Category Archives: Human oral

September 28, 2020

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In today’s digest read about ureteral stent microbiota, metagenomic growth estimators, social transmission as a major shaper of gut microbiota in wild mice [spoiler: mice with many friends in separate social circles have the richest microbiota], and give a listen to the first episode of Lonely Pipette, a brand new podcast about doing better science!

General microbiome

Review: Searching for principles of microbial physiology – Frank J Bruggeman – FEMS Microbiology Reviews

Metagenomics

*Benchmarking microbial growth rate predictions from metagenomes – Andrew M. Long – The ISME Journal

Metabolomics

Review: Gut microbial metabolites as multi-kingdom intermediates – Kimberly A. Krautkramer – Nature Reviews Microbiology

Multi-omics

Integration of absolute multi-omics reveals dynamic protein-to-RNA ratios and metabolic interplay within mixed-domain microbiomes – Francesco Delogu – Nature
Behind the paper: What can absolute multi-omics add to microbial ecology?

Gut microbiome

Macrophages Maintain Epithelium Integrity by Limiting Fungal Product Absorption – Aleksandra S. Chikina – Cell

Review: Anorexia nervosa and gut microbiota: A systematic review and quantitative synthesis of pooled microbiological data – Laura Di Lodovico – Progress in Neuro-Psychopharmacology and Biological Psychiatry

In search for interplay between stool microRNAs, microbiota and short chain fatty acids in Crohn’s disease – a preliminary study – Filip Ambrozkiewicz – BMC Gastroenterology

Vaginal microbiome

Slipped strand mispairing in the gene encoding cell wall associated sialidase NanH3 in Gardnerella spp – Shakya P. Kurukulasuriya – bioRxiv

The vaginal microbiome in pregnant women: knowledge gaps in relation to clinical relevance – Steven S. Witkin – BJOG: An International Journal of Obstetrics and Gynaecology

Urinary microbiome

*Ureteral Stent Microbiota Is Associated with Patient Comorbidities but Not Antibiotic Exposure – Kait F. Al – Cell Reports Medicine

Novel Antibiotic-Loaded Particles Conferring Eradication of Deep Tissue Bacterial Reservoirs for the Treatment of Chronic Urinary Tract Infection – Wai Lau – Journal of Controlled Release

Respiratory microbiome

Altered respiratory microbiota composition and functionality associated with asthma early in life – Mohammad T. AL Bataineh – BMC Infectious Diseases

Oral microbiome

Comparative evaluation of microbial profiles of oral samples obtained at different collection time points and using different methods – Michi Omori – Clinical Oral Investigations

Alteration of salivary microbiome in periodontitis with or without type-2 diabetes mellitus and metformin treatment – Xiaoyu Sun – Scientific Reports

Animal microbiome

Habitat disturbance influences the skin microbiome of a rediscovered neotropical-montane frog – Randall R. Jiménez – BMC Microbiology

Lactobacillus spp. attenuate antibiotic-induced immune and microbiota dysregulation in honey bees – Brendan A. Daisley – Communications Biology

Animal experiment

Antibiotics increase aggression behavior and aggression-related pheromones and receptors in Drosophila melanogaster – Michal Grinberg – bioRxiv

*Social networks strongly predict the gut microbiota of wild mice – Aura Raulo – bioRxiv

Plant/root/soil microbiome

Insights into the diversity and survival strategies of soil bacterial isolates from the Atacama Desert – Alicyn Reverdy – bioRxiv

Rhizobacterial species richness improves sorghum growth and soil nutrient synergism in a nutrient-poor greenhouse soil – Mohammad Radhi Sahib – Scientific Reports

Water microbiome

Bacterial Opportunistic Pathogen Gene Markers in Municipal Drinking Water are Associated with Distribution System and Household Plumbing Characteristics – Sarah Haig – Environmental Science: Water Research & Technology

Collection system investigation microbial source tracking (CSI-MST): Applying molecular markers to identify sewer infrastructure failures – Dana Gonzalez – Journal of Microbiological Methods

New insights into the vertical distribution and microbial degradation of microplastics in urban river sediments – Lihua Niu – Water Research

Unveiling dynamics of size-dependent antibiotic resistome associated with microbial communities in full-scale wastewater treatment plants – Kaifeng Yu – Water Research

Aerobic microbial communities in the sediments of a marine oxygen minimum zone – Sabyasachi Bhattacharya – FEMS Microbiology Letters

Phages and viruses

Identification of Bacteriophages in the Vagina of Pregnant Women: A Descriptive Study – Antonio Charlys da Costa – BJOG: An International Journal of Obstetrics and Gynaecology

The Protective Effect of Staphylococcus epidermidis Biofilm Matrix against Phage Predation – Luís D.R. Melo – Viruses

Bioinformatics

Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation – Dileep Kishore – bioRxiv

GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure – Yu Wan – BMC Genomics

A network approach to elucidate and prioritize microbial dark matter in microbial communities – Tatyana Zamkovaya – The ISME Journal

Podcast

*TLP #1: Navigating the path to team leader, guest: Maxim Greenberg – Renaud Pourpre and Jonathan Weitzman – The Lonely Pipette: helping scientists do better science

Burnout Syndrome, guest: Beth Thompson – Christine Boinett – Your Digital Mentor Podcast

August 2020 Pod: From the deep sea to the lost sense of smell – Bengtsson-Palme Lab – Microbiology Lab Pod

Events &c

Black In Microbiology Week [September 28 – October 4]
a vibrant celebration of Black microbiologists, with talks & panels featuring microbiologists across career stages and subdisciplines

How CHROMagar™ Revolutionized Microbe Identification – Andrea Prinzi – ASM
*Submit a Masterpiece to ASM Agar Art 2020!

The National Summer Undergraduate Research Project (NSURP) #nolabnoproblem initiative – Projects & Presentations

September 23, 2020

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General microbiome
Chemotaxis under flow disorder shapes microbial dispersion in porous media – Pietro de Anna – Nature Physics

REVIEW: A piece of the pie: engineering microbiomes by exploiting division of labor in complex polysaccharide consumption – Stephen RLindemann – Current Opinion in Chemical Engineering

Benchmarking microbial growth rate predictions from metagenomes – Andrew M. Long – The ISME Journal

Integration of absolute multi-omics reveals dynamic protein-to-RNA ratios and metabolic interplay within mixed-domain microbiomes – F. Delogu – Nature Communications

Spatial Variance of Species Distribution Predicts the Interspecies Interactions within a Microbial Metacommunity – So-Yeon Jeong & Tae Gwan Kim – Microbial Ecology

Human microbiome
The Social Distancing Imposed To Contain COVID-19 Can Affect Our Microbiome: a Double-Edged Sword in Human Health – Célia P. F. Domingues – mSphere

Gut microbiome
Auto-reactivity against gut bacterial peptides in patients with late-onset diabetes – Mohammad Sajid – Autoimmunity

REVIEW: The gut microbiome in pediatric patients undergoing allogeneic hematopoietic stem cell transplantation – Riccardo Masetti – Pediatric Blood & Cancer

Gut Microbiota and Metabolome Alterations Associated with Parkinson’s Disease – Sarah Vascellari – mSystems

REVIEW: Gut Microbiota Resilience: Definition, Link to Health and Strategies for Intervention – Shaillay Kumar Dogra – Frontiers in Microbiology

Deciphering the impact of diet and host physiology on the mammalian gut microbiome by multi-omics approaches – Christian Milani – Applied and Environmental Microbiology

Oral microbiome
High altitude as a possible factor for dysbiosis of salivary microbiome in orthodontic patients – Ibrahim AlShahrani – Archives of Oral Biology

Pregnancy and early life microbiome
Changes in Gut Microorganism in Patients with Positive Immune Antibody-Associated Recurrent Abortion – Min Jin – BioMed Research International

Contrasting microbiota profiles observed in children carrying either Blastocystis spp. or the commensal amoebas Entamoeba coli or Endolimax nana – Juan F. Alzate – Scientific Reports

Biological observations in microbiota analysis are robust to the choice of 16S rRNA gene sequencing processing algorithm: case study on human milk microbiota – Shirin Moossavi – BMC Microbiology

Microbiome of near sterile sites
Metagenome analysis using serum extracellular vesicles identified distinct microbiota in asthmatics – Ji-Hyang Lee – Scientific Reports

Lung microbiome
REVIEW: Reconsidering ventilator-associated pneumonia from a new dimension of the lung microbiome – Laia Fernández-Barata – EBioMedicine

Animal microbiome
The impact of anthelmintic treatment on gut bacterial and fungal communities in diagnosed parasite-free sika deer Cervus nippon – Xiaolong Hu – Applied Microbiology and Biotechnology

Host phylogeny and life history stage shape the gut microbiome in dwarf (Kogia sima) and pygmy (Kogia breviceps) sperm whales – Elizabeth R. Denison – Scientific Reports

Animal experiment
Altered gut microbiome accompanying with placenta barrier dysfunction programs pregnant complications in mice caused by graphene oxide – Xiaojing Liu – Ecotoxicology and Environmental Safety

Comparative analysis of the pulmonary microbiome in healthy and diseased pigs – Zongjie Li – Molecular Genetics and Genomics

Diet posttranslationally modifies the mouse gut microbial proteome to modulate renal function – Lior Lobel – Science

Plant, root, and soil microbiome
REVIEW: Overhauling the assessment of agrochemical-driven interferences with microbial communities for improved global ecosystem integrity – Mengcen Wang & Tomislav Cernava – Environmental Science and Ecotechnology

Susceptibility and resilience of the soil ciliate community to high temperatures – Takaaki Oshima – Soil Science and Plant Nutrition

Food microbiology
Novel approaches for the identification of microbial communities in kimchi: MALDI-TOF MS analysis and high-throughput sequencing – Eiseul Kim – Food Microbiology

Water microbiome
The Nutrient Removal Ability and Microbial Communities in a Pilot-Scale Horizontal Subsurface Flow Constructed Wetland Fed by Slightly Polluted Lake Water – Weigang Wang – Wetland

Pre-print
Impact of temporal pH fluctuations on the coexistence of nasal bacteria – Sandra Dedrick – bioRxiv

Study of growth, metabolism, and morphology of Akkermansia muciniphila with an in vitro advanced bionic intestinal reactor – Xiaobei Zhan – bioRxiv

September 8, 2020

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Greetings, friends!

Today’s digest is a very heavy grab bag of articles! Included are many reviews on everything from the microbiome in forensic science to the gut-lung axis. Also included are original research articles focused on a variety of subjects including microplastics, extremophiles, and the bicycle microbiome! Finally, for those of you looking for practical advice, I’ve highlighted an article focused on best practices for writing genome announcements.

Happy reading!

General microbiome

Manipulating denitrifying sulfide removal of Pseudomonas sp. C27 with nitrite as sole nitrogen source: Shotgun proteomics analysis – Guo et al. – Bioresource Technology

Pseudomonas aeruginosa – Candida interplay: Effect on in vitro antibiotic susceptibility of Pseudomonas aeruginosa when grown in the presence Candida culture – Mcllroy et al. – British Journal of Biomedical Science

Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates – Nouws et al. – Scientific Reports

Evolution of diversity explains the impact of pre-adaptation of a focal species on the structure of a natural microbial community – Padfield et al. – The ISME Journal

Biomass-degrading glycoside hydrolases of archaeal origin – Suleiman et al. – Biotechnology for Biofuels

Mining for novel antibiotics in the age of antimicrobial resistance – Udaondo and Matilla – Microbial Biotechology

Multi-site human microbiome

Association between the microbiomes of tonsil and saliva samples isolated from pediatric patients subjected to tonsillectomy for the treatment of tonsillar hyperplasia – Choi et al. – Experimental & Molecular Medicine

Review: The impact of the human microbiome in forensic sciences: A systematic review – García et al. – Applied and Enviornmental Microbiology

Human respiratory microbiome

Review: The evolving role of the lung microbiome in pulmonary fibrosis – Lipinski et al. – Lung Cellular and Molecular Physiology

Review: Recent advances in understanding the ecology of the lung microbiota and deciphering the gut-lung axis – Willis et al. – Lung Cellcular and Molecular Physiology

Human gut microbiome

Altered gut microbiota correlated with systemic inflammation in children with Kawasaki disease – Chen et al. – Scientific Reports

Review: Gut microbiota in human metabolic health and disease – Fan and Pedersen – Nature Reviews Microbiology

Lactose-reduced infant formula with added corn syrup solids is associated with a distinct gut microbiota in Hispanic infants – Jones et al. – Gut Microbes

Animal experiments

Gut bacterial communities and their contribution to performance of specialist Altica flea beetles – Wei et al. – Microbial Ecology

Dynamic changes of gut microbiota of discus fish (Symphysodon haraldi) at different feeding stages – Zhang et al. – Aquaculture

Plant, root, and soil microbiome

Diversity of cultivable microbes from soil of the Fildes Peninsula, Antarctica, and their potential application – Cong et al. – Frontiers in Microbiology

Structural and functional microbial diversity of sandy soil under cropland and grassland – Frąc et al. – PeerJ

Microbiome–environment interactions in antimony-contaminated rice paddies and the correlation of core microbiome with arsenic and antimony contamination – Li et al. – Chemosphere

Review: Implications of endophytic microbiota in Camellia Sinensis: A review on current understanding and future insights – Xie et al. – Bioengineered

Characterizing the nectar microbiome of the non-native tropical milkweed, Asclepias curassavica, in an urban environment – Warren et al. – PLOS ONE

Water and extremophile microbiome

Prokaryotic diversity in stream sediments affected by acid mine drainage – Carlier et al. – Extremophiles

Combination of genetic tools to discern Bacillus species isolated from hot springs in South Africa – Jardine and Ubomba-Jaswa – African Journal of Mirobiology Research

Bioleaching of pyritic coal wastes: bioprospecting and efficiency of selected consortia – Joulian et al. – Research in Microbiology

Genotypic and phylogenetic diversity of new isolates of terrestrial Xanthophyceae (Stramenopiles) from maritime sandy habitats – Rybalka et al. – Phycologia

Paucihalobacter ruber gen. nov., sp. nov., isolated from a haloalkaline lake sediment sample – Wu et al. – Microbiology Society

Comparative analysis of bacterial diversity and community structure in the rhizosphere and root endosphere of two halophytes, Salicornia europaea and Glaux maritima, collected from two brackish lakes in Japan – Yamamoto et al. – Microbes and Environments

Fungal diversity in deep-sea sediments from Magellan seamounts environment of the western Pacific revealed by high-throughput Illumina sequencing – Yang et al. – Journal of Microbiology

Effect of Ferrous Iron Addition on Ammonium Nitrogen Removal and Microbial Communities in Horizontal Subsurface Flow Constructed Wetlands – Zhang et al. – Wetlands

Built environment

Microplastics negatively affect soil fauna but stimulate microbial activity: insights from a field-based microplastic addition experiment – Lin et al. – Proceedings of the Royal Society B

Shared bicycle microbial community: a potential antibiotic-resistant bacteria warehouse – Wu et al. – Folia Microbiologica

Microbial carrying capacity and carbon biomass of plastic marine debris – Zhao et al. – The ISME Journal

Food microbiology

Proteolysis, lipolysis, texture and sensory properties of cheese ripened by Monascus fumeus – Xia et al. – Food Research International

Bioinformatics

Announcement: Best practices for successfully writing and publishing a genome announcement in microbiology resource announcements – Hotopp et al. – Microbiology Resource Announcements

Techniques

Flow-through stable isotope probing (Flow-SIP) minimizes cross-feeding in complex microbial communities – Mooshammer et al. – The ISME Journal

September 2, 2020

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Greetings for the month of September: the Haervest-monath (Harvest Month). Today’s microbiome digest consists of a cool editorial article on hidden theatre of microbes. The digest also features two interesting reviews; first one detailing the role of skin microbiota in forensic sciences and the second one with focus on association of sponges and their microbiome.

Let’s celebrate the month of September with some fascinating microbiome studies.

There are flowers enough in the summertime,
More flowers than I can remember—
But none with the purple, gold, and red
That dye the flowers of September!
—Mary Howitt (1799-1888)

General microbiome
*Editorial: Unveiling the Hidden Theatre of Microbes – Böttcher T – ChemBioChem

Chitosan-chelated zinc modulates cecal microbiota and attenuates inflammatory response in weaned rats challenged with Escherichia coli – Feng et al – Journal of Microbiology

Multi-site human microbiome
Potential Associations Among Alteration of Salivary miRNAs, Saliva Microbiome Structure, and Cognitive Impairments in Autistic Children – Ragusa et al – Int. J. Mol. Sci.

Human respiratory microbiome
Review: The importance of airway and lung microbiome in the critically ill – Martin-Loeches et al – Critical Care

Human skin microbiome
A Novel Mycovirus Evokes Transcriptional Rewiring in the Fungus Malassezia and Stimulates Beta Interferon Production in Macrophages – Clancey et al – mBio

A Novel Virus Alters Gene Expression and Vacuolar Morphology in Malassezia Cells and Induces a TLR3-Mediated Inflammatory Immune Response – Park et al – mBio

*Review: Challenges in Human Skin Microbial Profiling for Forensic Science: A Review – Neckovic et al – Genes

Human gut microbiome
Context-aware dimensionality reduction deconvolutes gut microbial community dynamics – Martino et al – Nat Biotechnol

Animal microbiome
*The relationship between microbiomes and selective regimes in the sponge genus Ircinia – Kelly et al – bioRxiv

Techniques
Flow cytometry with cell sorting and sequencing as a tool for the study of the Humboldt Current krill stomach microbiota – Henriquez-Castillo et al – bioRxiv

Microbes in the news
EurekAlert News: Researchers receive $3 million NSF grant to ‘understand the rules of life – Zhou J

August 23, 2020

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Hello from the Sonoran Desert! In today’s digest, you’ll find quite a few exciting papers! For those interested in soil microbiology, you’ll find in today’s digest a very interesting piece on the the biodiversity and ecology of protists in the soils of the McMurdo Dry Valleys (Antarctica). This piece is particularly exciting given that the role and impact of protists in polar regions is largely unknown and understudied.

Curious readers should also take a look at the amazing study by Dunaj and collaborators focusing on spider’s associated microbiome. This piece examines the host-microbe co-evolution of different widow spider species showing a strong congruence of the microbiome beta-diversity and the host phylogeny.

Finally, in today’s non-microbiology pick, I recommend a preprint, that explored the relationship between the use of jargon and citations in cave research articles. Interestingly the authors suggest that the juse of jargon in title and abstract significantly reduces the number of citations a paper recieves!

Have a great Sunday!

Human vaginal microbiome

Review: The vaginal microbiome of sub-Saharan African women: revealing important gaps in the era of next-generation sequencing – Martina Odogwy et al. – PeerJ

Human gut microbiome

Review: Association or Causation? Exploring the Oral Microbiome and Cancer Links – Teles et al. – Journal of Dental research

Animal microbiome

Learning machine approach reveals microbial signatures of diet and sex in dog – Scarsella et al.- Plos One

Spider phylosymbiosis: divergence of widow spider species and their tissues’ microbiomes – Dunaj et al. – BMC Evolutionary Biology

Plant, root, and soil microbiome

Review: The rhizosphere microbiome: functions, dynamics, and role in plant protection – Rabelo de Faria et al. – Tropical Plant Pathology

Review: The Floral Microbiome: Plant, Pollinator, and Microbial Perspectives – Vannette – Annual review of Ecology, Evolution and systematics

Response of soil microbial communities to natural and managed vegetation restoration in a subtropical karst region – Hu et al. – CATENA

Water and extremophile microbiome

Shotgun metagenomics reveal a diverse assemblage of protists in a model Antarctic soil ecosystem – Thompson et al.- Envirmental Microbiology

Phages and viruses

Evolution of a major virion protein of the giant pandoraviruses from an inactivated bacterial glycoside hydrolase – Krupovic et al. – Virus Evolution

Bioinformatics

Predicting Host Phenotype Based on Gut Microbiome Using a Convolutional Neural Network Approach – Reiman et al.- Methods in Molecular Biology, vol 2190. Humana, New York, NY.

Database limitations for studying the human gut microbiome – Dias et al. – PeerJ

Techniques

Review: Microbial High Throughput Phenomics: The Potential of an Irreplaceable Omics – Acin-Albiac et al. – Computational and Structural Biotechnolgy Journal

My non-microbiology pick

Preprint: Specialized terminology limits the reach of new scientific knowledge – Martinez et al. – BioRxiv

August 21, 2020

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Events
HAPPENING TODAY: Microbiome sequencing in high-host and low biomass samples. August 21, 2020.

Webinar Series on the Gut-Brain Axis and the Microbiome
August 28, 2020 – September 25, 2020

Funding
Functional effects of the human gut microbiome on autism. Biocodex Microbiota Foundation

Human microbiome
Focus on Microbiome in Health and Disease – A special microbiome issue in Cell Host Microbe

REVIEW: The Impact of the Microbiome on Immunity to Vaccination in Humans. Sanne E. de Jong et al. Cell Host & Microbe.

REVIEW: The Gut Microbiota and Unhealthy Aging: Disentangling Cause from Consequence. Erica N. DeJong et al. Cell Host & Microbe.

Helminth coinfection and COVID-19: An alternate hypothesis. Russell Hays et al. PLoS Negleced Tropical Diseases.

Gut microbiome
REVIEW: Mitochondria, the gut microbiome and ROS. and ROS. J. William O.Ballard & Samuel G. Towarnicki. Cellular Signalling.

Stool Microbiome Profiling of Patients with Metastatic Renal Cell Carcinoma Receiving Anti–PD-1 Immune Checkpoint Inhibitors. Nicholas J. Salgia et al. European Urology.

Programing of an Intravascular Immune Firewall by the Gut Microbiota Protects against Pathogen Dissemination during Infection. Braedon McDonald et al. Cell Host & Microbe

Oral microbiome
Analysis of microbial changes in the tonsillar formalin-fixed paraffin-embedded tissue of Chinese patients with IgA nephropathy. Anchao Zhu. Pathology – Research and Practice

Early life microbiome
Breastmilk Feeding Practices Are Associated with the Co-Occurrence of Bacteria in Mothers’ Milk and the Infant Gut: the CHILD Cohort Study. Kelsey Fehr et al. Cell Host & Microbe.

Animal microbiome
Effects of Urbanization and Landscape on Gut Microbiomes in White-Crowned Sparrows. Mae Berlow. Microbial Ecology

Built environment
Passenger-surface microbiome interactions in the subway of Mexico City. Daniela Vargas-Robles et al. PLoS One.

Plant, root, and soil microbiome
Plant resistance and leaf chemical characteristic jointly shape phyllosphere bacterial community. Tian Xueliang. World Journal of Microbiology and Biotechnology.

The role of land management and elevation in shaping soil microbial communities: Insights from the Central European Alps. Nadine Praega. Soil Biology and Biochemistry.

Composition, predicted functions, and co-occurrence networks of fungal and bacterial communities_ Links to soil organic carbon under long-term fertilization in a rice-wheat cropping system. Jie Chen. European Journal of Soil Biology

Diversity and structure of prokaryotic communities within organic and conventional farming systems in central highlands of Kenya. Edward Nderitu Karanja et al. PLoS One.

Water and wastewater
Turning harmful algal biomass to electricity by microbial fuel cell: A sustainable approach for waste management. Jafar Ali. Environmental Pollution.

Combining physicochemical properties and microbiome data to evaluate the water quality of South African drinking water production plants. Tawanda E. Maguvu et al. PLoS One.

Viruses
They are what you eat: Shaping of viral populations through nutrition and consequences for virulence. Rebekah Honce & Stacey Schultz-Cherry. PLoS Pathogens.

Bioinformatics
Assembly methods for nanopore-based metagenomic sequencing: a comparative study. Adriel Latorre-Pérez. Scientific Report.

Completion of draft bacterial genomes by long-read sequencing of synthetic genomic pools. Hooman Derakhshani et al. BMC Genomics.

Modeling microbial cross-feeding at intermediate scale portrays community dynamics and species coexistence. Chen Liao et al. PLoS Computational Biology

Pre-print
Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity. Cameron Martino et al. bioRxiv

Evaluation of Compatibility of 16S rRNA V3V4 and V4 Amplicon Libraries for Clinical Microbiome Profiling. Po-Yu Liu et al.bioRxiv

Shirin’s non-microbiology picks
MICROBIOME ART: François-Joseph Lapointe, when biology meets art. Jihane Mossalim. Convergence Initiative.

BEHIND THE PAPER: Early-life microbiota diversification facilitates enterocyte proliferation. Michael Dougherty. Nature Microbiology Research Community

JOP OPPURTUNITY: PhD positions in the ecology and evolution of metabolic cross-feeding interactions in soil-living bacterial communities and the gut microbiota in protecting the host against intestinal colonisation by multidrug-resistant organisms

August 14, 2020

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Good morning from Massachusetts! Dr. Elisabeth Bik will be giving a Zoom talk today on research misconduct in biomedical research. You can register at the link under events. Fittingly, today’s digest includes a preprint on the effects of retraction after misconduct on citations. Other highlights today include an entire theme issue on the microbiome and host evolution and a paper on phylogenomic analyses of archaea attempting to elucidate the DPANN lineage. In early life, the placental microbiome debate rages on with a paper demonstrating evidence for contamination rather than an actual placental microbiome. Finally, I have highlighted a paper studying whether soil archives can give us a glimpse into soil microbial communities of the past.

Have a great weekend!

Events

Dr. Bik is discussing “The Dark Side of Science: Misconduct in Biomedical Research” today at 12PM EDT! Register here.

General microbiome

Theme Issue: The role of the microbiome in host evolution – Philosophical Transactions of the Royal Society B

Pregnancy and early life

Evidence for contamination as the origin for bacteria found in human placenta rather than a microbiota – Rémi Gschwind – PloS One

Human milk microbiome

SARS-CoV-2 in human milk is inactivated by Holder pasteurization but not cold storage – Gregory J. Walker – Journal of Paediatrics and Child Health

Human oral microbiome

Review: Oral microbiome geography: Micron-scale habitat and niche – Jessica L. Mark Welch – Cell Host & Microbe

Human gut microbiome

Epidemiology and associated microbiota changes in deployed military personnel at high risk of traveler’s diarrhea – William A. Walters – PloS One

Animal experiments

Differential alteration in gut microbiome profiles during acquisition, extinction, and reinstatement of morphine-induced CPP – Jianbo Zhang – Progress in Neuro-Psychopharmacology and Biological Psychiatry

Modulation of the intestinal microbiota of broilers supplemented with monensin or functional oils in response to challenge by Eimeria spp. – Alexandre Maciel Vieira – PloS One

Herpes simplex virus infection, Acyclovir and IVIG treatment all independently cause gut dysbiosis – Chandran Ramakrishna – PloS One

Animal microbiome

Raw milk and fecal microbiota of commercial Alpine dairy cows varies with herd, fat content and diet – Francesca Albonico – PloS One

Hydrolytic bacteria associated with natural helminth infection in the midgut of Red Sea marbled spinefoot rabbit fish Siganus rivulatus – Ghada Abd-Elmonsef Mahmoud – Microbial Pathogenesis

Plant, root, and soil microbiome

Book: Agriculturally Important Fungi for Sustainable Agriculture Vol 2: Functional Annotation for Crop Protection – Eds. Ajar Nath Yadav et al. – Springer

Patient propagules: Do soil archives preserve the legacy of fungal and prokaryotic communities? – Gian Maria Niccolò Benucci – PloS One

Labile carbon limits late winter microbial activity near Arctic treeline – Patrick F. Sullivan – Nature Communications

Enhanced biodegradation of crude oil by constructed bacterial consortium comprising salt-tolerant petroleum degraders and biosurfactant producers – Weiwei Chen – International Biodeterioration & Biodegradation

Plant–archaea relationships: a potential means to improve crop production in arid and semi-arid regions – Elizabeth Temitope Alori – World Journal of Microbiology and Biotechnology

First report of Fusarium equiseti causing crown rot and damping-off on durum wheat in Algeria – Amor Bencheikh – Archives of Phytopathology and Plant Protection

Soil microbial diversity and composition: Links to soil texture and associated properties – Qing Xia – Soil Biology and Biochemistry

Water, air, and extremophile microbiome

Effects of different habitats on the bacterial community composition in the water and sediments of Lake Taihu, China – Wenjie Chang – Environmental Science and Pollution Research

Genomic and enzymatic evidence of acetogenesis by anaerobic methanotrophic archaea – Shanshan Yang – Nature Communications

Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution – Nina Dombrowski – Nature Communications

Preprint: Occurrence, identification and antibiogram signatures of selected Enterobacteriaceae from Tsomo and Tyhume rivers in the Eastern Cape Province, Republic of South Africa – Fadare Temitope Folake — BioRxiv

Built environment

The microbiome of drinking water biofilters is influenced by environmental factors and engineering decisions but has little influence on the microbiome of the filtrate – Ben Ma – Environmental Science & Technology

In-situ remediation of acid mine drainage from abandoned coal mine by filed pilot-scale passive treatment system: Performance and response of microbial communities to low pH and elevated Fe – Haiyan Chen – Bioresource Technology

Bioinformatics and other techniques

De novo sequence assembly requires bioinformatic checking of chimeric sequences – Laila Sara Arroyo – PloS One

Review on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the rapid screening of microbial species: A promising bioanalytical tool – Suresh Kumar Kailasa – Microchemical Journal

Microbes in the News

Using the infant stool microbiome to predict NEC: New machine learning tool predicts devastating intestinal disease in premature infants – Science Daily

Science Publishing and Career

Preprint: Does retraction after misconduct have an impact on citations? A pre-post study – Cristina Candal-Pedreira – bioRxiv

August 4, 2020

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Greetings Everyone. Today’s Microbiome Digest comprises of a wide variety of topics covering soil microbiota, tumor to water to extremophile microbiome. The digest has some reviews, books, as well as interesting articles on how synthetic microbial communities facilitate sustainable growth and the role of microbial communities in balancing the environment. A terrific news article covering the isolation of microbes buried beneath the sea floor for more than 100 million years. Today’s digest can be summarized by a quote by Julie Morley.

“Every being devotes and dedicates itself to some innate purpose. Single cells, microbes, plants, insects, animals – every being makes it own unique contribution” – Julie J. Morley

General microbiome

*Shifts in the microbiota associated with male mosquitoes (Aedes aegypti) exposed to an obligate gut fungal symbiont (Zancudomyces culisetae) – Jonas Frankel-Bricker – Scientific Reports

Microbiome-derived metabolites reproduce the mitochondrial dysfunction and decreased insulin sensitivity observed in type 2 diabetes – Ormsby et al – bioRxiv

*Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth – Zuñiga et al – Nature Communications

Multi-site human microbiome

Microbiome harbored within tumors: a new chance to revisit our understanding of cancer pathogenesis and treatment – Zhao et al – Signal Transduction and Targeted Therapy

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

Human gut microbiome
Review: Gut microbiota and atherosclerosis: role of B cell for atherosclerosis focusing on the gut-immune-B2 cell axis – Chen et al – Journal of Molecular Medicine

Gut microbiome a promising target for management of respiratory diseases – Trivedi et al – Biochemical Journal

*A carbohydrate-active enzyme (CAZy) profile links successful metabolic specialization of Prevotella to its abundance in gut microbiota – Aakko et al – Scientific Reports

Effects of antibiotic treatment on gut microbiota and how to overcome its negative impacts on human health – Ribeiro et al – ACS Infect. Dis

Animal experiments
Dynamics of uterine microbiota in postpartum dairy cows with clinical or subclinical endometritis – Pascottini et al – Scientific Reports

Plant, root, and soil microbiome
Book chapter: The Extended Microbiota: How Microbes Shape Plant-Insect Interactions – Mayoral-Peña et al – Evolutionary Ecology of Plant-Herbivore Interaction

Response of Soil Microbial Community to C:N:P Stoichiometry along a Caragana korshinskii Restoration Gradient on the Loess Plateau, China – Zhang et al – forests

Review: The endosphere microbial communities, a great promise in agriculture – Adeleke et al – International Microbiology

Water and extremophile microbiome
Influence of microorganisms on initial soil formation along a glacier forefield on King George Island, maritime Antarctica – Krauze et al – Biogeosciences

Review: Microbial communities of soda lakes and pans in the Carpathian Basin: a review – Tamás Felföldi – Biologia Futura

Fungal Community in Antarctic Soil Along the Retreating Collins Glacier (Fildes Peninsula, King George Island) – dos Santos et al – microorganims

Culture Independent Diversity of Bacterial Communities Indigenous to Lower Altitude at Laohugou Glacial Environment – Ali et al – Geomicrobiology Journal

Review: Methanosarcina acetivorans: A Model for Mechanistic Understanding of Aceticlastic and Reverse Methanogenesis – James G. Ferry – Front.Microbiol

The Composition of Microbial Communities in Six Streams, and Its Association With Environmental Conditions, and Foodborne Pathogen Isolation – Chung et al – Front.Microbiol

Food microbiology
FoodOmics as a new frontier to reveal microbial community and metabolic processes occurring on table olives fermentation – Vaccalluzzo et al – Food Microbiology


Bioinformatics
Book: A Bioinformatics Primer for the Analysis of Illumina MiSeq Data of Litter-Associated Fungi and Bacteria – Seena et al – Methods to Study Litter Decomposition

Techniques
Review: Method development for cross-study microbiome data mining: challenges and opportunities – Su et al – Computational and Structural Biotechnology Journal

Microbes in the news
*Scientists pull living microbes, possibly 100 million years old, from beneath the sea – Elizabeth Pennnisi – Science

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

June 17, 2020

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Hello and welcome to Wednesday’s Digest! Today’s selection includes two separate but complementary papers from Cell Host & Microbe. The first, from Brett Finlay’s lab, investigates what drives the loss of Immunoglobulin A recognition by beneficial bacteria in the gut of undernourished children. The second, from Jeffrey Gordon’s lab, examines the impact of prebiotic and microbial interventions on oral vaccination responses in a mouse model of childhood undernutrition. These papers both highlight the important relationship between nutrition, the microbiota, and host mucosal immunity.

There are also a few fungi-focused papers today as well as some interesting animal microbiome research. Tan et al. compare the microbiome of pigs and their farmers and Andrade-Oliveira et al. found that antimicrobial resistance genes from a feline oral commensal can be transferred to a human-associated staphylococci. I also want to call attention to the techniques section, especially a paper by Song and Xie in which they used CRISPR/Cas9 to deplete host contamination in 16S rRNA gene amplicon samples.

Happy reading, y’all!

Pregnancy and Early-life
Analysis of Immune, Microbiota and Metabolome Maturation in Infants in a Clinical Trial of Lactobacillus Paracasei CBA L74-fermented Formula. Roggero, P. et al. Nature Communications.

Ecological Succession in the Vaginal Microbiota During Pregnancy and Birth. Rasmussen, M.A. et al. The ISME Journal.

Neonatal Diet Alters Fecal Microbiota and Metabolome Profiles at Different Ages in Infants Fed Breast Milk or Formula. Brink, L.R. et al. American Journal of Clinical Nutrition.

Human Milk Fungi: Environmental Determinants and Inter-Kingdom Associations With Milk Bacteria in the CHILD Cohort Study. Moossavi, S. et al. BMC Microbiology.

Profiles of Human Milk Oligosaccharides and Their Relations to the Milk Microbiota of Breastfeeding Mothers in Dubai. Ayoub, C. et al. Nutrients.

Human Milk Microbiota Development During Lactation and Its Relation to Maternal Geographic Location and Gestational Hypertensive Status. Wan, Y. et al. Gut Microbes.

Skin Microbiome
Skin Microbiota Analysis-Inspired Development of Novel Anti-Infectives. Liu, Y. et al. Microbiome.

Review: Skin Microbiome Analysis for Forensic Human Identification: What Do We Know So Far? Tozzo, P. et al. Microorganisms.

Review: Protecting the Outside: Biological Tools to Manipulate the Skin Microbiota. O’Sullivan, J.N. et al. FEMS Microbiology and Ecology.

Vaginal Microbiome
Recovery of Vaginal Microbiota After Standard Treatment for Bacterial Vaginosis Infection: An Observational Study. Lehtoranta, L. et al. Microorganisms.

Alterations in Vaginal Microbiota and Associated Metabolome in Women With Recurrent Implantation Failure. Fu, M. et al. mBio.

Gut Microbiome
Alterations of the Gut Microbiota in Patients With COVID-19 or H1N1 Influenza. Gu, S. et al. Clinical Infectious Diseases.

Alterations in the Gut Microbiome and Suppression of Histone Deacetylases by Resveratrol Are Associated with Attenuation of Colonic Inflammation and Protection Against Colorectal Cancer. Alrafas, H.R. et al. Journal of Clinical Medicine.

Long-term Dietary Intervention Reveals Resilience of the Gut Microbiota Despite Changes in Diet and Weight. Fragiadakis, G.K. et al. American Journal of Clinical Nutrition.

Oral Microbiome
Intraoral Microbial Metabolism and Association With Host Taste Perception. Gardner, A. et al. Journal of Dental Research.

Animal Experiments
Combined Prebiotic and Microbial Intervention Improves Oral Cholera Vaccination Responses in a Mouse Model of Childhood Undernutrition. Di Luccia, B. et al. Cell Host & Microbe.

Commensal Bacteria Modulate Immunoglobulin A Binding in Response to Host Nutrition. Huus, K.E. et al. Cell Host & Microbe.

The interplay between the gut microbiota and NLRP3 activation affects the severity of acute pancreatitis in mice. Xueyang, L. et al. Gut Microbes.

Structural and functional changes of gut microbiota in ovariectomized rats and their correlations with altered bone mass. Ma, S. et al. Aging (Albany NY).

Animal Microbiome
Comparative assessment of faecal microbial composition and metabonome of swine, farmers and human control. Tan, S.C. et al. Scientific Reports.

Staphylococcus nepalensis, a Commensal of the Oral Microbiota of Domestic Cats, Is a Reservoir of Transferrable Antimicrobial Resistance. Andrade-Oliveira, A.L. et al. Microbiology.

Increasing the Hindgut Carbohydrate/Protein Ratio by Cecal Infusion of Corn Starch or Casein Hydrolysate Drives Gut Microbiota-Related Bile Acid Metabolism To Stimulate Colonic Barrier Function. Pi, Y. mSystems.

The Microbial Biogeography of the Gastrointestinal Tract of Preterm and Term Lambs. Chong, C.Y.L. et al. Scientific Reports.

Microbial Ecology of Atlantic Salmon (Salmo Salar) Hatcheries: Impacts of the Built Environment on Fish Mucosal Microbiota. Minich, J.J. et al. Applied and Environmental Microbiology.

Dysbiosis in the Gut Microbiota of Soil Fauna Explains the Toxicity of Tire Tread Particles. Ding, J. et al. Environmental Science and Technology.

Insect Microbiome
Dietary Adaptation of Microbiota in Drosophila Requires NF-κB-Dependent Control of the Translational Regulator 4E-BP. Vandehoef, C. et al. Cell Reports.

Responses of soil and earthworm gut bacterial communities to heavy metal contamination. Liu, P. et al. Environmental Pollution.

Effect of Life Stage and Pesticide Exposure on the Gut Microbiota of Aedes Albopictus and Culex Pipiens L. Juma, E.O. et al. Scientific Reports.

Caterpillar Gut and Host Plant Phylloplane Mycobiomes Differ: A New Perspective on Fungal Involvement in Insect Guts. Višňovská, D. et al. FEMS Microbiology Ecology.

Plant, Root, and Soil Microbiome
The Response of Soil and Phyllosphere Microbial Communities to Repeated Application of the Fungicide Iprodione: Accelerated Biodegradation or Toxicity? Katsoula, A. et al. FEMS Microbiology Ecology.

Host Genotype Explains Rhizospheric Microbial Community Composition: The Case of Wild Cotton Metapopulations (Gossypium Hirsutum L.) in Mexico. Hernández-Terán, A. et al. FEMS Microbiology Ecology.

Review: Microbiome Approaches Provide the Key to Biologically Control Postharvest Pathogens and Storability of Fruits and Vegetables. Kusstatscher, P. et al FEMS Microbiology and Ecology.

Review: The Plant Microbiome: From Ecology to Reductionism and Beyond. Fitzpatrick, C.R. et al. Annual Review of Microbiology.

Water Microbiome
Persistence of Wastewater Antibiotic Resistant Bacteria and Their Genes in Human Fecal Material. Scaccia, N. et al. FEMS Microbiolgy Ecology.

Review: Microorganisms Populating the Water-Related Indoor Biome. Babič, M.N. et al. Applied Microbiology and Biotechnology.

Phage
Introducing Lu-1, a Novel Lactobacillus Jensenii Phage Abundant in the Urogenital Tract. Miller-Ensminger, T. et al. PLoS ONE.

Review: Bacteriophage-mediated Manipulation of the Gut Microbiome – Promises and Presents Limitations. Rasmussen, T.S. et al. FEMS Microbiology Reviews.

Bioinformatics
gutMEGA: A Database of the Human Gut MEtaGenome Atlas. Zhang, Q. et al. Briefings in Bioinformatics.

Techniques
Engineering CRISPR/Cas9 to mitigate abundant host contamination for 16S rRNA gene-based amplicon sequencing. Song, L. and Xie, K. Microbiome.

Optimization and Standardization of the Culturomics Technique for Human Microbiome Exploration. Diakite, A. et al. Scientific Reports

Direct detection of mRNA expression in microbial cells by fluorescence in situ hybridization using RNase H-assisted rolling circle amplification. Takahashi, H. et al. Scientific Reports.