Category Archives: General Microbiome

Probiotics to precision probiotics

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After “precision medicine”, it is now time to conceptualize the term “precision probiotics”. In simple words, fundamental idea of precision medicine is to develop “new taxonomy” of disease employing molecular characterization of disease based on individual data that will enable better stratification of patients and determining most effective treatments. On similar lines, Veiga and colleagues offer strategies to develop precision probiotics, combine with multi-omics host response data to find most optimal probiotic modality in stratified individuals/populations.

I would recommend to read the review in full. To motivate you, following are some excerpts from the review:

“Historically, the discovery of probiotics relied on a top-down approach, where a microorganism enriched in healthy individuals (compared to an altered health state) is suggested to be beneficial and correlates with a health benefit upon administration to humans…While this empirical top-down approach provides robust leads for the development of probiotics, in the absence of prior mechanistic information, it inherently necessitates multiple cycles of trial and error to identify health benefits.”

Problems with top-down approach

  • “Probiotic efficacy being both strain- and indication-specific
  • Person-specific factors also contribute to heterogeneity in the outcome of probiotic supplementations, including diet, age and the microbiome. Colonization-resistant microbiomes are more resilient to probiotic interventions compared to colonization-permissive individuals.”

Bottom up approach

“The phenotypic approach is based on screening for probiotic effects using in vitro and ex vivo cell cultures as well as animal models with immune, neuronal, metabolic or microbial read-outs.

Target-based discovery relies on the selection of probiotic candidates based primarily on in silico prediction of their capacity to produce molecular effectors that are potentially able to modulate host or microbial pathways, which are foreseen to play a critical role in health or disease. Such in silico predictions would require the use of multi-omics (such as genomics, transcriptomics, metabolomics and proteomics) possibly coupled to metabolic reconstruction to infer the metabolic capacity of the screened microorganisms.”

Challenges with bottom-up approach

  • “A greater challenge lies in applying a person-specific approach to predict efficacy, which likely requires obtaining profound individualized host data (including genetics, anthropometrics and immune profiling) and microbiome data (such as strain-level composition, transcriptomics and metabolomics), as well as identifying relevant biomarkers that predict colonization resistance and/or a health outcome.
  • As stool samples do not accurately reflect colonization and impact on the gut microbiota along the gastrointestinal tract during probiotic supplementation, there is a great need to devise non-invasive means for identifying compatible probiotic–individual matches.
  • Another important factor to consider is safety, as exogenous microorganisms can have unexpected effects on the microbiome, and can even compromise the health of vulnerable subjects and result in bacteraemia or fungaemia.”

I believe that these challenges also hold true for top-down approach

Precision probiotics strategies

The big aim

“…developing algorithms that, when provided with these individualized parameters, can suggest the optimal probiotic modality that would result in a beneficial outcome.”

  • “To achieve this goal, on one hand, scientists need to better characterize the physiological or pathological pathways that can be modulated by probiotics, in line with the increasing effort to use bottom-up approaches.
  • On the other hand, further digitization of tools for the collection and processing of person-specific data, and their integration with genomic and metabolomic host and microbiome profiles, will be required.
  • Setting up standardized protocols that allow bio-citizens to self-experiment in ‘N-of-1 trials’ and report their experiences with probiotics, coupled with individualized measurements, would greatly expand our understanding of differential probiotic activity in the heterogenous human population. This approach will require devising strict validation and safety measurements for promising centralized data collection while maintaining participants’ anonymity.“

“…While today, this (refers to microbiome data) personal information is poorly actionable, tomorrow it could serve as the basis for microbiome-centred precision nutrition and preventive medicine, including precision probiotics.”

May 8, 2020.

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The highlighted paper of the day looked at the relationship between statins and gut microbiome / enterotype prevalence, mined from data collected from the MetaCardis study which looked at over 2000 participants all across the EU and collected over 1,400 parameters.

If you’re looking for a review/news article of the paper head to: Statin drugs might boost healthy gut microbes

If you’re looking for the paper: Statin therapy is associated with lower prevalence of gut microbiota dysbiosis – Sara Silva – Nature

COVID-19


Identification of Drugs Blocking SARS-CoV-2 Infection using Human Pluripotent Stem Cell-derived Colonic Organoids – Xiaohua Duan – bioRxiv

Whose coronavirus strategy worked best? Scientists hunt most effective policies – Elizabeth Gibney – Nature

Coronavirus activates a stem cell-mediated defense mechanism that accelerates the activation of dormant tuberculosis: implications for the COVID-19 pandemic – Lekhika Pathak – bioRxiv

General Microbiome

Multi ‘Omics Profiling of the HIV Airway Epithelium: Integration of the Microbiome, Methylome, and Transcriptome – MS Jude – Am J Respir Crit Care Med

Intracellular Staphylococcus aureus persisters upon antibiotic exposure – Frederuc Peyrusson – Nature Communications

Isolation and characterization of bacteriophages that infect Citrobacter rodentium, a model pathogen for investigating human intestinal diseases – Carolina Mizuno – bioRxiv

MiniReview: A toxic environment: a growing understanding of how microbial communities affect Shiga toxin expression by E. coli O157:H7 – Erin M. Nawrocki – American Society for Microbiology, Applied and Environmental Microbiology

Pregnancy and early life

Gut microbiota derived metabolites contribute to intestinal barrier maturation at the suckling-to- weaning transition – Martin Beaumont – Gut Microbes

Gut Microbiome Derived 12,13 Dihome Promotes Antigen Presenting Cell Dysfunction In Vitro and Airway Allergic Inflammation In Vivo – S Levan – Atsjournal


Multi-site human microbiome

The Microbiome and the Gut‐Liver‐Brain Axis for CNS Clinical Pharmacology: Challenges in Specifying and Integrating In Vitro and In Silico Models – Kyle Hawkins – Clinical Pharmacology and Therapeutics

Gut Check: The Intestinal Microbiome Does Not Predict or Protect from Vancomycin- Resistant Enterococcus Acquisition Among Critically Ill Patients – Chanderraj – Atsjournal

The Tumour-Resident Microbiome Is Associated with Cancer Hypomethylation Status in Lung Adenocarcinoma – Marshall – atsjournal

An association between the gut microbiota and immune cell dynamics in humans. – Jonas Schluter – bioRxiv

Metabolomics

Analyzing the impact of Mycobacterium tuberculosis infection on primary human macrophages by combined exploratory and targeted metabolomics – Vrieling Frank

Review: Metabolome–Microbiome Crosstalk and Human Disease – Kathleen Lee-Sarwar – metabolites

Animal Microbiome

Review – Mycobacterium bovis: From Genotyping to Genome Sequencing – Ana Guimaraeas – Microorganism

Animal experiments

Staphylococcus aureus-induced proteomic changes in the mammary tissue of rats: A TMT-based study – Lirong Cai – Plos One

Plant, root, and soil microbiome


Effects of earthworms on the microbiomes and antibiotic resistomes of detritus fauna and phyllosphere – Dong Zhu – Environmental Science and Technology

Surface runoff alters cave microbial community structure and function – Madison Davis – Plos One

Water and extremophile microbiome

Culturing of ‘Unculturable’ Subsurface Microbes: Natural Organic Carbon Source Fuels the Growth of Diverse and Distinct Bacteria from Groundwater – Xiaoqin Wu – bioRxiv

Bioinformatics & Techniques

Sequence count data are poorly fit by the negative binomial distribution – Stjin Hawinkel – Plos One

Book Chappter: Meta-Pangenome: At the Crossroad of Pangenomics and Metagenomics – Bing MA – The Pangenome, Springer.

Snipe: Highly sensitive pathogen detection from metagenomic sequencing data – Lihong Huang – bioRxiv

Validated Method for the Study of Human Lung Microbiota from Excised Tissue – Dumont-Leblond – atsjounal

Microbes in the news

Bad to the Bone – Matthew Greseth- MUSC Health

Meet the ‘psychobiome’: the gut bacteria that may alter how you think, feel, and act – Elizabeth Pennisi – ScienceMag

Decoding the Microbiome: Essential to Advancing Precision Medicine – Heather Hall – rdworldonline

Harithaa’s non-microbiology picks!

Mass spectrometry for future atomic clocks – Marianna Safrova – Nature (news & views)

May 7, 2020

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Good morning! There’s a particularly broad collection of microbiome papers to share with you today, from the bacteria that hang onto wounds after debridement to the biofilms that form in the ancient ruins of a town buried by the eruption of Mount Vesuvius. A few unusual highlights include the sexually transmitted microbiome of bedbugs and the gut microbes that colonize a sea cucumber after it grows up, remove its own digestive tract and grows a new one. Some interesting new software tools are hiding in the “Bioinformatics” section at the bottom as well.

General microbiome

Intracellular Staphylococcus aureus persisters upon antibiotic exposure, Frédéric Peyrusson et al., Nature Communications

Human respiratory microbiome

Investigation of the human nasal microbiome in persons with long- and short-term exposure to methicillin-resistant Staphylococcus aureus and other bacteria from the pig farm environment, Md Zohorul Islam et al., PLOS ONE

Human skin microbiome

Microbial predictors of healing and short-term effect of debridement on the microbiome of chronic wounds, Samuel Verbanic et al., npj Biofilms and Microbiomes

Human gut microbiome

Systemic short chain fatty acids limit antitumor effect of CTLA-4 blockade in hosts with cancer, Clélia Coutzac et al., Nature Communications

Functional and phylogenetic alterations in gut microbiome are linked to graft-versus-host disease severity, Mathilde Payen et al., Blood Advances

Animal experiments

Preprint: Metagenomic alterations in gut microbiota precede and predict onset of colitis in the IL10 gene-deficient murine model, Miyoshi and Lee et al., bioRxiv

Dietary Fiber Protects against Diabetic Nephropathy through Short-Chain Fatty Acid–Mediated Activation of G Protein–Coupled Receptors GPR43 and GPR109A, Yan Jun Li et al., Journal of the American Society of Nephrology

Probiotic strain Lactobacillus plantarum YYC-3 prevents colon cancer in mice by regulating the tumour microenvironment, Yuanchun Yue et al., Biomedicine & Pharmacotherapy

Effect of stevia on the gut microbiota and glucose tolerance in a murine model of diet-induced obesity, Sarah L. Becker et al., FEMS Microbiology Ecology

Animal microbiome

Sea cucumber intestinal regeneration reveals deterministic assembly of the gut microbiome, Brooke L. Weigel, Applied and Environmental Microbiology

Mating changes the genital microbiome in both sexes of the common bedbug Cimex lectularius across populations, Sara Bellinvia et al., Proceedings of the Royal Society B

Plant, root, and soil microbiome

Mutualist and pathogen traits interact to affect plant community structure in a spatially explicit model, John W. Schroeder et al., Nature Communications

Preprint: Seasonal dynamics of methane cycling microbial communities in Amazonian floodplain sediments, Julia B. Gontijo et al., bioRxiv

Preprint: Community succession of the grapevine fungal microbiome in the annual growth cycle, Liu and Howell, bioRxiv

Characterizing changes in soil microbiome abundance and diversity due to different cover crop techniques, Wang and Wu et al., PLOS ONE

Preprint: Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field, Selma Cadot et al., bioRxiv

Water and extremophile microbiome

The role of changing temperature in microbial metabolic processes during permafrost thaw, Komi S. Messan et al., PLOS ONE

Built environment

Microbial biofilm community structure and composition on the lithic substrates of Herculaneum Suburban Baths, De Natale and Mele et al., PLOS ONE

Probiotics/prebiotics

Comparative effectiveness of probiotic-based formulations on cecal microbiota modulation in broilers, Denise R. Rodrigues et al., PLOS ONE

Phages and viruses

Weirdo19ES is a novel singleton mycobacteriophage that selects for glycolipid deficient phage-resistant M. smegmatis mutants, Cristian Alejandro Suarez et al., PLOS ONE

Bioinformatics

Decoding the language of microbiomes using word-embedding techniques, and applications in inflammatory bowel disease, Tataru and David, PLOS Computational Biology

Sequence count data are poorly fit by the negative binomial distribution, Stijn Hawinkel et al., PLOS ONE

Preprint: sPepFinder expedites genome-wide identification of small proteins in bacteria, Li and Chao, bioRxiv

Logicome Profiler: Exhaustive detection of statistically significant logic relationships from comparative omics data, Fukunaga and Iwasaki, PLOS ONE

May 6, 2020

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General microbiome

Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the ‘ancestral’ sub-Saharan African intestinal microbiome – Rifkin et al – Microbiome

The neovaginal microbiome of transgender women post-gender reassignment surgery  – Birse et al – Microbiome

Pregnancy and early life

The stepwise assembly of the neonatal virome is modulated by breastfeeding – Liang et al – Nature

Human gut microbiome

Impact of smoking cessation, coffee and bread consumption on the intestinal microbial composition among Saudis: A cross-sectional study – Harakeh et al – PLOS One

Animal experiments

Altered Immunity of Laboratory Mice in the Natural Environment Is Associated with Fungal Colonization – Yeung et al – Cell Host & Microbe

Infection with the sheep gastrointestinal nematode Teladorsagia circumcincta increases luminal pathobionts – Cortés et al – Microbiome

Vitamin D receptor promotes healthy microbial metabolites and microbiome – Chatterjee et al – Nature Scientific Reports

Phages and viruses

Phages Actively Challenge Niche Communities in Antarctic Soils – Bezuidt et al – mSystems

Evolution

The Syntrophy hypothesis for the origin of eukaryotes revisited – López-García & Moreira – Nature Microbiology

Microbes in the news

State-of-the-art imaging method provides new insights into how bacteria move and exchange genetic information

May 2nd, 2020

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Another month has passed! Hope everyone is staying at home and being well. Today’s highlights include a paper applying NMR to monitor neonatal metabolic adaptations, how oil influence microbial community assembly off the Gulf of Mexico and a preprint for a Bayesian Multi-task method to identify global microbiome associations.

COVID-19 Articles 

Why the Coronavirus Is So Confusing – Ed Yong – The Atlantic

Aerodynamic analysis of SARS-CoV-2 in two Wuhan hospitals – Liu & Ning et al. – Nature

Human microbiome

Fucosidases from the human gut symbiont Ruminococcus gnavus – Wu & Rebello et al. – Cellular and Molecular Life Sciences

Temporal Dysbiosis of Infant Nasal Microbiota Relative to Respiratory Syncytial Virus Infection – Grier et al. – bioRxiv **preprint**

Sex-specific Alterations in the Urinary and Tissue Microbiome in Therapy-naïve Urothelial Bladder Cancer Patients – Pederzoli et al.  – European Urology Oncology

Microbiome and Metabolomics 

Metabolic changes in early neonatal life: NMR analysis of the neonatal metabolic profile to monitor postnatal metabolic adaptations – Georgakopoulou, I., Chasapi, S.A., Bariamis, S.E. et al – Metabolomics

Analyzing the impact of Mycobacterium tuberculosis infection on primary human macrophages by combined exploratory and targeted metabolomics – Vrieling & Kostidis et al. – Nature Scientific Reports

Soil microbiome

Structural and microbial evidence for different soil carbon sequestration after four-year successive biochar application in two different paddy soils – Bi & Cai et al. – Chemosphere

Soil pH and C/N ratio determines spatial variations in soil microbial communities and enzymatic activities of the agricultural ecosystems in Northeast China: Jilin Province case – Xu et al. – Applied Soil Ecology

Animal microbiome

Viral metagenomics revealed diverse CRESS-DNA virus genomes in faeces of forest musk deer – Liu & Wang et al. – Virology Journal

Links between the rumen microbiota, methane emissions and feed efficiency of finishing steers offered dietary lipid and nitrate supplementation – Bowen & Cormican et al. – PLOS One

Microbiomes of the built environment 

Influence of oil, dispersant, and pressure on microbial communities from the Gulf of Mexico – Noirungsee et al. – Nature Scientific Reports

Passenger-surface microbiome interactions in the subway of Mexico City – Vargas-Robles et al.  – bioRxiv **preprint**

Pathogens 

Intra-species signaling between Pseudomonas aeruginosa genotypes increases production of quorum sensing controlled virulence factors – Mould et al. – bioRxiv **preprint**

Statistics and bioinformatics 

A Bayesian Multi-Task Approach for Detecting Global Microbiome Associations – Hatami et al. – bioRxiv (soon to be published in Bioinformatics) **preprint**

Extremophiles

Genomic sequencing of Gracilibacillus dipsosauri reveals key properties of a salt-tolerant a-amylase – Deutch & Yang – Antonie van Leeuwenhoek

Aquatic environments  

Cyanobacteria in inland waters: new monitoring, reporting, modelling and ecological research – Mitrovic et al. – Marine & Freshwater Research **review**

Contrast diversity patterns and processes of microbial community assembly in a river-lake continuum across a catchment scale in northwestern China – Tang et al. – Environmental Microbiome

Microbiome in the News

Coffee plants have a small but consistent core microbiome of fungi and bacteria – American Phytopathological Society – EurekAlert!

May 1, 2020

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Greetings from Durham, NC!

Hope everyone is doing well and staying healthy. Today’s digest includes several host-microbiome studies, environmental microbiome studies, and an intriguing EurekAlert news article.
In this light digest of today, I wanted to highlight a cool review about correlation of the oral microbiome with children’s health and a very interesting article on cell wall architecture of the gram-positive bacteria.
COVID-19 pandemic has opened a sort of Pandora’s box filled with great science along with pseudoscience. So, the digest has these two great articles from Nature: one about chloroquine and other about the race for coronavirus vaccines.
Staying at home is difficult for everyone, here is a fun activity to do: coloring space microbes book.

Stay Safe and entertained at home!!!!

COVID-19 news articles

The race for coronavirus vaccines: a graphical guide – Callaway – Nature

Chloroquine hype is derailing the search for coronavirus treatments – Ledford – Nature

General microbiome
*The architecture of the Gram-positive bacterial cell wall– Pasquina-Lemonche et al. – Nature

Pregnancy and early life
Maternal H. pylori is associated with differential fecal microbiota in infants born by vaginal delivery – Hernandez et al. – Scientific Reports

Metabolic Effects of Bovine Milk Oligosaccharides on Selected Commensals of the Infant Microbiome—Commensalism and Postbiotic Effects – Jakobsen et al. – Metabolites

Multi-site human microbiome
*Review: Oral microbiome: possible harbinger for children’s health – Xiao et al. – Nature International Journal of Oral Science

Animal microbiome
Links between the rumen microbiota, methane emissions and feed efficiency of finishing steers offered dietary lipid and nitrate supplementation – Bowen et al. – PLOS ONE

Plant, root, and soil microbiome
Variation in rhizosphere microbial communities and its association with the symbiotic efficiency of rhizobia in soybean – Han et al. – The ISME Journal

Water and extremophile microbiome
Review: Exopolysaccharides from marine bacteria: production, recovery and applications – Dave et al. – Environmental Sustainability

Stromatolitic digitate sinters form under wide‐ranging physicochemical conditions with diverse hot spring microbial communities – Sriaporn et al. – gebiology

Built environment
Comparative analysis of bacterial community and functional species in oil reservoirs with different in situ temperatures – Tian et al. – International Microbiology

Bioinformatics
Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions – Medlock et al. – PLOS Computational Biology

Review: The National Microbiome Data Collaborative: enabling microbiome science – Wood-Charlson et al. – Nature Reviews Microbiology

Probiotics / prebiotics
Lactobacillus plantarum NA136 ameliorates nonalcoholic fatty liver disease by modulating gut microbiota, improving intestinal barrier integrity, and attenuating inflammation – Zhao et al. -Applied Microbiology and Biotechnology

Microbes in the news
Scientists explore links between genetics, gut microbiome and memory – DOE/PACIFIC NORTHWEST NATIONAL LABORATORY

April 28, 2020

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Today’s post covers a divers selection of new microbiome related articles. Of particular interested in an article by Zagato et al. who describe two anti-tumourigenic strains of the microbiota.

Stay healthy!

Covid-19

Functional and Genetic Analysis of Viral Receptor ACE2 Orthologs Reveals Broad Potential Host Range of SARS-CoV-2 – Liu et al. – bioRxiv

Mapping the Immunodominance Landscape of SARS-CoV-2 Spike Protein for the Design of Vaccines against COVID-19 – Zhang et al. – bioRxiv

Probiotics and COVID-19: one size does not fit all – Mak, Chan, Ng – Lancet Gastroenterol Hepatol

Human skin microbiome

Isolation and characterization of diverse microbial representatives from the human skin microbiome – Timm et al. – Microbiome

Human Neurology

Spinal cord injury and the human microbiome: beyond the brain–gut axis – Wallace et al. – Journal of Neurosurgery

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

Engineered butyrate-producing bacteria prevents high fat diet-induced obesity in mice – Bai et al. – Microbial Cell Factories

Gut-seeded α-synuclein fibrils promote gut dysfunction and brain pathology specifically in aged mice – Challis et al. – Nat. Neurosci.

Endogenous murine microbiota member Faecalibaculum rodentium and its human homologue protect from intestinal tumour growth. – Zagato et al. – Nat. Microbiol.

Plant, root, and soil microbiome

Microbiome-Mediated Stress Resistance in Plants – Liu et al. – Trends in Plant Science

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

Disentangling the mechanisms shaping the surface ocean microbiota – Logares et al. – Microbiome

Microbes in the news

A news feature on a recent medRxiv article
Can the gut microbiome predict severe COVID-19?

Microbiome Sequencing Services Market 2020: Remarking Enormous Growth with Recent Trends

April 26, 2020

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Greetings from Pittsburgh, PA!

Today’s digest includes several reviews, numerous host-microbiome studies, a wide variety of environmental microbiome studies, and a new book focused on Emerging Technologies in Environmental Bioremediation.

I also wanted to highlight the virtual Fermentation Mini-Seminars offered by the Applied Ecology Department at my alma mater, NC State University. During the first seminar of the series I learned about the Wild Sourdough Project, which is a community-science/citizen-science project where participants can submit observational data about their sourdough culture. If you’re missing the lab, this might be the perfect project for you!

Virtual Events

NCSU Fermentation Mini-Seminars offered every Thursday at 4pm EST from April through August

General microbiome

Special Issue: Stochasticity in microbiology: managing unpredictability to reach the Sustainable Development Goals – De Vrieze et al. – Microbial Biotechnology

Review: Biofilm matrixome: Extracellular components in structured microbial communities – Karygianni et al. – Trends in Microbiology

Review: Microbial symbiosis: A network towards biomethanation – Saha et al. – Trends in Microbiology

Multi-site human microbiome

Microbiota in cerebrovascular disease: A key player and future therapeutic target – Tonomura et al. – Journal of Cerebral Blood Flow & Metabolism

Review: Role of microbiome and antibiotics in autoimmune diseases – Vangoitsenhoven and Cresci – Nutrition in Clinical Practice

Human skin microbiome

Isolation and characterization of diverse microbial representatives from the human skin microbiome – Timm et al. – BMC Microbiology

Human gut microbiome

Altered gut microbial profile is associated with abnormal metabolism activity of Autism Spectrum Disorder – Dan et al. – Gut Microbes

Seasonal variation in gut microbiota composition: cross-sectional evidence from Ukrainian population – Koliada et al. – BMC Microbiology

Gut microbiome reveals specific dysbiosis in primary osteoporosis – Xu et al. – Frontiers in Cellular and Infection Microbiology

Animal experiments

The clinical drug Ebselen attenuates inflammation and promotes microbiome recovery in mice after antibiotic treatment for CDI – Garland et al. – Cell Reports Medicine

Effect of oxytetracycline treatment on the gastrointestinal microbiome of critically endangered white abalone (Haliotis sorenseni) treated for withering syndrome – Parker-Graham et al. – Aquaculture

Effects of hydrolyzed fish protein and autolyzed yeast as substitutes of fishmeal in the gilthead sea bream (Sparus aurata) diet, on fish intestinal microbiome – Rimoldi et al. – BMC Veterinary Research

Animal microbiome

(My microbiome) would walk 10,000 miles: Maintenance and turnover of microbial communities in introduced dung beetles – Parker et al. – Invertebrate Microbiology

Plant, root, and soil microbiome

Nocardiopsis deserti sp. nov., isolated from a high altitude Atacama Desert soil – Asem et al. – International Journal of Systemic and Evolutionary Microbiology

Steel slag amendment impacts on soil microbial communities and activities of rice (Oryza sativa L.) – Das et al. – Scientific Reports

Peat properties, dominant vegetation type and microbial community structure in a tropical peatland – Girkin et al. – Wetlands

Integrating transcriptomics and metabolomics to studies key metabolism, pathways and candidate genes associated with drought-tolerance in Carthamus tinctorius L. under drought stress – Wei et al. – Industrial Crops and Products

Dynamics of ammonia oxidizers and denitrifiers in response to compost addition in black soil, Northeast China – Yang et al. – PeerJ

Water and extremophile microbiome

Impacts of an eruption on cold-seep microbial and faunal dynamics at a mud volcano – Girard et al. – Frontiers in Marine Science

Unraveling heterogeneity of coral microbiome assemblages in tropical and subtropical corals in the South China Sea – Gong et al. – Microorganisms

Anode potential-dependent protection of electroactive biofilms against metal ion shock via regulating extracellular polymeric substances – Hou et al. – Water Research

Microbial ecology and biogeochemistry of hypersaline sediments in Orca Basin – Nigro et al. – PLOS One

Near streambed flow shapes microbial guilds within and across trophic levels in fluvial biofilms – Risse-Buhl et al. – Limnology and Oceanography

Heterotrophic sulfide-oxidizing nitrate-reducing bacteria enables the high performance of integrated autotrophic-heterotrophic denitrification (IAHD) process under high sulfide loading – Zhang et al. – Water Research

Built environment (subways, indoor surfaces)

Ecological processes affecting long-term eukaryote and prokaryote biofilm persistence in nitrogen removal from sewage – Angell et al. – Genes

Long-term microbial community dynamics in a pilot-scale gas sparged anaerobic membrane bioreactor treating municipal wastewater under seasonal variations – Kannan et al. – Bioresource Technology

Book: Emerging Technologies in Environmental Bioremediation – Edited by Shah et al.

Food microbiology

How processing methods affect the microbial community composition in a cereal-based fermented beverage – Phiri et al. – LWT – Food Science and Technology

High-throughput sequencing and metabolomics reveal differences in bacterial diversity and metabolites between red and white sufu – Tang et al. – Frontiers in Microbiology

April 24, 2020

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Events

Virtual Podium 2020 – Session 5 (Microbiome) – April 24, 2020

Scientific career and work-life balance – April 24, 2020

World Malaria Day – April 25, 2020 – Draws attention to the impact of the disease and (re)urges us to find a way to overcome it once and for all.
Join the #talkingmalaria tweetchat on April 24, 2020 at 12 noon BST.

COVID-19

GRAND CHALLENGE: A billion molecules against COVID-19 – Joint European Disruptive Initiative

General microbiome

Reversibility of propionic acid inhibition to anaerobic digestion: Inhibition kinetics and microbial mechanism – Youl Han – Chemosphere

Responses of microbial structures, functions, metabolic pathways and community interactions to different C/N ratios in aerobic nitrification – Hongwei Sun – Bioresource Technology

PERSPECTIVE: Cultivating fungal research – Heidi H. Kong – Science

Human microbiome

REVIEW: Microbiota–immune interactions in asthma pathogenesis and phenotype – Nicholas W.Lukacs – Current Opinion in Immunology

CANCER IN TRANSLATION: Microbiome genomics for cancer prediction – Lorenz Adlung – Nature Cancer

Human skin microbiome

BOOK CHAPTER: The wound microbiome – Aayushi Uberoi – In: Wound Healing, Tissue Repair, and Regeneration in Diabetes.

Human gut microbiome

BOOK CHAPTER: Dietary Fiber and Gut Microbiota – Carolina Senés-Guerrero – In: Science and Technology of Fibers in Food Systems

Animal experiments

Effect of in feed administration of different butyrate formulations on Salmonella Enteritidis colonization and cecal microbiota in broilers – Lonneke Onrust – Veterinary Research

Stochasticity constrained by deterministic effects of diet and age drive rumen microbiome assembly dynamics – Ori Furman – Nature Communications

Sequence variant analysis reveals poor correlations in microbial taxonomic abundance between humans and mice after gnotobiotic transfer – Farnaz Fouladi – ISME Journal

Temporal changes in microbial communities attached to forages with different lignocellulosic compositions in the cattle rumen – Javad Gharechahi – FEMS Microbiology Ecology

Animal microbiome

Host-microbiota interaction helps to explain the bottom-up effects of climate change on a small rodent species – Guoliang Li – ISME Journal

Plant, root, and soil microbiome

Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions – Stien Beirinckx – Microbiome

Regulatory relationship between quality variation and environment of Cistanche deserticola in three ecotypes based on soil microbiome analysis – Xiao Sun – Scientific Reports

Effects of biodegradable plastic film mulching on soil microbial communities in two agroecosystems – Sreejata Bandopadhyay – PeerJ

Water microbiome

Total Microbial Activity and Sulfur Cycling Microbe Changes in Response to the Development of Hypoxia in a Shallow Estuary – Yunjung Park – Ocean Science Journal

Built environment

Associations Between Respiratory Infections and Bacterial Microbiome in Student Dormitories in Northern China – Xi Fu – Indoor Air

Bacterial community analysis of floor dust and HEPA filters in air purifiers used in office rooms in ILAS, Beijing – Jianguo Guo – Scientific Reports

Microbes in space

The influence of spaceflight on the astronaut salivary microbiome and the search for a microbiome biomarker for viral reactivation – Camilla Urbaniak – Microbiome

Food microbiology

Insights into the Microbiological Safety of Wooden Cutting Boards Used for Meat Processing in Hong Kong’s Wet Markets: A Focus on Food-Contact Surfaces, Cross-Contamination and the Efficacy of Traditional Hygiene Practices – Patrick T. Sekoai – Microorganisms

Pre-print

MicrobioLink: An integrated computational pipeline to infer functional effects of microbiome-host interactions – Tahila Andrighetti – bioRxiv

Repeatability and reproducibility assessment in a large-scale population-based microbiota study: case study on human milk microbiota – Shirin Moossavi – bioRxiv

Mendelian randomization analysis revealed causal effects from gut microbiota to abdominal obesity – Qian Xu – bioRxiv

A quantitative measure of functional redundancy in microbial ecosystems – Taylor M Royalty – bioRxiv

Host association induces genome changes in Candida albicans which alters its virulence – Amanda C Smith – bioRxiv

Shirin’s non-microbiology picks

CAREER FEATURE: Safely conducting essential research in the face of COVID-19 – Virginia Gewin – Nature

Reaching a Large Urban Undergraduate Population through Microbial Ecology Course-Based Research Experiences – Samantha Parks – Journal of Microbiology & Biology Education

POLICY FORUM: Against pandemic research exceptionalism – Alex John London – Science

WORLD VIEW: On the 50th Earth Day, take collective action for the planet – Emma Marris – Nature

BEHIND THE PAPER: Annotating the unknown: Functional Gene Annotation using Untargeted Metabolomics – Robert Jansen – Nature Microbiology Community

April 20, 2020

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God morgon!

Good morning from Sweden. To all my friends who have lost the track of time during the quarantine, it is Monday and the beginning of a new week. Today’s digest is a very light one. However, it carries a super interesting preprint that studies the impact of the pandemic on publication speed of different medical journals. The study reports that, on average, the COVID-19 related papers were expedited through the peer-review process at a 49% (up to 80% in case of certain journals) higher pace than the mean pre-pandemic publishing speed (Yes, there is a pre-pandemic and, possibly, a post-pandemic era now). Although this is a controversial topic, I guess the preprint did a very good job of discussing the reasons behind and impact of accelerated publishing.

In my personal opinion, it is great to be able to get valuable scientific information as soon as it is produced. However, as the paper points out, there has to be some sort of trade-off between the quality of a publication and the time taken by the peer-review process. It could be argued that the quarantine measures might have made it easier for some reviewers to focus their attention on the peer-review, making it faster, but there is no information on ‘who’ reviewed these papers. Also, the article highlights what a lot of scholars have been warning about – the amount of post-publishing corrections that these papers would require (more work for Ms Bik!).

What do you think could be the reasons behind this unprecedented celerity of publishing? Could it be the availability of more spare time to review papers? or could this be an instance of politicization of science (as someone pointed out in the comments section of the article)? What could be the impact of this swiftness, both positive and negative, on the scientific realm? Would it be possible, or advisable, to keep up this trend of swift publishing in the post-pandemic era? Let’s discuss in the comments section.

Apart from this highly thought-provoking article, there is another interesting article on the identification of bacterial strains that may promote maize (corn, for my American friends) growth in chilling conditions.

There is another interesting article that tries to establish a link between the gut microbiome and memory. The study focused on microbiome-specific genetic and metabolomic changes that may impact memory. The study was performed in mice.

Enjoy the articles, have a great week, and stay safe!

COVID 19

Preprint: Pandemic Publishing: Medical journals drastically speed up their publication process for Covid-19 – Serge P.J.M. Horbach

Preprint: Coronavirus Infection and PARP Expression Dysregulate the NAD Metabolome: A Potentially Actionable Component of Innate Immunity – Collin D Heer, et al.

Animal microbiome

Genetic and metabolic links between the murine microbiome and memory – Jian-Hua Mao, et al. – Microbiome

Plant root-soil microbiome

Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions – Stien Beirinckx, et al. – Microbiome

Microbial interactions

Preprint: Expanding the diversity of bacterioplankton isolates and modeling isolation efficacy with large scale dilution-to-extinction cultivation – Michael W. Henson, et al.