May 18, 2020

God morgon!

Good morning from Sweden. It’s Monday and the beginning of another week. I am quite excited to write today’s digest because there is a super impressive paper that concerns my area of research. Research efforts in Shigella infections have always suffered from the lack of a mouse model of infection. This notorious bacterium causes enteric infections only in humans and all the infection models, that have been in use so far,  are not physiologically that relevant. It was extremely thrilling to read the development of a mouse model that replicates the typical features of human infections. Talking about infection models, there is another interesting development. A group of researchers has reported an African green monkey model for CoViD-19. This is an important development for clinical assessment of potential vaccine and drug candidates against nCoV-19.

Speaking of vaccines, another group has reported a Neisseria meningitidis outer membrane vesicle (OMV) based vaccine that provides cross-species protection against Neisseria gonorrhoeae. This report assumes great importance when you consider the fact that no Neisseria gonorrhoeae vaccine has entered clinical testing for the past 30 years! In addition to this, there is a structural study of budding in Cryptococcus neoformans that has some really beautiful pictures like this one:

Screenshot 2020-05-18 at 14.57.43

Elsewhere in the digest are some interesting reports on the virulence of a root pathogen, Fusarium; metagenomic identification of diverse viruses; a potent mycobacteriophage; and commentary on Coronaviruses as pathogens responsible for pandemics.

Hope you enjoy today’s selection and have a great week!


Preprint: Establishment of an African green monkey model for COVID-19 – Courtney B. Woolsey, et al.

Preprint: Coronavirus, as a source of pandemic pathogens – Tomokazu Konishi

Bacteria Hysteria

Preprint: NAIP-NLRC4-deficient mice are susceptible to shigellosis – Patrick S Mitchell, et al.

Preprint: The serogroup B meningococcal outer membrane vesicle-based vaccine 4CMenB induces cross-species protection against Neisseria gonorrhoeae – Isabelle Leduc, et al.

Preprint: Antimycobacterial potential of Mycobacteriophage under pathophysiological conditions – Yeswanth C Kalapala, et al.

Preprint: A Division of Labor in the Recruitment and Topological Organization of a Bacterial Morphogenic Complex – Paul D Caccamo, et al.

Preprint: Comparative genomics of ocular Pseudomonas aeruginosa strains from keratitis patients with different clinical outcomes – Kathirvel Kandasamy, et al.

Human gut

Preprint: Higher prevalence of Bacteroides fragilis in Crohn’s disease exacerbations and strain-dependent increase of epithelial resistance – Heike E.F. Becker, et al.


Preprint: Let it bud: an ultrastructural study of Cryptococcus neoformans surface during budding events – Glauber R. de S. Araujo, et al.


Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets – Isabel F. Escapa, et al. – Microbiome

A powerful microbial group association test based on the higher criticism analysis for sparse microbial association signals – Hyunwook Koh and Ni Zhao – Microbiome


Preprint: Metagenomic identification of diverse animal hepaciviruses and pegiviruses– Ashleigh F. Porter, et al.


Preprint: Transcriptome analysis reveals infection strategies employed by Fusarium graminearum as a root pathogen – Yi Ding, et al.

Microbes in the News

Living on The Space Station Leaves a Microbial ‘Fingerprint’ on Astronauts – Science Alert

What are the best foods to increase happiness? – Eastern Daily Press

May 2nd, 2020

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**


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**


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

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

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

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!


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 22, 2020

Welcome to another post from a new volunteer! I’m a Ph.D student studying the infant gut microbiome and I’m excited to be volunteering with Microbiome Digest.

There are several preprints today, including another great study from the CHILD cohort. This one is on maternal consumption of artificially sweetened beverages and the infant gut microbiota. There is also a preprint calling for improvement in scientific conferences. Both are highlighted in green.

Pregnancy and early life

Preprint: Consumption of artificially sweetened beverages during pregnancy impacts infant gut microbiota and body mass index – Isabelle Laforest-Lapointe — bioRxiv

Oral microbiome

Preprint: Genotypic and phenotypic characterization of Streptococcus mutans isolated from dental caries – Mohammad Shahnoor Hossain – bioRxiv

Pyruvate secretion by oral streptococci modulates hydrogen peroxide dependent antagonism – Sylvio Redanz – ISME Journal

Synergism between Corynebacterium and Streptococcus sanguinis reveals new interactions between oral commensals – Puthayalai Treerat – ISME Journal

Animal experiments

The gut microbiota response to helminth infection depends on host sex and genotype – Fei Ling – ISME Journal

Animal microbiome

Lipids and small metabolites provisioned by ambrosia fungi to symbiotic beetles are phylogeny-dependent, not convergent – Yin-Tse Huang – ISME Journal

Comparative genomics: Dominant coral-bacterium Endozoicomonas acroporae metabolizes dimethylsulfoniopropionate (DMSP) – Kshitij Tandon – ISME Journal

Plant, root, and soil microbiome

Active sulfur cycling in the terrestrial deep subsurface – Emma Bell – ISME Journal

Preprint: An antagonistic driver of the microbial phyllosphere suppresses infection of Arabidopsis thaliana by the oomycete pathogen Albugo laibachii via a secreted hydrolase – Katharina Eitzen – bioRxiv

Preprint: Grapevine pruning time affects natural wound colonization by wood-invading fungi – Maria del Pilar Martinez-Diz – bioRxiv

Water and extremophile microbiome

Mixotrophy in marine picocyanobacteria: use of organic compounds by Prochlorococcus and Synechococcus – M.C. Muñoz-Marín – ISME Journal

Food microbiology

Preprint: Antibiotic-resistant Salmonella species and Escherichia coli in broiler chickens from farms, abattoirs and open markets in selected districts of Zambia – Nelson Phiri – bioRxiv

Microbes in the news

Breastfeeding may lead to fewer human viruses in infants

Science, publishing, and career

Preprint: Evaluating features of scientific conferences: A call for improvements – Sarvenaz Sarabipour – bioRxiv

April 7, 2020

Hi everyone! This is my first contribution to the daily digest, and I’ll follow others’ lead by starting with the latest preprints concerning Covid-19. Away from the ongoing pandemic, some of the highlights include a look at how commensal gut microbes interact with pathogens, and an insight into deep sea oceanic crust microbiomes.

It seems to be a relatively quiet day today, so I’ve included an article from the University of Bristol which looks at how nanoscopic pillars on the surface of some insect wings protect them against bacteria. Perhaps only loosely a microbiome paper, but it’s worth a read for its electron microscopy alone!


Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor – Lan et al. – Nature

Preprint: Atazanavir inhibits SARS-CoV-2 replication and pro-inflammatory cytokine production – Fintelman-Rodrigues et al.

Preprint: Amantadine disrupts lysosomal gene expression; potential therapy for COVID19 – Smieszek et al.

Preprint: Potent Antiviral Activities of Type I Interferons to SARS-CoV-2 Infection – Mantlo et al.

Human gut microbiome

Dissecting individual pathogen-commensal interactions within a complex gut microbiota community – Hassall and Unnikrishnan

Animal microbiome

Antibacterial effects of nanopillar surfaces are mediated by cell impedance, penetration and induction of oxidative stress – Jenkins et al. – Nature Communications

Water and extremophile microbiome

Deep microbial proliferation at the basalt interface in 33.5–104 million-year-old oceanic crust – Suzuki et al.Communications Biology

Food microbiology

How does the microbiome impact pig health? – Sarah Mikesell – The Pig Site

Microbes in the news

Lifestyle trumps geography in determining makeup of gut microbiomeEurekAlert!

Microbes on the market

Gilead taps Second Genome for microbiome biomarker help in a potential $1.5B deal – Connor Hale –

April 6, 2020

God morgon!

Good morning from Sweden. This is my first post and following the current trend, it starts with some articles on the COVID19 pandemic. Today’s digest is headlined by some interesting preprints reporting inhibitors of SARS-CoV2 virus, followed by another interesting read suggesting the link between the gut microbiome and ADHD, some articles on our struggle against pathogenic bacteria, virus and fungi, and capped off with a small but informative news article on things one should not do during the COVID19 lockdown.

You might notice that today’s post is dominated by preprints. These preprints, while being an excellent way to disperse information as rapidly as it emerges, aren’t peer-reviewed. Hence, always read them with a pinch of salt!


Preprint: In vitro screening of a FDA approved chemical library reveals potential inhibitors of SARS-CoV-2 replication – Franck Touret, et al.

Preprint: LY6E Restricts the Entry of Human Coronaviruses, including the currently pandemic SARS-CoV-2 – Xuesen Zhao, et al.

Preprint: Indomethacin has a potent antiviral activity against SARS CoV-2 in vitro and canine coronavirus in vivo – Tianhong Xu, et al.

Preprint: Potent Antiviral Activities of Type I Interferons to SARS-CoV-2 Infection – Emily K. Mantlo, et al.

Microbial interactions

Preprint: Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria – Ryan K Fritts, et al.

Structure and function of the Arctic and Antarctic marine microbiota as revealed by metagenomics – Weipeng Zhang, et al. – Microbiome

Preprint: Accumulation of dead cells from contact killing facilitates coexistence in bacterial biofilms – Gabi Steinbach, et al.

Human microbiome

Preprint: Gut microbiota from persons with attention-deficit/hyperactivity disorder affects the brain in mice – Anouk C. Tengeler, et al.

Lung function and microbiota diversity in cystic fibrosis – Leah Cuthbertson, et al. – Microbiome

Animal microbiome

Preprint: Functional maturation of the gut microbiota at weaning is influenced by maternal environment in piglets – Martin Beaumont, et al.

Bacteria Hysteria

Preprint: The adaptive transcriptional response of pathogenic Leptospira to peroxide reveals new defenses against infection-related oxidative stress – Crispin Zavala-Alvarado, et al.

Preprint: Cytotoxicity of the effector protein BteA was attenuated in Bordetella pertussis by insertion of an alanine residue – Jan Bayram, et al.

Preprint: Antimicrobial peptide induced-stress renders Staphylococcus aureus susceptible to toxic nucleoside analogues – Alexandro Rodriguez-Rojas, et al.

Preprint: (p)ppGpp and malonyl-CoA set the pace for Staphylococcus aureus adaptation to FASII antibiotics and provide a basis for bi-therapy inhibition – Amit Pathania, et al.

Phages and viruses

Preprint: Viral RNA is a target for Wolbachia-mediated pathogen blocking – Tamanash Bhattacharya, et al.

Preprint: Synchronized infection identifies early rate-limiting steps in the hepatitis B virus life cycle – Anindita Chakraborty, et al.


Preprint: Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota – Takeo Shibata, et al.

Preprint: Biotinylated surfome profiling identifies potential biomarkers for diagnosis and therapy of Aspergillus fumigatus infection – Lei-Jie Jia, et al.


Preprint: Interpretable machine learning framework reveals novel gut microbiome features in predicting type 2 diabetes – Wanglong Gou, et al.

Preprint: Comprehensive single cell analysis of pandemic influenza A virus infection in the human airways uncovers cell-type specific host transcriptional signatures relevant for disease progression and pathogenesis – Jenna N Kelly, et al.

MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics – Eli Levy Karin, et al. – Microbiome

Preprint: Whole genome sequences of multi-drug resistant Escherichia coli isolated in a Pastoralist Community of Western Uganda: Phylogenomic changes, virulence and resistant genes – Jacob Stanley Iramiot, et al.

Microbes in news

News article: Experts study banana disease in Tanzania – The Guardian

News article: What not to do while on COVID-19 lockdown – Jamaica Observer

I know a lot of my fellow researchers are unable to continue their experiments and are yearning to get back to their respective labs. It is a testing time and I believe that patience and perseverance are the biggest strengths of a researcher. So, let’s bank on our strength and hope to see each other on the other side of this global pandemic soon!

With new information emerging every day about COVID19, there is a plethora of misinformation and myths surrounding the virus and the disease. As science enthusiasts, it is pertinent for us to dispel these myths. Here is a small list that I complied a few days back. Check it out!

March 24, 2020

Today’s Digest features a study to use engineered Acinetobacter to boost host immunity against bacterial pneumonia, and a review on the relationship between plant-microbe symbiosis and agriculture.The coronavirus is probably on the mind of all of us. Listen to Dr. Blaser talk about it. Stay well and keep reading.


Research Tech II – CHOP Microbiome Center


Editorial: Coronavirus: three things all governments and their science advisers must do now – Nature

World View: Don’t rush to deploy COVID-19 vaccines and drugs without sufficient safety guarantees – Shibo Jiang – Nature

Q&A: The novel coronavirus outbreak causing COVID-19 – Dale Fisher & David Heymann – BMC Medicine

** Dr. Martin Blaser answers coronavirus questions from Twitter (full video available) –

General microbiology

Regulation of fungal decomposition at single-cell level – Michiel Op De Beeck et al. – The ISME Journal

Antimicrobial resistance

** Broad-spectrum suppression of bacterial pneumonia by aminoglycoside-propagated Acinetobacter baumannii – M. Indriati Hood-Pishchany et al. – PLoS Pathogens

Vulnerability and resistance in the spatial heterogeneity of soil microbial communities under resource additions – Kelly Gravuer et al. – PNAS

Discovery of a novel integron-borne aminoglycoside resistance gene present in clinical pathogens by screening environmental bacterial communities – Maria-Elisabeth Böhm et al. – Microbiome

Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection – Lingdi Zhang et al. – Microbiome

Human gut microbiome

The role of gut microbiota in bone homeostasis – Jyotirmaya Behera et al. – Bone

Animal experiments

Docosahexaenoate-enriched fish oil and medium chain triglycerides shape the feline plasma lipidome and synergistically decrease circulating gut microbiome-derived putrefactive postbiotics – Matthew I. Jackson & Dennis E. Jewell – PLoS One

Animal microbiome

The rodent vaginal microbiome across the estrous cycle and the effect of genital nerve electrical stimulation – Micah Levy et al. – PLoS One

The different dietary sugars modulate the composition of the gut microbiota in honeybee during overwintering – Hongfang Wang et al. – BMC Microbiology

Most dominant roles of insect gut bacteria: digestion, detoxification, or essential nutrient provision? – Tian-Zhong Jing et al. – Microbiome

Predictive ability of host genetics and rumen microbiome for subclinical ketosis – Grum Gebreyesus et al. – Journal of Dairy Science

Plant, root and soil microbiome

** Review: Agriculture and the Disruption of Plant–Microbial Symbiosis – Stephanie S. Porter & Joel L. Sachs – Trends in Ecology & Evolution

Taxon-specific microbial growth and mortality patterns reveal distinct temporal population responses to rewetting in a California grassland soil – Steven J. Blazewicz et al. – The ISME Journal

Reusing oil and gas produced water for agricultural irrigation: Effects on soil health and the soil microbiome – Hannah Miller et al. – Science of the Total Environment

Network analysis reveals the strengthening of microbial interaction in biological soil crust development in the Mu Us Sandy Land, northwestern China – Hong Zhou et al. – Soil Biology and Biochemistry

Water and extremophile microbiome

Performance and functional microbial communities of denitrification process of a novel MFC-granular sludge coupling system – Qiujin Deng et al. – Bioresource Technology

Microbial community structure and functional properties in permanently and seasonally flooded areas in Poyang Lake – Yang Liu et al. – Scientific Reports

Associations between redox-sensitive trace metals and microbial communities in a Proterozoic ocean analogue – Kathryn I. Rico et al. – Geobiology

Reactor configuration influences microbial community structure during high-rate, low-temperature anaerobic treatment of dairy wastewater – Paul G McAteer et al. – Bioresource Technology


Multiple-Disease Detection and Classification across Cohorts via Microbiome Search – Xiaoquan Su et al. – mSystems

Microbes in the news

How the mi­cro­biome is in­volved in the de­vel­op­ment of can­cer – Christian Urban – MedicalXpress

How a Fiber-Rich Plant-Based Diet Keeps Your Gut Microbiome Happy and Healthy – Chelsea Debret – One Green Planet

Gerhart: Keeping well during a pandemic – Timothy Gerhart – Your Valley

Study shows positive effect of cover crops on soil microbiome – AgriNews

Microbiome search engine can increase efficiency in disease detection and diagnosis – Chinese Academy of Sciences – EurekAlert

7 Ways A Gastroenterologist Supports His Microbiome & Overall Health – Marvin Singh – mbg Health

Infliximab Helps Gut Microbiome in Children with Crohn’s, Study Finds – Ana Pena – IBD News Today

Microbes on the market

DuPont, APC Microbiome Ireland link up for babies – Melody M. Bomgardner – C&EN

March 14, 2020


NYSCC Microbiome Program Postponed – Happi

General microbiome

Weakest link dynamics predict apparent antibiotic interactions in a model cross-feeding community – EM Adamowicz – bioRxiv

Simultaneous copper removal and electricity production and microbial community in microbial fuel cells with different cathode catalysts – Y Wu – Bioresource Technology

Multi-site human microbiome

Disrupted tongue microbiota and detection of nonindigenous bacteria on the day of allogeneic hematopoietic stem cell transplantation – S Oku – PLoS Pathogens

Human vaginal microbiome

Changes in key vaginal bacteria among postpartum African women initiating intramuscular depot-medroxyprogesterone acetate – BM Whitney – PLoS One

Human gut microbiome

Gut Microbial Protein Expression in Response to Dietary Patterns in a Controlled Feeding Study: A Metaproteomic Approach – S Pan – Microorganisms

A Story of Liver and Gut Microbes: How Does the Intestinal Flora Affect Liver Disease? A Review of the Literature – M Giuffrè – American Journal of Physiology

Fecal microbiota transplantation for the improvement of metabolism in obesity: The FMT-TRIM double-blind placebo-controlled pilot trial – EW Yu – PLoS Medicine

Animal experiments 

Early-life microbial intervention reduces colitis risk promoted by antibiotic-induced gut dysbiosis – J Miyoshi – bioRxiv

Low mutational load and high mutation rate variation in gut commensal bacteria – RS Ramiro – PLoS Biology

Response to mechanical loading in rat Achilles tendon healing is influenced by the microbiome – F Dietrich-Zagonel – PLoS One

Plant, root, and soil microbiome

Testing the two-step model of plant root microbiome acquisition under multiple plant species and soil sources – HR Barajas – bioRxiv

A survey of invasive plants on grassland soil microbial communities and ecosystem services – JK Bell – Scientific Data

Host identity is more important in structuring bacterial epiphytes than endophytes in a tropical mangrove forest – H Yao – FEMS Microbiology Ecology

Water and extremophile microbiome 

Metagenomic Insights into Microbial Metabolisms of a Sulfur-Influenced Glacial Ecosystem – CB Trivedi – bioRxiv

Diel, daily, and spatial variation of coral reef seawater microbial communities – L Weber – PLoS One

Food microbiology

Shotgun Metagenomic Analysis Reveals New Insights on Bacterial Community Profiles in Tempeh – A Yulandi – bioRxiv

Phages and viruses

Identification of viruses belonging to the family Partitiviridae from plant transcriptomes – Y Jo – bioRxiv

The Restrictome of Flaviviruses – L Berthoux – Virologica Sinica

Plasma virome of 781 Brazilians with unexplained symptoms of arbovirus infection include a novel parvovirus and densovirus – E Fahsbender – PLoS One


Intestinal Organoids: A Tool for Modelling Diet–Microbiome–Host Interactions – J Rubert – Trends in Endocrinology and Metabolism

Microbes in the news

Microbiome studies may require correction for PPI use – MD edge

As You Age, So Does Your Microbiome – Technology Networks

DuPont Nutrition & Biosciences and APC Microbiome Ireland on infant gut health project – Nutra Ingredients

The Role of Zinc: It’s More Important than You Think –  UMass Lowell

Microbiome Therapeutics Market to Make Great Impact in near Future by 2026 – Nyse News Times

Mapping Bacterial Neighborhoods in Gut – Mirage News

Non-microbe picks

Sorry, we’re open: Golden Open Access and inequality in the natural sciences – RJ Gray – bioRxiv

Quantifying and contextualizing the impact of bioRxiv preprints through automated social media audience segmentation – J Carlson – bioRxiv

Comparing quality of reporting between preprints and peer-reviewed articles in the biomedical literature – CFD Carneiro – bioRxiv

Studying the dynamics of the gut microbiota using metabolically stable isotopic labeling and metaproteomics – P Smyth – bioRxiv

March 5, 2020

Today’s Digest is heavy, so you might want to pace yourself. It’s hard to pick the highlights, but I’m biased towards fungal research, so first about a wake-up call to look at the fungi seriously. The insects might provide for remedy against antibiotic resistance and is the dust settled on the sparse fetal intestinal microbiota? Stay healthy and keep reading.


Call for papers – Global Outbreaks and Responses – BMC Medicine

General microbiology

** Viewpoints: Fungal diseases as neglected pathogens: A wake-up call to public health officials – Marcio L. Rodrigues & Joshua D. Nosanchuk – PLoS NTD

Inducible cell-to-cell signaling for tunable dynamics in microbial communities – Arianna Miano et al. – Nature Communications

Antimicrobial resistance

** The insect antimicrobial peptide cecropin A disrupts uropathogenic Escherichia coli biofilms – Miriam Kalsy et al. – npj Biofilms and Microbiomes

Using comparative genomics to understand molecular features of carbapenem-resistant Acinetobacter baumannii from South Korea causing invasive infections and their clinical implications – Min Hyung Kim – PLoS One

Factors associated with sufficient knowledge of antibiotics and antimicrobial resistance in the Japanese general population – Shinya Tsuzuki et al. – Scientific Reports

Faeces and vaccines could be the key to tackling antimicrobial resistance – Elisabeth Mahase – BMJ

A survey of extended-spectrum beta-lactamase-producing Enterobacteriaceae in urban wetlands in southwestern Nigeria as a step towards generating prevalence maps of antimicrobial resistance – Olawale Olufemi Adelowo et al. – PLoS One

Pregnancy and early life

** Viable bacterial colonization is highly limited in the human intestine in utero – E. Rackaityte et al. – Nature Medicine

Perinatal Antibiotic Exposure Affects the Transmission between Maternal and Neonatal Microbiota and Is Associated with Early-Onset Sepsis – Ping Zhou et al. – mSphere

Combined analysis of microbial metagenomic and metatranscriptomic sequencing data to assess in situ physiological conditions in the premature infant gut – Yonatan Sher et al. – PLoS One

Human skin microbiome

A microbiome and metabolomic signature of phases of cutaneous healing identified by profiling sequential acute wounds of human skin: An exploratory study – Mohammed Ashrafi et al. – PLoS One

Human oral microbiome

Review: Single-Cell Genomics and the Oral Microbiome – M. Balachandran et al. – Journal of Dental Research

Insights Obtained by Culturing Saccharibacteria With Their Bacterial Hosts – B. Bor et al. – Journal of Dental Research

Electronic Cigarette Aerosol Modulates the Oral Microbiome and Increases Risk of Infection – Smruti Pushalkar et al. – iScience

Press: Oral Microbiome Changes Implicated in Gum Inflammation in E-Cigarette Users – GenomeWeb

In vitro: A salivary metabolite signature that reflects gingival host-microbe interactions: instability predicts gingivitis susceptibility – Marcela M. Fernandez-Gutierrez et al. – Scientific Reports

Human respiratory microbiome

Review: The Role of Lung and Gut Microbiota in the Pathology of Asthma – Weronika Barcik et al. – Immunity

Cancer and microbiome

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

Escherichia coli adhesion portion FimH functions as an adjuvant for cancer immunotherapy – Wei Zhang et al. – Nature Communications

Temporal changes in gut microbiota profile in children with acute lymphoblastic leukemia prior to commencement-, during-, and post-cessation of chemotherapy – Ling Ling Chua et al. – BMC Cancer

Review: Interplay between Dietary Polyphenols and Oral and Gut Microbiota in the Development of Colorectal Cancer – Carolina Cueva & Mariana Silva – Nutrients

Human gut microbiome

In vitro: Short-term supplementation of celecoxib-shifted butyrate production on a simulated model of the gut microbial ecosystem and ameliorated in vitro inflammation – Emma Hernandez-Sanabria et al. – npj Biofilms and Microbiomes

Review: Crosstalk Between Gut Microbiota and Innate Immunity and Its Implication in Autoimmune Diseases – Yuhao Jiao et al. – Frontiers in Immunology

An empirically derived method for measuring human gut microbiome alpha diversity: Demonstrated utility in predicting health-related outcomes among a human clinical sample – Sarah L. Hagerty et al. – PLoS One

Proof-of-concept study of the efficacy of a microbiota-directed complementary food formulation (MDCF) for treating moderate acute malnutrition – Ishita Mostafa et al. – BMC Public Health

Microbiota as Predictor of Mortality in Allogeneic Hematopoietic-Cell Transplantation – Jonathan U. Peled et al. – New England Journal of Medicine

Human multi-site microbiome

Age-Related Variation of Bacterial and Fungal Communities in Different Body Habitats across the Young, Elderly, and Centenarians in Sardinia – Lu Wu et al. – mSphere

Response of the human gut and saliva microbiome to urbanization in Cameroon – Ana Lokmer et al. – Scientific Reports

The gut-microbiota-brain axis

Therapeutic Effects of the In Vitro Cultured Human Gut Microbiota as Transplants on Altering Gut Microbiota and Improving Symptoms Associated with Autism Spectrum Disorder – Kainan Chen et al. – Microbial Ecology

Built environment microbiome

A preliminary study on the potential of Nanopore MinION and Illumina MiSeq 16S rRNA gene sequencing to characterize building-dust microbiomes – Anders B. Nygaard et al. – Scientific Reports


Spatial metabolomics of in situ host–microbe interactions at the micrometre scale – Benedikt Geier et al. – Nature Microbiology

Global chemical effects of the microbiome include new bile-acid conjugations – Robert A. Quinn et al. – Nature

Animal experiments

PM2.5 exposure perturbs lung microbiome and its metabolic profile in mice – Jingli Li et al. – Science of the Total Environment

Growth hormone deficiency and excess alter the gut microbiome in adult male mice – Elizabeth A Jensen et al. – Endocrinology

Dissociation of Adaptive Thermogenesis from Glucose Homeostasis in Microbiome-Deficient Mice – Tibor L. Krisko et al. – Cell Metabolism

Fecal IgA Levels Are Determined by Strain-Level Differences in Bacteroides ovatus and Are Modifiable by Gut Microbiota Manipulation – Chao Yang et al. – Cell Host & Microbe

Animal microbiome

Can rumen bacteria communicate to each other? – Mi-Young Won et al. – Microbiome

Entomopathogenic nematode-associated microbiota: from monoxenic paradigm to pathobiome – Jean-Claude Ogier et al. – Microbiome

The canine oral microbiome: variation in bacterial populations across different niches – Avika Ruparell et al. – BMC Microbiology

Evolutionary analysis of Mycobacterium bovis genotypes across Africa suggests co-evolution with livestock and humans – Osvaldo Frederico Inlamea et al. – PLoS NTD

Nanopore sequencing of microbial communities reveals the potential role of sea lice as a reservoir for fish pathogens – Ana Teresa Gonçalves et al. – Scientific Reports

Plant, root and soil microbiome

Insights on aquatic microbiome of the Indian Sundarbans mangrove areas – Paltu Kumar Dhal et al. – PLoS One

Ganoderma lucidum cultivation affect microbial community structure of soil, wood segments and tree roots – Fei Ren et al. – Scientific Reports

Effect of long-term destocking on soil fungal functional groups and interactions with plants – Jie Wang et al. – Plant and Soil

Comparative Analysis of Root Microbiomes of Rice Cultivars with High and Low Methane Emissions Reveals Differences in Abundance of Methanogenic Archaea and Putative Upstream Fermenters – Zachary Liechty et al. – mSystems

Fungal diversity and community composition of wheat rhizosphere and non-rhizosphere soils from three different agricultural production regions of South Africa – Magalane Pheladi Gqozo et al. – Applied Soil Ecology

Microbial and volatile profiling of soils suppressive to Fusarium culmorum of wheat – Adam Ossowicki & Vittorio Tracanna et al. – Proceedings of the Royal Society B

Industrial development as a key factor explaining variances in soil and grass phyllosphere microbiomes in urban green spaces – Zhen-Zhen Yan et al. – Environmental Pollution

Plant communities mediate the interactive effects of invasion and drought on soil microbial communities – Catherine Fahey et al. – The ISME Journal

Water and extremophile microbiome

Methyl t-butyl ether-degrading bacteria for bioremediation and biocontrol purposes – Giada d’Errico et al. – PLoS One

Uncovering microbial responses to sharp geochemical gradients in a terrace contaminated by acid mine drainage – Rui Xu et al. – Environmental Pollution

Snapshot: Microbial Extremophiles – Amy K. Schmid et al. – Cell

Denitrification performance and microbial communities of solid-phase denitrifying reactors using poly (butylene succinate)/bamboo powder composite – Wanhe Qi et al. – Bioresource Technology

Meta-omics Provides Insights into the Impact of Hydrocarbon Contamination on Microbial Mat Functioning – Johanne Aubé et al. – Microbial Ecology

Role of microbial diversity for sustainable pyrite oxidation control in acid and metalliferous drainage prevention – Omy T. Ogbughalu et al. – Journal of Hazardous Materials

Phages and viruses

** Coronavirus research highlights – BMC

Fecal Viral Community Responses to High-Fat Diet in Mice – Anjelique Schulfer et al. – mSphere


Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens – Richard M. Leggett et al. – Nature Microbiology

Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities – John Beaulaurier et al. – Genome Research


Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing – Karel Břinda et al. – Nature Microbiology

Microbes in the news

Tough microbe’s DNA could be a lasting archive – Steve Nadis – Science

How Bacteria Can ‘Sculpt The Gut’ – Maya Trabulsi – KPBS

The bee microbiome can fight back against fungi that cause Colony Collapse Disorder – Lauren Sara McKee – Massive Science

Ancient gut microbiomes shed light on human evolution – Newswise

Launch of the Marine Microbiome Roadmap – NIOZ

Understanding Microbiome Resilience on a Changing Planet – Michigan State University

Adaptations in gut microbes helped our ancestors thrive in new geographical territories: Study – New Kerala

Scientists Announce VIRGO, First Comprehensive Gene Catalog To Decode the Vaginal Microbiome – PR Newswire

Metabolomics Reveals Connection Between Gut Microbiome and Blood – Metabolon

Study shows universally positive effect of cover crops on soil microbiome –

New Center of Microbiome Science is in the works at Ohio State – Emily Caldwell – Ohio State University News

Common diseases may be communicable through microbiome, says UBC researcher – Stephanie Blain – The Ubyssey

The microbes in your mouth, and a reminder to floss and go to the dentist – Science Daily

For Your Microbiome, How You Eat Could Be As Important As What You Eat – Technology Networks

Study: Infectious gut bacteria may predict UTI risk – Sue Treiman – Cornell Chronicle

The Best Way to Avoid Getting Sick Is to Wash Your Hands — But You’re Probably Doing It Wrong – Bojana Galic – Live Strong

Microbes on the market

DuPont carries on microbiome momentum with metabolic disease collaboration – Will Chu – Nutraingredients

Non-microbiology picks

Invest 5% of research funds in ensuring data are reusable – Barend Mons – Nature