April 2, 2020

Today’s digest starts with a recent study from The Lancet linking antibiotic usage and the gut microbiome with asthma incidence, before moving onto a range of other papers covering multiple human body sites and environmental microbiome studies.

General microbiome
*** Decreasing antibiotic use, the gut microbiota, and asthma incidence in children: evidence from population-based and prospective cohort studies – Patrick et al. – The Lancet

Human respiratory microbiome

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

Human gut microbiome

Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease – Ryan et al. – Nature Communications

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

Effects of underfeeding and oral vancomycin on gut microbiome and nutrient absorption in humans – Basolo et al. – Nature Medicine

The Gut Microbial Diversity of Newly Diagnosed Diabetics but Not of Prediabetics Is Significantly Different from That of Healthy Nondiabetics – Gaike et al. – MSystems

Shotgun Metagenomics of Gut Microbiota in Humans with up to Extreme Longevity and the Increasing Role of Xenobiotic Degradation – Rampelli et al. MSystems

Animal experiments

Gut microbiota from persons with attention-deficit/hyperactivity disorder affects the brain in mice – Tengeler et al. – BMC Microbiome

Unraveling Assemblage, Functions and Stability of the Gut Microbiota of Blattella germanica by Antibiotic Treatment – Domínguez-Santos et al. – Frontiers in Microbiology

Plant, root, and soil microbiome

Novel phosphate-solubilizing bacteria enhance soil phosphorus cycling following ecological restoration of land degraded by mining – Liang et al.  – ISME

Water and extremophile microbiome

Genomic and transcriptomic evidence of light-sensing, porphyrin biosynthesis, Calvin-Benson-Bassham cycle, and urea production in Bathyarchaeota – Pan et al. BMC Microbiome

Microbial community profiling of ammonia and nitrite oxidizing bacterial enrichments from brackishwater ecosystems for mitigating nitrogen species – Baskaran et al. – Nature Scientific Reports


Lactobacillus reuteri 5454 and Bifidobacterium animalis ssp. lactis 5764 improve colitis while differentially impacting dendritic cells maturation and antimicrobial responses – Hrdý et al. Nature Scientific Reports

March 27, 2020

We begin with a few updates about the recent research news about COVID 19 and how as a scientist you might be able to help. As a result of the global lock down, many conferences and seminars have moved online. You will find some of the microbiome-related online events in today’s post. Please also have a look at a special issue of the Philosophical Transactions of the Royal Society for conceptual challenges in microbial community ecology.

Coronavirus vaccines: five key questions as trials begin – Nature News

How blood from coronavirus survivors might save lives – Nature News

COVID-19 Pandemic: Scientist volunteer form

An initiative to redirect scientific resources towards the fight against COVID-19

Virtual Events
Virtual Conference: 6th Annual Translational Microbiome Conference

Guts & Bugs: A virtual GI seminar series by Edelblum Lab

Let’s go viral: online microbiology seminars in partnership with International Society of Microbial Ecology
Schedule can be found via Twitter #MicroSeminar @MicroSeminar

General microbiome
SPECIAL ISSUE: Phillosophical Transactions of the Royal Society B : Conceptual challenges in microbial community ecology

Human respiratory microbiome
Review: Respiratory microbiome and epithelial interactions shape immunity in the lungs – Invernizzi et al. – Immunology

Human oral microbiome
Polymicrobial periodontal disease triggers a wide radius of effect and unique virome – Gao et al. – npj Biofilms and Microbiomes

Metagenomic analysis of bacterial species in tongue microbiome of current and never smokers – Sato et al. – npj Biofilms and Microbiomes

Spatial Ecology of the Human Tongue Dorsum Microbiome – Wilbert et al. – Cell Reports

Oral biofilms exposure to chlorhexidine results in altered microbial composition and metabolic profile – Chatzigiannidou et al. – npj Biofilms and Microbiomes

Dysbiotic oral microbiota and infected salivary glands in Sjögren’s syndrome – Alam et al. – PLOS ONE

Animal experiments
Drosophila-associated bacteria differentially shape the nutritional requirements of their host during juvenile growth – Consuegra et al. – PLOS Biology

Bacterially produced metabolites protect C. elegans neurons from degeneration – Urrutia et al. – PLOS Biology

Dynamic interactions within the host-associated microbiota cause tumor formation in the basal metazoan Hydra – Rathje et al. – PLOS Pathogens

Association of colitis with gut-microbiota dysbiosis in clathrin adapter AP-1B knockout mice – Jangid et al. – PLOS ONE

Variations in microbiota composition of laboratory mice influence Citrobacter rodentium infection via variable short-chain fatty acid production – Osbelt et al. – PLOS Pathogens

Changes in the faecal microbiota of horses and ponies during a two-year body weight gain programme – Langner et al. – PLOS ONE

Animal microbiome
Microbiomes in the insectivorous bat species Mops condylurus rapidly converge in captivity – Edenborough et al. – PLOS ONE

Plant, root, and soil microbiome
Towards Nutrition-Sensitive Agriculture: An evaluation of biocontrol effects, nutritional value, and ecological impact of bacterial inoculants – Passera et al. – Science of The Total Environment

Book Chapter: Rhizobacteria Versus Chelating Agents: Tool for Phytoremediation – Kaur et al. – Microbial Technology for Health and Environment

Book Chapter: Applications of Microorganisms in Agriculture – Doley et al. – Microbial Technology for Health and Environment

Plant Invasion Has Limited Impact on Soil Microbial alpha Diversity: A Meta-Analysis – Custer & van Diepen – Diversity

Water microbiome
Carbonate facies‐specific stable isotope data record climate, hydrology, and microbial communities in Great Salt Lake, UT – Ingalls et al. – Geobiology

The microbiome of modern microbialites in Bacalar Lagoon, Mexico – Yanez-Montalvo et al. – PLOS ONE

Food microbiology
Variations in Fungal Community and Diversity in Doushen With Different Flavors – Luo et at. – Frontiers in Microbiology

MetaBridge: An Integrative Multi‐Omics Tool for Metabolite‐Enzyme Mapping – Blimkie et al. – Current Protocols in Bioinformatics

Validating metabarcoding-based biodiversity assessments with multi-species occupancy models: A case study using coastal marine eDNA – McClenaghan et al. – PLOS ONE

PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph – Gautreau et al. – PLOS Computational Biology

The Community Simulator: A Python package for microbial ecology – Marsland et al. – PLOS ONE

Genome-based species-specific primers for rapid identification of six species of Lactobacillus acidophilusgroup using multiplex PCR – You & Kim – PLOS ONE

Pathogens and microbiome
Commensal Neisseria cinerea impairs Neisseria meningitidis microcolony development and reduces pathogen colonisation of epithelial cells – Custodio et al. – PLOS Pathogens

Swimming motility of a gut bacterial symbiont promotes resistance to intestinal expulsion and enhances inflammation – Wiles et al. – PLOS Biology

March 26th, 2020

This is my first post on the site! There weren’t a lot of alerts today, so I dug around for other papers I can find. Today’s digest includes mostly human microbiome research, most notably a study identifying a staph peptide that induces acute exacerbation of pulmonary fibrosis, as well as a very diverse epidemiological study of the impact of diet on the gut microbiome in the United States.

General Human Microbiome

US nativity and dietary acculturation impact the gut microbiome in a diverse US population  – Peters, B.A., Yi, S.S., Beasley, J.M. et al. – ISME

Microbiome in Pregnancy and Birth

Maternal carriage of Prevotella during pregnancy associates with protection against food allergy in the offspring – Vuillermin, P.J., O’Hely, M., Collier, F. et al. – Nature Communications

Vaginal Microbiome of Pregnant Indian Women: Insights into the Genome of Dominant Lactobacillus Species – Mehta, O., Ghosh, T.S., Kothidar, A. et al. – Microbial Ecology

Translational human microbiome research

A Staphylococcus pro-apoptotic peptide induces acute exacerbation of pulmonary fibrosis – D’Alessandro-Gabazza, C.N., Kobayashi, T., Yasuma, T. et al. – Nature Communications

Effect of probiotics during vonoprazan‐containing triple therapy on gut microbiota in Helicobacter pylori infection: A randomized controlled trial – Kakiuchi et al. – Helicobacter

Rosuvastatin alters the genetic composition of the human gut microbiome – Kummen, M., Solberg, O.G., Storm-Larsen, C. et al. – Scientific Reports

Microbiome and Cancer

Metaproteomics characterizes human gut microbiome function in colorectal cancer – Long, S., Yang, Y., Shen, C. et al. – npj Biofilms and Microbiomes

Plant microbiome

Genome‐resolved metagenomics to study co‐occurrence patterns and intraspecific heterogeneity among plant pathogen metapopulations – Newberry et al. – Environmental Microbiology

Symbiotic nitrogen fixation and endophytic bacterial community structure in Bt-transgenic chickpea (Cicer arietinum L) – Alok, D., Annapragada, H., Singh, S. et al. – Scientific Reports

Soil microbiome

Soil Microbial Diversity Affects the Plant-Root Colonization by Arbuscular Mycorrhizal Fungi – Ferreira et al. – Microbial Ecology

Bioinformatics/Sequencing analysis methods

Joining Illumina paired-end reads for classifying phylogenetic marker sequences – Liu et al. – BMC Bioinformatics

M2IA: a Web Server for Microbiome and Metabolome Integrative Analysis – Ni et al. – Bioinformatics


Alcohol pretreatment of stools effect on culturomics – Afouda, P., Hocquart, M., Pham, T. et al. – Scientific Reports

Pre-prints on bioRxiv to look forward to

Infant gut microbiome

Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics – West et al. (Side note: The Banfield lab produces a lot of good work!)

Laboratory work on bacterial motility in the gut

Bacterial Swarmers exhibit a Protective Response to Intestinal Stress – Chen et al.

Long-read sequencing of gut mycobiome

Assessing anaerobic gut fungal (Neocalliamstigomycota) diversity using PacBio D1/D2 LSU rRNA amplicon sequencing and multi-year isolation – Hanafy et al.


HumGut: A comprehensive Human Gut prokaryotic genomes collection filtered by metagenome data


March 23, 2020

In today’s digest, review on biliary tract microbiome, effect of disinfection on water microbiome, resveratrol on adipose tissue browning via gut microbiome modelling and influence of livestock farm environment on human gut microbiota and antibiotic resistome.

Hope all readers are staying safe at home!

General microbiome

Intestinal microbiota and its association with colon cancer and red/processed meat consumption – Nadine Abu‐Ghazaleh – Journal of Gastroenterology and Hepatology

Is it time to consider gut microbiome readouts for precision diagnosis and treatment of alcoholic liver disease? – Gail A.M. Cresci – Hepatology

Biliary tract microbiota: a new kid on the block of liver diseases? – Nicoletti A – European Review for Medical and Pharmacological Sciences

Human microbiome

Characteristics of the urinary microbiome in kidney stone patients with hypertension – Fengping Liu – Journal of Translational Medicine

Pregnancy associates with alterations to the host and microbial proteome in vaginal mucosa – Christina Farr Zuend – American Journal of Reproductive Immunology

Prebiotics inhibit proteolysis by gut bacteria in a host diet-dependent manner: a three stage continuous in vitro gut model experiment – Xuedan Wang – Applied and Environmental Microbiology

Animal experiments

Resveratrol enhances brown adipose tissue activity and white adipose tissue browning in part by regulating bile acid metabolism via gut microbiota remodeling – Suocheng Hui – International Journal of Obesity

Environmental remodeling of human gut microbiota and antibiotic resistome in livestock farms – Jian Sun – Nature Communications

Effects of the dietary fibre inulin and Trichuris suis products on inflammatory responses in lipopolysaccharide-stimulated macrophages – Laura J. Myhill – Molecular Immunology

Deoxycholic Acid-Induced Gut Dysbiosis Disrupts Bile Acid Enterohepatic Circulation and Promotes Intestinal Inflammation – Mengque Xu – Digestive Diseases and Sciences

Commensal Bacteria Impact a Protozoan’s Integration into Murine Gut Microbiota in a Dietary Nutrient-dependent Manner – Applied and Environmental Microbiology

Plant, root and soil microbiome

Rhizosphere fungal communities of wild and cultivated soybeans grown in three different soil suspensions – Chunling Chang – Applied Soil Ecology

Straw decreased N2O emissions from flooded paddy soils via altering denitrifying bacterial community compositions and soil organic carbon fractions – Ning Wang – FEMS Microbial Ecology

Water microbiome

Microbial communities from subglacial water of naled ice bodies in the forefield of Werenskioldbreen, Svalbard – Sławomir Sułowicz – Science of the Total Environment

Disinfection exhibits systematic impacts on the drinking water microbiome – Zihan Dai – Microbiome

Microbial diversity in deep subsurface hot brines of the North West Poland: from a community structure to isolate characteristics – Agnieszka Kalwasińska – Applied and Environmental Microbiology

Non microbiology picks

Identification of antiviral drug candidates against SARS-CoV-2 from FDA-approved drugs – Sangeun Jeon – BioRxiv

Comparative Pathogenesis Of COVID-19, MERS And SARS In A Non-Human Primate Model – Barry Rockx – 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 – Phys.org

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


Antibiotic resistance- can reducing outpatient prescription help?

Antibiotic resistance is increasing at a rapid rate making pathogens and other bacterial species resistant to currently available antibiotics. Its impact is already visible globally and clock is ticking faster than ever pushing scientists all over the world to develop better antibiotics with higher specificity (only!) for pathogens. Antibiotic consumption is directly related to antibiotic resistance and policies across the continents are underway to control the consumption and prescription of antibiotics.

A recent article in elife introduces the problem of unnecessary antibiotic use and provides data to avert it.

Inappropriate antibiotic use leads to increased risk of adverse events, disruption of colonization resistance and other benefits of the microbial flora, and bystander selection for antibiotic resistance, with little to no health gains for the patient.”

To address the problem, Christine et al. used publically available data (NAMCS/NHAMCS) and mathematical models to find what would happen if antibiotic consumption is averted in hypothetical scenarios.

What they did?
The analysis included sixteen antibiotics that are frequently prescribed in the outpatient setting and nine potentially pathogenic bacterial species that are commonly carried in the normal human microbiome. For each antibiotic-species pair, they estimated the proportion of antibiotic exposures experienced by that species that could be averted under four hypothetical scenarios.

1) Eliminate unnecessary antibiotic use across all outpatient conditions.
2) Eliminate all antibiotic use for outpatient respiratory conditions for which antibiotics are not indicated.
3) Eliminate all antibiotic use for acute sinusitis.
4) Prescribe nitrofurantoin* for all cases of cystitis in women.”

“*Nitrofurantoin- a recommended first-line therapy with good potency against common uropathogens, low levels of resistance, and decreased risk of collateral damage to the intestinal microbiome”



Heatmaps showing the estimated percentage of species exposures to each antibiotic or antibiotic class that could be averted if A: unnecessary antibiotic prescriptions across all outpatient conditions, B: all antibiotic use for outpatient respiratory conditions for which antibiotics are not indicated, C: all antibiotic use for acute sinusitis, or D: non-nitrofurantoin treatment of cystitis in women was eliminated. Drug class results include prescriptions of all antibiotics in that class, as identified by the Lexicon Plus classification system.
Abbreviations: Antibiotics (y-axis): AMX-CLAV=amoxicillin-clavulanate,, MACR/LINC=macrolides/lincosamides, TMP-SMX=sulfamethoxazole-trimethoprim;

Organisms (x-axis): EC=E. coli, HI=H. influenzae, KP=K. pneumoniae, MC=M. catarrhalis, PA=P. aeruginosa, SA=S. aureus, SAg=S. agalactiae, SP=S. pneumoniae, SPy=S. pyogenes; PY=person-years

The darker shades in panel A (scenario 1) clearly indicated that “elimination of unnecessary antibiotic prescriptions across all outpatient conditions would prevent 6 to 48% (IQR: 17 to 31%) of antibiotic-species exposures. If all unnecessary antibiotic use could be prevented, over 30% of exposures to amoxicillin-clavulanate, penicillin, azithromycin, clarithromycin, levofloxacin, and doxycycline across most potential pathogens of interest could be averted.

In panel D (scenario 4), they found that prescribing nitrofurantoin not only averted antibiotic exposure in non-causative bacterial species (bystanders) but also in causative species for cystitis in women.
Overall, 27% of ciprofloxacin use is associated with acute cystitis in women. Organisms that are not causative pathogens of cystitis have proportions of avertable exposures close to or less than 27%, but a substantially higher proportion of exposures could be averted among causative pathogens – 33%, 36%, and 44% of ciprofloxacin exposures to E. coli, K. pneumoniae, and P. aeruginosa, respectively.

The study addresses the limitations with regard to data availability and reporting in public database. Authors are cautious and point out,

It is important to note that the reduction in antibiotic exposures estimated here does not translate to the same reduction in the prevalence of resistance or in the morbidity and mortality attributable to resistance. Additionally, in this analysis, we give each exposure equal weight. However, the selective pressure imposed by a single exposure depends on a number of variables, including pharmacokinetics, pharmacodynamics, distribution of bacteria across body sites, and bacterial population size. For example, we might expect that the probability of resistance scales with population size, and thus that an exposure received by an individual with higher bacterial load will have a larger impact on resistance.

Overall, this study indeed provides evidence that “improved prescription of antibiotics has the potential to prevent antibiotic exposure experienced by bacterial species throughout microbiome.

January 22, 2020

In today’s digest read about Lactobacillus mulieris sp. nov. isolated from healthy female urinary tract, diversity of Escherichia coli phages in the Danish wastewater, PLate Coverage Algorithm (PLCA) in culture-enriched metagenomics, and more. Happy reading!

General microbiome

Microbiomes Reduce Their Host’s Sensitivity to Interspecific Interactions – Sara L. Jackrel – mBio

Gut microbiome

Klebsiella michiganensis transmission enhances resistance to Enterobacteriaceae gut invasion by nutrition competition – Rita A. Oliveira – Nature Microbiology

Long-term impact of fecal transplantation in healthy volunteers – Oleg V. Goloshchapov – BMC Microbiology

Efficacy of faecal microbiota transplantation in Crohn’sdisease: a new target treatment?– Liyuan Xiang – Microbial Biotechnology

Resident microbial communities inhibit growth and antibiotic resistance evolution of Escherichia coli in human gut microbiome samples – Michael Baumgartner – bioRxiv

Microreview: Causalities of war: The connection between type VI secretion system and microbiota – Luke P. Allsopp – Cellular Microbiology

Urinary microbiome

*Lactobacillus mulieris sp. nov., a new species of Lactobacillus delbrueckii group – Joana Rocha – International Journal of systematic and evolutionary microbiology

Vaginal microbiome

Vaginal Microbiota Transplantation: The Next Frontier – Kevin DeLong – The Journal of Law, Medicine, & Ethics

Respiratory microbiome

*Culture-enriched metagenomic sequencing enables in-depth profiling of the cystic fibrosis lung microbiota – Fiona J. Whelan – Nature Microbiology

A Refined View of Airway Microbiome in Chronic Obstructive Pulmonary Disease at Species and Strain-levels– Zhang Wang – bioRxiv

Eye microbiome

The closed eye harbors a unique microbiome in dry eye disease – Kent A. Willis – medRxiv

Plant/root/soil microbiome

Root ethylene mediates rhizosphere microbial community reconstruction when chemically detecting cyanide produced by neighbouring plants – Yan Chen – Microbiome

Warming-induced permafrost thaw exacerbates tundra soil carbon decomposition mediated by microbial community– Jiajie Feng – Microbiome

Microbiome composition differs in hybrid and inbred maize – Maggie R. Wagner – bioRxiv

Diversity and plant growth-promoting functions of diazotrophic/N-scavenging bacteria isolated from the soils and rhizospheres of two species of Solanum – Zuluaga Mya – PlosOne

Water microbiome

Molecular Characteristics of Dissolved Organic Nitrogen and Its Interaction with Microbial Communities in a Prechlorinated Raw Water Distribution System – Hang Xu – Environmental Science and Technology

Effects of geographic location and water quality on bacterial communities in full-scale biofilters across North America – Ben Ma – FEMS Microbiology Ecology

Phages and viruses

*Exploring the remarkable diversity of Escherichia coli Phages in the Danish Wastewater Environment, Including 91 Novel Phage Species – Nikoline S. Olsen – bioRxiv


Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences – Nicole R. Narayan – BMC Genomics

Network-Based Prediction of Novel CRISPR-Associated Genes in Metagenomes – Jake L. Weissman and Philip L. F. Johnson – mSystems

Review: Integrating Computational Methods to Investigate the Macroecology of Microbiomes – Rilquer Mascarenhas – Frontiers in Genetics

Assessment of single cell RNA-seq statistical methods on microbiome data – Matteo Calgaro – bioRxiv