Category Archives: Animal experiments

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 27, 2020

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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 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 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 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 09, 2020

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COVID-19
Face masks: what the data say – Lynne Peeples – Nature

Pregnancy and early life

[REVIEW] Can we prevent allergic disease? Understanding the links between the early life microbiome and allergic diseases of childhood – Petersen & Turvey – Current Opinions in Pediatrics

Human skin microbiome

Atopic Dermatitis and the Role of the Skin Microbiome in Choosing Prevention, Treatment, and Maintenance Options – Baldwin ety al. – Journal of Drugs in Dermatology

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

[PREPRINT] Western-style diet impedes colonization and clearance of gut bacterial pathogens – Gewirtz et al. – bioRxiv

Animal microbiome (for animals in the wild)

Taxonomic profiling of individual nematodes isolated from copse soils using deep amplicon sequencing of four distinct regions of the 18S ribosomal RNA gene – Kenmotsu et al. – PLOS One

The red flour beetle Tribolium castaneum: A model for host-microbiome interactions – Agarwal & Agashe – PLOS One

[PREPRINT] Meta-transcriptomic identification of divergent Amnoonviridae in fish – Turnbull et al. – bioRxiv

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Metagenome analysis from the sediment of river Ganga and Yamuna: In search of beneficial microbiome – Behera et al. – PLOS One

Phages and viruses

[PREPRINT] Thousands of previously unknown phages discovered in whole-community human gut metagenomes – Benler et al. – bioRxiv

Bioinformatics

Metabolic pathway inference using multi-label classification with rich pathway features – Basher, McLaughlin & Hallam – PLOS Computational Biology

Big Data in metagenomics: Apache Spark vs MPI – Abuin et al. – PLOS One

October 8, 2020

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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

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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 2, 2020

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

General microbiome

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

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

Human microbiome

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

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

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

Animal microbiome

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

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

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

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

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

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

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

Plant microbiome

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

Techniques

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

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

Non-microbiology picks

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

October 1, 2020

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Greetings, friends!

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

Enjoy!

Events

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

Human respiratory microbiome

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

Human gut microbiome

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

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

Animal experiments

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

Plant, root, and soil microbiome

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

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

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

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

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

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

Water and extremophile microbiome

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

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

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

Built environment

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

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

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

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

Microbes in the news

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

Science, publishing, and career

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