July 31, 2020

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Today’s digest features studies on hospital-associated bacterial communities on window components, the effect of urbanization on the vaginal microbiota of Amerindians, nitrate as a potential prebiotic for oral health, and the latest news in bioinformatics. Happy reading!

General microbiome

Microbial species interactions determine community diversity in fluctuating environments – Shota Shibasaki – bioRxiv

Review: The host-associated archaeome – Guillaume Borrel – Nature Reviews Microbiology

Oral microbiome

*Nitrate as a potential prebiotic for the oral microbiome – Bob T. Rosier – Scientific Reports

Skin microbiome

Deep skin dysbiosis in vitiligo patients: link with mitochondrial and immune changes – Hanene Bzioueche – medRxiv

Gut microbiome

Review: The microbiome: An emerging key player in aging and longevity– Minhoo Kim and Bérénice A. Benayoun – Translational Medicine of Aging

Immunoglobulin recognition of fecal bacteria in stunted and non-stunted children: findings from the Afribiota study – Kelsey E. Huus – Microbiome

Vaginal microbiome

*Changes in the vaginal microbiota across a gradient of urbanization – Daniela Vargas-Robles – Scientific Reports

Comparison between a novel molecular tool and conventional methods for diagnostic classification of bacterial vaginosis: is integration of the two approaches necessary for a better evaluation? – Margherita Scapaticci – New Microbiologica

Genome-wide mutagenesis identifies factors involved in Enterococcus faecalis vaginal adherence and persistence – Norhan Alhajjar – bioRxiv

Association between Vaginal Bacterial Microbiota and Vaginal Yeast Colonization – McKenna C Eastment – The Journal of Infectious Diseases

Urinary microbiome

Review: The microbiome in urological diseases – Kwang Woo Lee – Investigive and Clinical Urology

Review: FimH and Anti-Adhesive Therapeutics: A Disarming Strategy Against Uropathogens – Meysam Sarshar – Antibiotics

Characterization of urinary microbiome in patients with bladder cancer: Results from a single-institution, feasibility study – Juan Chipollini – Urologic Oncology: Seminars and Original Investigations

Animal microbiome

Resistance to change: AMR gene dynamics on a commercial pig farm with high antimicrobial usage – Jolinda Pollock – Scientific Reports

Vaginal Microbiota Changes During Estrous Cycle in Dairy Heifers – Juan J. Quereda – Frontiers in Veterinary Science

Animal experiment

The gut microbiome switches mutant p53 from tumour-suppressive to oncogenic – Eliran Kadosh – Nature

An Enteric Pathogen Subverts Colonization Resistance by Evading Competition for Amino Acids in the Gut – Gustavo Caballero-Flores – Cell Host & Microbe

Consumption of a Western-Style Diet Modulates the Response of the Murine Gut Microbiome to Ciprofloxacin – Damien J. Cabral – mSystems

Water and extremophile microbiome

Determining the primary sources of fecal pollution using microbial source tracking assays combined with land-use information in the Edwards Aquifer – Jessica Hinojosa – Water Research

Diverse Microorganisms in Sediment and Groundwater Are Implicated in Extracellular Redox Processes Based on Genomic Analysis of Bioanode Communities – Tyler J. Arbour – Frontiers in Microbiology

Food microbiome

Discovering microbiota and volatile compounds of surströmming, the traditional Swedish sour herring – Luca Belleggia – Food Microbiology

Built environment

*Viable bacterial communities on hospital window components in patient rooms – Patrick F. Horve – PeerJ

Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation – Ganesh Babu Malli Mohan – mSystems

Phages and viruses

Viral Metagenomic Content Reflects Seawater Ecological Quality in the Coastal Zone – Anastasia Tsiola – Viruses

Bioinformatics

Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets – Yi Yue – BMC Bioinformatics

Untangling Species-Level Composition of Complex Bacterial Communities through a Novel Metagenomic Approach – Christian Milani – mSystems

Automated prediction and annotation of small proteins in microbial genomes– Matthew G Durrant and Ami S Bhatt – bioRxiv

Accurate and sensitive detection of microbial eukaryotes from metagenomic shotgun sequencing data – Abigail L. Lind – bioRxiv

MicrobeAnnotator: a user-friendly, comprehensive microbial genome annotation pipeline – Carlos A. Ruiz-Perez – bioRxiv

Topological and kernel-based microbial phenotype prediction from MALDI-TOF mass spectra – Caroline Weis – Bioinformatics

NetCoMi: Network Construction and Comparison for Microbiome Data in R – Stefanie Peschel – bioRxiv

Review: Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses – Ana Elena Pérez-Cobas – Microbial Genomics

Podcast

Machine learning for drug development with Marinka Zitnik – Jacob Schreiber – The Bioinformatics Chat

July 30, 2020

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Hello from Lübeck! This week started slowly but our todays post covers quite a range of topics with a couple of reviews about our understanding of the gut microbiome related to digestive diseases. Of particular note is a publication by Kadosh et al. (Nature 2020) linking the gut microbiome and p53 in mice. This highlights the role of the microenvironment on cancer in general.

● Human vaginal microbiome

Changes in the vaginal microbiota following antibiotic treatment for Mycoplasma genitalium, Chlamydia trachomatis and bacterial vaginosis – Ahrens et al. – Plos One

● Human gut microbiome

[REVIEW] Gut Microbiome Modulates Response to Cancer Immunotherapy – Khan et al. – Digestive Diseases and Sciences

[REVIEW] Healthy Human Gastrointestinal Microbiome: Composition and Function After a Decade of Exploration – Ruan et al. – Digestive Diseases and Sciences

[REVIEW] Microbiome and Its Role in Irritable Bowel Syndrome – Pimentel and Lembo – Digestive Diseases and Sciences

[REVIEW] Diet and Gut Microbes Act Coordinately to Enhance Programmed Cell Death and Reduce Colorectal Cancer Risk – Chapkin et al. – Digestive Diseases and Sciences

Diversity of Gut Microbiota and Bifidobacterial Community of Chinese Subjects of Different Ages and from Different Regions – Yang et al. – Microorganisms

[PREPRINT] Gut Microbiota Changes in Nonalcoholic Fatty Liver Disease and Concomitant Cardiovascular Diseases – Kurinna – bioarxiv

Lactobacillus plantarum-Mediated Regulation of Dietary Aluminum Induces Changes in the Human Gut Microbiota: an In Vitro Colonic Fermentation Study – Yu et al. – Probiotics and Antimicrobial Proteins

Troublesome friends within us: the role of gut microbiota on rheumatoid arthritis etiopathogenesis and its clinical and therapeutic relevance – Reyes-Castillo et al. – Clinical and Experimental Medicine

Duodenal Microbiota in Stunted Undernourished Children with Enteropathy – Chen et al. – The New Englang Journal of Medicine

Small molecules, big effects: microbial metabolites in intestinal immunity – Glotfelty, Wong and Levy – AJP Gastrointestinal and Liver Physiology

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

The gut microbiome switches mutant p53 from tumour-suppressive to oncogenic – Kadosh et al. – Nature

Impact of PepT1 deletion on microbiota composition and colitis requires multiple generations – Viennois et al. – npj Biofilms and Microbiomes

● Plant, root, and soil microbiome

[REVIEW] Recent advances in the role of plant metabolites in shaping the root microbiome – Jacoby et al. – F1000

● Food microbiology

Selection of cereal-sourced lactic acid bacteria as candidate starters for the baking industry – Milanovic et al. – Plos One

The sources and transmission routes of microbial populations throughout a meat processing facility – Zwirzitz et al. – npj Biofilms and Microbiomes

● Phages and viruses

[PREPRINT] Characterization of the gut DNA and RNA viromes in a cohort of Chinese residents and visiting Pakistanis – Yan – bioarxiv

● Bioinformatics

[REVIEW] Tools for Analysis of the Microbiome – Galloway-Pena and Hanson – Digestive Diseases and Sciences

● Techniques

Microbial community dissimilarity for source tracking with application in forensic studies – Carter et al. – Plos One

● Microbes in the news

Pilot study examines facial microbiome diversity – Petrou – Dermatology Times

The 2020 Way To Treat Your Skin Is All About Bacteria, Bugs And Microbiomes – Driver – ELLE

July 29, 2020

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● General microbiome

[REVIEW] The dialogue between unconventional T cells and the microbiota – Lin et al. – Mucosal Immunology

● Human skin microbiome

Stability of Skin Microbiome at Sacral Regions of Healthy Young Adults, Ambulatory Older Adults, and Bedridden Older Patients After 2 Years – Ogai et al. – Biological Research For Nursing

The skin microbiome as a clinical biomarker in atopic eczema: Promises, navigation, and pitfalls – Reiger et al. – Journal of Allergy and Clinical Immunology

● Human gut microbiome

Feeding Bugs to Bugs: Edible Insects Modify the Human Gut Microbiome in an in vitro Fermentation Model – Young et al. – Front. Microbiol.

● Plant, root, and soil microbiome/metabolome

[REVIEW] The Application of Metabolomics for the Study of Cereal Corn (Zea mays L.) – Lena Gálvez Ranilla – Metabolites

Elevational is the main factor controlling the soil microbial community structure in alpine tundra of the Changbai Mountain – Tang et al. – Scientific Reports

● Techniques

A guide to deciphering microbial interactions and metabolic fluxes in microbiome communities – Maciek R Antoniewicz – Current Opinion in Biotechnology

July 27, 2020

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Greetings from Pittsburgh!

Saturday and Sunday’s digests were packed full of great articles, which means the week is off to a slower start than usual. We’ve got two environmentally focused preprints that I am super excited about, a paper demonstrating how microbiota can be dosed in order to help mice mitigate intestinal cancer and inflammation, and a paper focused on the eco-thermodynamics of methanogenic bioprocesses. Enjoy!

Animal experiments

Microbiota from alginate oligosaccharide-dosed mice successfully mitigated small intestinal mucositis – Zhang et al. – Microbiome

Water and extremophile microbiome

Preprint: Distinct microbial communities along the chronic oil pollution continuum of the Persian Gulf converge with oil spill accidents – Somee et al. – BioRxiv

Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses – Nobu et al. – Microbiome

Preprint: Freshwater monitoring by nanopore sequencing – Urban et al. – bioRxiv

July 26, 2020

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General microbiome

No endospore formation confirmed in members of the phylum Proteobacteria – Polina Beskrovnaya – bioRxiv

Interbacterial competition and anti-predatory behavior of environmental Vibrio cholerae strains – Natalia C. Drebes Doerr – bioRxiv

The kleboxymycin biosynthetic gene cluster is encoded by several species belonging to the Klebsiella oxytoca complex – Preetha Shibu – bioRxiv

Plant, root, and soil microbiome

POPULATION GENOMICS REVEALS MOLECULAR DETERMINANTS OF SPECIALIZATION TO TOMATO IN THE POLYPHAGOUS FUNGAL PATHOGEN BOTRYTIS CINEREA – Alex Mercier – bioRxiv

Phages and viruses

Scientometric Trends for Coronaviruses and Other Emerging Viral Infections – Dima Kagan – bioRxiv

Bioinformatics

Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae – Liam P Shaw – bioRxiv

Techniques

Comparing DNA Extraction and 16s Amplification Methods for Plant-Associated Bacterial Communities – Cecelia Giangacomo – bioRxiv

Microrisk Lab: an online freeware for predictive microbiology – Yangtai Liu – bioRxiv

Microbes in the news 

Human microbiome project paved way for poultry research – WATTAgNet

Microbes on the market

SeqBiome’s clients already include Nestlé, Mars Petcare, Atlantia and Microbion, among others. – Silicon Republic

Global Human Microbiome Sequencing Market 2020 Industry Research Strategy, Outlook and Product Development to 2025 – Bandera County Courier

July 25, 2020

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Good morning and happy Saturday y’all! Today’s digest is brief, but covers some fascinating papers including: small RNAs regulating gut microbe metabolism; epigenetics linking the early-life airway microbiota with allergic rhinitis; and the impact of gut microbial composition on vagal innervation. I’ve also included a non-microbiome pick discussing how to spot and resolve common statistical mistakes in research manuscripts. The authors of the article hope this will help improve robustness of scientific research. Happy reading!

Gut Microbiome
A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron. Ryan, D. et al. Nature Communications.

Depicting SARS-CoV-2 faecal viral activity in association with gut microbiota composition in patients with COVID-19. Zuo, T. et al. Gut.

High microbiota reactivity of adult human intestinal IgA requires somatic mutations. Kabbert, J. et al. Journal of Experimental Medicine.

A unified catalog of 204,938 reference genomes from the human gut microbiome. Almeida, A. et al. Nature Biotechnology.

Airway Microbiome
Epigenetic landscape links upper airway microbiota in infancy with allergic rhinitis at 6 years of age. Morin, A. et al. Journal of Allergy and Clinical Immunology.

Early-Life Microbiome
Butyrate producing colonic Clostridiales metabolise human milk oligosaccharides and cross feed on mucin via conserved pathways. Pichler, M.J. et al. Nature Communications.

Animal Experiments
Bile acids drive the newborn’s gut microbiota maturation. van Best, N. et al. Nature Communications.

Gut microbiota composition modulates inflammation and structure of the vagal afferent pathway. Kim, J.S. et al. Physiology & Behavior.

TNFα regulates intestinal organoids from mice with both defined and conventional microbiota. Sun, L. et al. International Journal of Biological Macromolecules.

Water Microbiome
Nutrient and microbial water quality of the upper Ganga River, India: identification of pollution sources. Bowed, M.J. et al. Environmental Monitoring and Assessment.

Plant, Root, and Soil Microbiome
Global warming shifts the composition of the abundant bacterial phyllosphere microbiota as indicated by a cultivation-dependent and -independent study of the grassland phyllosphere of a long-term warming field experiment. Aydogan, E.L. FEMS Microbiology and Ecology.

Non-Microbiome Pick
Science Forum: Ten common statistical mistakes to watch out for when writing or reviewing a manuscript. Makin, T.R. and Orban de Xivry, JJ. eLife.

July 24, 2020

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Good afternoon all!

Today’s digest is a bit on the lighter side, nevertheless, there are some great papers to sink your teeth into.

Those with an interest in tropical diseases will want to read an investigation into the three-way relationship between humans, their microbiotas and the protozoan cause of Chagas disease.

History buffs, and fans of the epic novel ‘Romance of the Three Kingdoms’ may be interested by an analysis of the soil microbiome of the Jinsha relic, which is found at the site of the former Chinese Shu state capital.

For those more philosophically inclined, there is an interesting discussion on the impact of human space activity on the search for extra-terrestrial life. So that’s ancient history and space-age wizardry all covered in today’s rather modest digest. What more could you want?!

COVID-19

Preprint: Rapid in vitro assays for screening neutralizing antibodies and antivirals against SARS-CoV-2 – Oark et al.

Preprint: The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner – Ogawa et al.

Preprint: Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants – Weisblum et al.

General microbiome

Mapping of host-parasite-microbiome interactions reveals metabolic determinants of tropism and tolerance in Chagas disease – Hossain et al. – Science Advances

Animal experiments

Host immunity and the colon microbiota of mice infected with Citrobacter rodentium are beneficially modulated by lipid-soluble extract from late-cutting alfalfa in the early stages of infection – Fries-Craft et al. – PLOS One

Plant, root, and soil microbiome

Diversity and structure of soil microbiota of the Jinsha earthen relic – Yang et al. – PLOS One

Quantitative detection of economically important Fusarium oxysporum f. sp. cubense strains in Africa in plants, soil and water – Matthews et al. – PLOS One

Fungi, bacteria and oomycota opportunistically isolated from the seagrass, Zostera marina – Ettinger and Eisen – PLOS One

Techniques

Majority sensing in synthetic microbial consortia – Alnahhas et al. – Nature Communications

Microbes in the news

Should we disinfect outer space?: Jenna Sutela and Sophia Roosth in conversation – Sutela and Roosth – Art in America

July 23, 2020

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In today’s digest – duodenal microbiota linked to stunting in children, differential effects of germfree and antibiotic treated mouse models on social behavior, microbial metabolite receptor GPBAR and its interaction with bile acids, review article on engineering microbes to treat diseases and many more…happy reading!

General microbiome

The Microbiota-Gut-Immune-Glia (MGIG) Axis in Major Depression – Leszek Rudzki – Molecular Neurobiology

Engineering the gut microbiota to treat chronic diseases – Noura S. Dosoky – Applied Microbiology and Biotechnology

Human microbiome

Acute and chronic improvement in postprandial glucose metabolism by a diet resembling the traditional Mediterranean dietary pattern: Can SCFAs play a role? – Marilena Vitale – Clinical Nutrition

Linking the duodenal microbiota to stunting in a cohort of undernourished Bangladeshi children with enteropathy – Robert Y. Chen – New England Journal of Medicine

Enterobacterales Infection after Intestinal Dominance in Hospitalized Patients – Krishna Rao – mSphere

Differences in the gut Firmicutes to Bacteroidetes ratio across age groups in healthy Ukrainian population – Alexander Vaiserman – BMC Microbiology

Preprint- Association of gut microbiota with cerebral cortex and cerebrovascular abnormality in human mild traumatic brain injury – Lijun Bai – BioRxiv

Real-world study in infants fed an infant formula with two human milk oligosaccharides – Enriqueta Román – Nutricion Hospitalaria

Animal experiments

Gut microbiome composition differences among breeds impact feed efficiency in swine – Matteo Bergamaschi – Microbiome

Opposing effects of antibiotics and germ-free status on neuropeptide systems involved in social behaviour and pain regulation – Katerina V. A. Johnson – BMC Neuroscience

Local Necrotic Cells Trigger Systemic Immune Activation via Gut Microbiome Dysbiosis in Drosophila – Hina Kosakamoto – Cell Reports

Peanut skin extract ameliorates the symptoms of type 2 diabetes mellitus in mice by alleviating inflammation and maintaining gut microbiota homeostasis – Lan Xiang – Aging

Preprint- Community composition and development of the post-weaning piglet gut microbiome – D. Gaio – BioRxiv

Gut microbiota regulate tumor metastasis via circRNA/miRNA networks – Zhuxian Zhua – Gut Microbes

Porcine circovirus type 2 (PCV2) and Campylobacter infection induce diarrhea in piglets: Microbial dysbiosis and intestinal disorder – Gang Yang – Animal Nutrition

Plant, root and soil microbiome

Populations of the Parasitic Plant Phelipanche ramosa Influence Their Seed Microbiota – Sarah Huet – Frontiers in Plant Science

Domestication-driven changes in plant traits associated with changes in the assembly of the rhizosphere microbiota in tetraploid wheat – Aymé Spor – Scientific Reports

Water microbiome

Preprint- Time series metagenomic sampling of the Thermopyles, Greece, geothermal springs reveals stable microbial communities dominated by novel sulfur-oxidizing chemoautotrophs – A. Meziti – BioRxiv

Preprint- Evaluation of the microbial community structure of potable water samples from occupied and unoccupied buildings using16S rRNA amplicon sequencing – Kimothy L. Smith – BioRxiv

Phages and Viruses

Preprint- Targeting of Mammalian Glycans Enhances Phage Predation in the Gastrointestinal Tract – Sabrina I. Green – BioRxiv

Techniques
Structural basis of GPBAR activation and bile acid recognition – Fan Yang – Nature

Microbes in News

Machine learning analysis reveals less diverse microbiome in children with type 1 diabetes – Healio

July 22, 2020

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Human microbiome

The Urinary Tract Microbiome in Older Women Exhibits Host Genetic and Environmental Influences – Adebayo et al. – Cell Host & Microbe

The vaginal microbiome as a predictor for outcome of in vitro fertilization with or without intracytoplasmic sperm injection: a prospective study – Koedooder et al. – Human reproduction

Comparison of Meconium Microbiome in Dizygotic and Monozygotic Twins Born by Caesarean Section (CS) – Yang et al. – Frontiers in Microbiology

Gut microbiome

Autoreactivity in naïve human fetal B cells is associated with commensal bacteria recognition – Chen et al. – Science

Prenatal stress increases IgA coating of offspring microbiota and exacerbates necrotizing enterocolitis-like injury in a sex-dependent manner – Brawner et al. – Brain, Behavior, and Immunity

General microbiome

* Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts – McLean et al. – Cell Reports

July 21, 2020

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Hello! We are in the midst of an unprecedented heat wave here in Western New York and I hope everyone is enjoying summer in the northern hemisphere. In todays post there is an interesting article by Kyung-Eon Lee, et al on the extracellular vesicle of a gut microbe Paenalcaligenes hominis as a risk factor for vagus nerve-mediated cognitive impairment. There also is a preprint on parthenogenesis in weevils as a possible Wolbachia-density dependent trait to ponder as well as a look at the experimental approaches to investigating the vaginal biofilm microbiome. Enjoy!

COVID-19

Preprint: ACE2-independent interaction of SARS-CoV-2 spike protein to human epithelial cells can be inhibited by unfractionated heparin. Lynda J Partridge, et al. bioRxiv

SARS-CoV-2 is not present in the vaginal fluid of pregnant women with COVID-19. MM Aslan, et al. – The Journal of Maternal…

GENERAL MICROBIOME

Preprint: Targeting methionine synthase in a fungal pathogen causes a metabolic imbalance that impacts cell energetics, growth and virulence. Jennifer Scott, et al. bioRxiv

HUMAN SKIN MICROBIOME

News Article: All-Natural Soap For Nourished And Balanced Microbiome Product Launched

HUMAN VAGINAL MICROBIOME

Experimental approaches to investigating the vaginal biofilm microbiome. PubMed – NIH

HUMAN GUT MICROBIOME

The extracellular vesicle of gut microbial Paenalcaligenes hominis is a risk factor for vagus nerve-mediated cognitive impairment. Kyung-Eon Lee, et al. Microbiome

Evolution of Gut Microbiome and Metabolome in Suspected Necrotizing Enterocolitis. MDPI

[PDF] Effect of a Nutritional Intervention on the Intestinal Microbiota of Vertically HIV-Infected Children: The Pediabiota Study. T Sainz,et al. – Nutrients

ANIMAL MICROBIOME

Preprint: Parthenogenesis in weevils of the tribe Naupactini (Coleoptera, Curculionidae): a Wolbachia-density dependent trait?Marcela Silvina Rodriguero, et al. bioRxiv

PLANT, ROOT AND SOIL MICROBIOME

Preprint: Humic acids enrich the plant microbiota with bacterial candidates for the suppression of pathogens. Maura SRA Silva, et al. bioRxiv

Predicting disease occurrence with high accuracy based on soil macroecological patterns of Fusarium wilt. J Yuan, et al. – The ISME Journal

ANIMAL EXPERIMENTS

The gut microbiota of brood parasite and host nestlings reared within the same environment: disentangling genetic and environmental effects. CY Lee, et al. – The ISME Journal

TECHNIQUES

Two possible candidate enzymes from Ulva lactuca-associated epiphytic bacteria obtained through PCR and functional evaluation. JS Ruiz-Toquica, et al. – Universitas Scientiarum

WATER AND EXTREMOPHILE MICROBIOME

Genomic insights into the salt tolerance and cold adaptation of Planococcus halotolerans SCU63 T. L Gan, et al. – Archives of Microbiology

PROBIOTICS / PREBIOTICS

The Benefits of Probiotic Interventions in Maternal-Fetal Health: An Appraise Review. P Dhillon, et al. – PharmaNutrition

PHAGES AND VIRUSES

[PDF] Low Host Abundance and High Temperature Determine Switching from Lytic to Lysogenic Cycles in Planktonic Microbial Communities in a Tropical Sea (Red Sea). R Abdulrahman Ashy, et al. – Viruses