bacteroides Colonization on Mucosal Reservoir to Prevent Antibiotic-Induced Dysbiosis. – Ou, J. et al., Frontiers in Immunology

In situ reprogramming of gut bacteria by oral delivery. – Hsu, B.B. et al., Nature Communications

The intestinal microbial metabolite desaminotyrosine is an anti‐inflammatory molecule that modulates local and systemic immune homeostasis. – Wei, Y. et al., The FASEB Journal

Modulation of experimental autoimmune encephalomyelitis through colonisation of the gut with Escherichia coli. – Libbey, J.E. et al., Beneficial Microbes

Molecular patterns from a human gut-derived Lactobacillus strain suppress pathogenic infiltration of leukocytes into the central nervous system. -Sanchez, J.M.S. et al., Journal of Neuroinflammation

Plant, Root, and Soil Microbiome
Soil-microorganism-mediated invasional meltdown in plants. – Zhang, Z. et al., Nature Ecology and Evolution

Microbiome Management by Biological and Chemical Treatments in Maize Is Linked to Plant Health. – Kusstatscher, P. et al., Microorganisms

Disruption of Firmicutes and Actinobacteria abundance in tomato rhizosphere causes the incidence of bacterial wilt disease. – Lee, S-M. et al., The ISME Journal

Keystone Microbiomes Revealed by 14 Years of Field Restoration of the Degraded Agricultural Soil Under Distinct Vegetation Scenarios. – Zhang, Z. et al., Frontiers in Microbiology

Dynamic Changes in the Microbiome of Rice During Shoot and Root Growth Derived From Seeds. – Wang, M. et al., Frontiers in Microbiology

Root-Secreted Coumarins and the Microbiota Interact to Improve Iron Nutrition in Arabidopsis. – Harbort, C.J. et al., Cell Host & Microbe

Review: Pinpointing secondary metabolites that shape the composition and function of the plant microbiome. – Jacoby, R.P. et al., Journal of Experimental Botany

Water and Extremophile Microbiome
Microbiomes of fish, sediment and seagrass suggest connectivity of coral reef microbial populations. – León-Zayas, R. et al., PeerJ

Size Shapes the Active Microbiome of Methanogenic Granules, Corroborating a Biofilm Life Cycle. – Trego, A.C. et al., mSystems

Self-regulating microbiome networks ensure functional resilience of biofilms in sand biofilters during manganese load fluctuations. – Zhao, X. et al., Water Research

Review: Groundwater Microbial Communities in Times of Climate Change. -Retter, A. et al., Current Issues in Molecular Biology

Probiotics/Prebiotics
Combining IL-2-based immunotherapy with commensal probiotics produces enhanced antitumor immune response and tumor clearance. – Shi, L. et al., Journal for the ImmunoTherapy of Cancer

Mom’s diet matters: Maternal prebiotic intake in mice reduces anxiety and alters brain gene expression and the fecal microbiome in offspring. – Hebert, J.C. et al., Brain, Behavior, and Immunity

Prophylactic effects of oral administration of Lactobacillus casei on house dust mite-induced asthma in mice. – Lingzhi, L. et al., Food & Function

Bioinformatics
INTEDE: interactome of drug-metabolizing enzymes. – Yin, J. et al., Nucleic Acid Research.

GIMICA: host genetic and immune factors shaping human microbiota. – Tang, J. et al., Nucleic Acid Research

metaFlye: scalable long-read metagenome assembly using repeat graphs. – Kolmogorov, M. et al., Nature Methods

Diagnosing and Predicting Mixed-Culture Fermentations with Unicellular and Guild-Based Metabolic Models. – Scarborough, M.J. et al., mSystems

Education
The Bean Beetle Microbiome Project: A Course-Based Undergraduate Research Experience in Microbiology. – Zelaya, A.J. et al., Frontiers in Microbiology

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 11, 2020

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Hello from the Sonoran Desert! In today’s digest, you’ll find quite a few exciting reads about ancient microbes!

Duchêne and collaborators review recents efforts in paleopathology leading to the genome sequencing of ancient pathogens of historical interest such as the pre-modern bubonic plague (Yersinia pestis), smallpox (Variola virus) and cholera (Vibrio cholerae). In their review, the authors explore this amazing topic that aims to broaden our understanding of the past infectious disease.

On the other hand, Eisenhofer and collaborators examine ancient microbial DNA preserved within dental calculus samples from two major cultural periods in Japan: the Jomon period circa 3000 years ago and the Edo period circa 400–150 ago. In this piece, they explore how human oral microbiomes have changed through time in ancient Japanese populations.

Finally, you’ll find in this digest a non-microbiology pick: a “10 simple rules” paper outlining best practices for annotating and submitting sequencing data! Indeed, metadata accompanying sequence datasets is critical to ensure data longevity and reusability by both human and machine agents, and poor metadata can drastically reduce the value of sequencing experiments by limiting its reuse in integrative analyses!

Have a great Sunday!

General Microbiology

Review: The Recovery, Interpretation and Use of Ancient Pathogen Genomes – Duchêne et al. – Current Biology

Multi-site human microbiome

Functional diversity of microbial ecologies estimated from ancient human coprolites and dental calculus – Jacobson et al. – Philosphical transactions of the royal society of Biological sciences.

Human respiratory and oral microbiome

Investigating the demographic history of Japan using ancient oral microbiota – Eisenhofer et al. – Philosphical transactions of the royal society of Biological sciences.

Human gut microbiome

Preprint: Distinct human gut microbial taxonomic signatures uncovered with different sample processing and microbial cell disruption methods for metaproteomic analysis – Garcia-Duran et al. – BioRxiv.

Review: Deciphering diet-gut microbiota-host interplay: Investigations of pectin. – Tan and Nie – Trends in Food Science & Technology

Plant, root, and soil microbiome

Book Chapter: Microbes and Environment: Global Warming Reverting the Frozen Zombies. In: Fahad et al. (eds) Environment, Climate, Plant and Vegetation Growth. Springer, Cham.

Taxonomic Diversity of Bacteria and Their Filterable Forms in the Soils of Eastern Antarctica (Larsemann Hills and Bunger Hills) – Kudinova et al. – Microbiology.

Preprint: Long-term warming effects on the microbiome and nitrogen fixation associated with the moss Racomitrium lanuginosum in Icelandic tundra – Klarenberg et al. – bioRxiv

Water and extremophile microbiome

Diversity of Eukaryotic Microorganisms in the Drainage Waters of a Coal Open-Cast Mine – Gruzdev et al. – Microbiology

Dissimilarity of microbial diversity of pond water, shrimp intestine and sediment in Aquamimicry system – Zeng et al. – AMB express.

Comparative diversity analysis of halophiles at two polar saltern systems in Indramayu, West Java, Indonesia – Chasanah et al. – Letters in Applied Microbiology.

Mechanistic model of nutrient uptake explains dichotomy between marine oligotrophic and copiotrophic bacteria – Norris et al. – BioRxiv.

Food microbiology

Review: Microbial diversity of seafood. Parlapani. Current Opinion in Food Science.

Phages and viruses

The first head‐tailed virus, MFTV1, produced by a hyperthermophilic methanogenic deep‐sea archaea – Thiroux et al. – Environmental microbiology.

Review: Single-virus genomics and beyond – Martinez et al. – Nature reviews Microbiology

Bioinformatics

A Rapid Automated Process for Organizing Bacterial Cluster Segments Using Deep Neural Networks – Elroy Martis et al. – IEEE conference

Techniques

FACS-iChip: a high-efficiency iChip system for microbial ‘dark matter’ mining – Liu et al. – Marine Life Science and Technology

Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses – Sabatier et al. – Microorganisms

Science, publishing, and career

Preprint: Advancing science or advancing careers? Researchers’ opinions on success indicators – Aubert Bonn and Pinxten – BioRxiv.

My non-microbiology picks

Ten simple rules for annotating sequencing experiments – Stevens et al. – Plos Computational Biology

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