October 27, 2020

Greetings from Pittsburgh, PA!

Today’s digest a contains articles focused on the oral microbiome, koala symbionts, soil microbial communities, and more. For those of you who are a bit too tired to digest cutting-edge research, I suggest using the 10 simple steps outlined in the highlighted editorial to colorize your own data visualizations. Finally, if you just need a break, I suggest bookmarking the article on the whale skin microbiome and revisiting the film Star Trek IV: The Voyage Home.

Happy reading (or movie watching)!

General microbiome

Taxonomic profiling and functional characterization of the healthy human oral bacterial microbiome from the north Indian urban sub-population – Verma et al. – Archives of Microbiology

Pregnancy and early life

Maternal and cord blood vitamin D level and the infant gut microbiota in a birth cohort study – Kassem et al. – Maternal Health, Neonatology and Perinatology

Human gut microbiome

Review: A review on preventive role of ketogenic diet (KD) in CNS disorders from the gut microbiota perspective – Rawat et al. – Reviews in Neurosciences

Animal experiments

Challenges in microbiological identification of aerobic bacteria isolated from the skin of reptiles – Brockmann et al. – PLOS ONE

Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum – Dahlhausen et al. – Peer J

Vertical transmission of zika virus in Aedes albopictus – Lai et al. – PLOS Neglected Tropical Diseases

Cultured-dependent and cultured-independent study of bacteria associated with Thai commercial stingless bee Lepidotrigona terminata – Suphaphimol et al. – Journal of Apicultural Research

Animal microbiome

**Skin microbiome of beluga whales: spatial, temporal, and health-related dynamics – Van Cise et al. – Animal Microbiome

Diversity of bacterial symbionts associated with Myzus persicae (Sulzer) (Hemiptera: Aphididae: Aphidinae) revealed by 16S rRNA Illumina sequencing – Xu et al. – Microbial Ecology

Plant, root, and soil microbiome

Protists and collembolans alter microbial community composition, C dynamics and soil aggregation in simplified consumer–prey systems – Erktan et al. – Biogeosciences

Responses of soil bacteria and fungi after 36 years fertilizer, straw cover, and irrigation management practices in northwest China – Zhang et al. – Soil Use and Management

Water and extremophile microbiome

Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance – Herold et al. – Nature Communications

Islands in the sand: Are all hypolithic microbial communities the same? – Lebre et al. – FEMS Microbiology Ecology

Shifts of sediment bacterial community and respiration along a successional gradient in a typical karst plateau lake wetland (China) – Xia et al. – Journal of Oceanology and Limnology

Salinity controls soil microbial community structure and function in coastal estuarine wetlands – Zhang et al. – Environmental Microbiology

Phages and viruses

Association of host proteins with the broad host range filamentous phage NgoΦ6 of Neisseria gonorrhoeae – Piekarowicz et al. – PLOS ONE

Bioinformatics

**Editorial: Ten simple rules to colorize biological data visualization – Hattab et al. – PLOS Computational Biology

NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy – de Koning et al. – GigaScience

Predicting antimicrobial resistance using conserved genes – Nguyen et al. – PLOS Computational Biology

Techniques

Review: Innovations to culturing the uncultured microbial majority – Lewis et al. – Nature Reviews Microbiology

Comparison of the diversity of cultured and total bacterial communities in marine sediment using culture-dependent and sequencing methods – Wang et al. – PeerJ

Science, publishing, and career

Comment: Crowdsourcing virtual summer research opportunities to support minorities in microbiology – Johnson et al. – Nature Microbiology

October 22, 2020

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

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 16, 2020

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 14, 2020

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

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

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 8, 2020

Greetings!!
Congratulations to the Nobel prize winners in Chemistry : Emmanuelle Charpentier and Jennifer A. Doudna for the discovery of “Genetic scissors: a tool for rewriting the code of life- the CRISPR/Cas9 genetic scissors.” Today’s brief digest covers a wide range of articles on early life microbiome to respiratory microbiome. Happy reading!!!

General microbiome
Electrochemical Investigation of Thiobacillus denitrificans in a Bacterial Composite – Abada et al – Journal of the Electrochemical Society

Pregnancy and early life
Review: Can we prevent allergic disease? Understanding the links between the early life microbiome and allergic diseases of childhood – Petersen and Turvey – Current Opinion in Pediatrics

Multi-site human microbiome
Nutritional Targeting of the Microbiome as Potential Therapy for Malnutrition and Chronic Inflammation – Schröder et al – Nutrients

Human respiratory microbiome
Airway bacterial and fungal microbiome in chronic obstructive pulmonary disease – Liu et al – bioRxiv

Human gut microbiome
Review: Mechanistic insight into the gut microbiome and its interaction with host immunity and inflammation – Xue et al – Animal Nutrition

Ethanol extract of Centella asiatica alleviated dextran sulfate sodium-induced colitis via restoration on mucosa barrier and gut microbiota homeostasis – Li et al – Journal of Ethnopharmacology

Development of a three-compartment in vitro simulator of the Atlantic Salmon GI tract and associated microbial communities: SalmoSim – Kazlauskaite et al – bioRxiv

Time-dependent modulation of gut microbiome in response to systemic antifungal agents – Udawatte et al – bioRxiv

Animal microbiome
North American fireflies host low bacterial diversity – Green et al – bioRxiv

Plant, root, and soil microbiome
Anthropogenic Invasion of Micromycetes to Undisturbed Ecosystems of the Larsemann Hills Oasis (East Antarctica) – Vlasov et al – Russian Journal of Biological Invasions

Larch or Mongolian pine? Effects of tree species on soil properties and microbial biomass with the consideration of afforestation time – Teng et al – Ecological Engineering

Water and extremophile microbiome
Understanding the microbial trends in a nitritation reactor fed with primary settled municipal wastewater – Pedrouso et al – Separation and Purification Technology

Microbiome community and complexity indicate environmental gradient acclimatisation and potential microbial interaction of endemic coral holobionts in the South China Sea – Chen et al – Science of The Total Environment

Microbial community structure in the river sediments from upstream of Guanting Reservoir: potential impacts of reclaimed water recharge – Xie et al – Science of The Total Environment

Food microbiology
Next-generation sequencing to enhance the taxonomic resolution of the microbiological analysis of meat and meat-derived products – Reckem et al – Current Opinion in Food Science

Techniques
CRISPR/Cas12a mediated genome engineering in photosynthetic bacteria – Zhang et al – bioRxiv

October 07, 2020

Grant application (US specific grant)
2020 Biocodex Microbiota Foundation US $50,000 grant, supporting cutting edge research on the relationship between gut microbiota and chronic disease.
Deadline: October 15th.
Link: https://www.biocodexmicrobiotafoundation.com/national-call-projects/usa

General microbiome

Understanding the potential of lactobacilli in recurrent UTI prevention – Vagios, Hesham & Mitchel – Microbial Pathogenesis

Throat microbial community structure and functional changes in post-surgery laryngeal carcinoma patients – Hsueh et al. – Applied and Environmental Microbiology

Bacterial diversity and prevalence of antibiotic resistance genes in the oral microbiome – Almeida et al. – PLOS One

Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on Streptococcus mutans and Streptococcus sobrinus – Achtman & Zhou – Philosophical Transactions of the Royal Society B

Pregnancy and early life

In utero human intestine harbors unique metabolomic features including bacterial metabolites – Li et al. – JCI insight

Interactions between Environmental Exposures and the Microbiome: Implications for Fetal Programming – Banerjee, Suter & Aagaard – Current Opinion in Endocrine and Metabolic Research

Human nearly-sterile sites (blood, organs, brain)

Alterations in blood microbiota after colonic cancer surgery – Søby et al. – BJS Open

Human gut microbiome

Estimating molecular preservation of the intestinal microbiome via metagenomic analyses of latrine sediments from two medieval cities – Sabin et al. – Philosophical Transactions of the Royal Society B

Gut microbiota composition in obese and non-obese adult relatives from the highlands of Papua New Guinea – Jonduo et al. – FEMS Microbiology Letters

Fecal Bacteria as Biomarkers for Predicting Food Intake in Healthy Adults – Shinn et al. – The Journal of Nutrition

Animal experiments

Inulin fermentation by lactobacilli and bifidobacteria from dairy calves – Zhu et al. – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Microbial Diversity and Community Structure in Alpine Stream Soil – Rasool et al. – Geomicrobiology Journal

Food microbiology

Impact of dietary fibers in infant formula on gut microbiota and the intestinal immune barrier – Kong et al. – Food & Function

Bioinformatics

[PREPRINT] A framework for comparing microbial networks reveals core associations – Rottjers et al. – bioRxiv

Microbes in the news (popular press, EurekAlert, ScienceDaily, Youtube, NPR, etc)

Gut health benefits begin in utero – Brita Belli – YaleNews

Medieval poo holds clues to health of modern-day gut microbiome – Sara Rigby – Science Focus

October 6, 2020

Starting today’s digest with a couple of very interest studies on COVID-19 in Nature and Science. There’s also multiple interesting virome papers today.

COVID-19 & Vaccines

Selective and cross-reactive SARS-CoV-2 T cell epitopes in unexposed humans – Mateus et al. Science

The major genetic risk factor for severe COVID-19 is inherited from Neanderthals – Zeberg et al. Nature

Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-PCR – Smyrlaki et al. Nature Communications. 

General microbiome

Identification of new enterosynes using prebiotics: roles of bioactive lipids and mu-opioid receptor signalling in humans and mice – Abot et al. Gut

Assessing the Variation within the Oral Microbiome of Healthy Adults – Nearing et al. mSphere

Strain-Level Analysis of Bifidobacterium spp. from Gut Microbiomes of Adults with Differing Lactase Persistence Genotypes – Schmidt et al. mSystems

Description of a new member of the family Erysipelotrichaceae: Dakotella fusiforme gen. nov., sp. nov., isolated from healthy human feces – Ghimire et al. PeerJ.

Gut microbiome

Distinct signatures of gut microbiome and metabolites associated with significant fibrosis in non-obese NAFLD – Lee et al. Nature Communications

Animal microbiome 

Fecal microbiota in client-owned obese dogs changes after weight loss with a high-fiber-high-protein diet – Bermudez-Sanchez. PeerJ

Plant microbiome

Achieving similar root microbiota composition in neighbouring plants through airborne signalling – Kong et al. ISME

Phages and viruses

Human-Gut-DNA Virome Variations across Geography, Ethnicity, and Urbanization – Zuo et al. Cell Host & Microbe

Phage gene expression and host responses lead to infection-dependent costs of CRISPR immunity – Meaden et al. ISME

Interaction of bacterial metagenome and virome in patients with cirrhosis and hepatic encephalopathy – Bajaj et al. Gut

Stability of the Virome in Lab- and Field-Collected Aedes albopictus Mosquitoes across Different Developmental Stages and Possible Core Viruses in the Publicly Available Virome Data of Aedes Mosquitoes – Shi et al. mSystems