Good Morning! Highlights of today’s digest include malaria parasite control by a symbiont: investigation of a host immune response and mosquito development in responds to the mosquito symbiont Asaia. On a relating note, please also check out Parasite Microbiome Project, which aims to provide interactive centralized platform and resources for researchers to dissect complex interactions between parasites, hosts and their respective microbiota. Finally, a plant-microbe interactions study aimed to define a core microbiota of wheat crop and a possibility to use certain microbial taxa for management of stripe rust, a widely occuring wheat leaf disease.

General microbiome
*Asaia Activates Immune Genes in Mosquito Eliciting an Anti-Plasmodium Response: Implications in Malaria Control – Cappelli et al. – Frontiers in Genetics

*Opinion: Parasite microbiome project: Grand challenges – Dheilly et al. – PLOS PATHOGENS

Human oral microbiome
Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules – Baker et al. – bioRxiv

Human gut microbiome
Review: Is there any association between gut microbiota and type 1 diabetes? A systematic review – Jamshidi et al. – Gut Pathogens

Differential Effects of Typical Korean Versus American-Style Diets on Gut Microbial Composition and Metabolic Profile in Healthy Overweight Koreans: A Randomized Crossover Trial – Shin et al. – Nutrients

Animal experiments
Colonic Microbiota and Metabolites Response to Different Dietary Protein Sources in a Piglet Model – Li et al. – Frontiers in Nutrition

Antibiotics and Host-Tailored Probiotics Similarly Modulate Effects on the Developing Avian Microbiome, Mycobiome, and Host Gene Expression – Ward et al. – mBio

Evaluation of the bacterial ocular surface microbiome in clinically normal cats before and after treatment with topical erythromycin – Darden et al. – PLOS ONE

Animal microbiome
Effects of Nutritional Deprivation and Re-Alimentation on the Feed Efficiency, Blood Biochemistry, and Rumen Microflora in Yaks (Bos grunniens) – Zou et al. – MDPI Animals

Plant, root and soil microbiome
* Wheat‐associated microbiota and their correlation with stripe rust reaction – Dai et al. – Journal of Applied Microbiology

Prophage induction mediated by quorum sensing signals alters soil bacterial community structure – Liang et al. – bioRxiv

Water and extremophile microbiome
Chemical and biological dispersants differently affect the bacterial communities of uncontaminated and oil-contaminated marine water – de Almeida Couto et al. – Brazilian Journal of Microbiology

Shift of Sediments Bacterial Community in the Black-Odor Urban River during In Situ Remediation by Comprehensive Measures – Zhang et al. – MDPI Water

Built environment
Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach – Hendriksen et al. – PLOS ONE

In today’s microbiome digest, several interesting studies have been covered including a) the relationships between multidrug-resistant bacteria (MDRB) colonization and dysbiosis after liver transplantation, b) microbiome and host transcriptome signature in patients with Atopic dermatitis or psoriasis, c) in the animal microbiome section- effect of host genetics on the gut microbiome composition of Avian, Bovine, and Drosophila models, d) a study which shows Composition of gut microbiota can modulate adaptive immune responses in chickens to vaccination against influenza viruses, e) CSMD, a bioinformatics pipeline specifically developed to generate accurate species-level microbiome profiles for clinical samples with low microbial loads and many more. Enjoy your Sunday with the latest microbiome feed.

General microbiome

Research highlight: Your microbiome is what you eat – Ashley York – Nature Reviews Microbiology

Gastro-intestinal and oral microbiome signatures associated with healthy aging – Harinder Singh – GeroScience

The future of microbiome‐based therapeutics in clinical applications – Anukriti Sharma – Clinical Pharmacology and Therapeutics

Human gut microbiome

Colonizing multidrug-resistant bacteria and the longitudinal evolution of the intestinal microbiome after liver transplantation – Medini K. Annavajhala – Nature Communication

Normal gut microbiome in NMDA receptor encephalitis – Julia Herken – Neurology, Neuroimmunology and Neuroinflammation

Urolithin Metabotypes Can Determine the Modulation of Gut Microbiota in Healthy Individuals by Tracking Walnuts Consumption over Three Days – Izaskun García-Mantrana – Nutrients 

Fecal microbiota transplantation results in bacterial strain displacement in patients with inflammatory bowel diseases – Manli Zou – FEBS openbio

Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men – Ryan R. Cook – Scientific Reports

Human skin microbiome

Microbe-host interplay in atopic dermatitis and psoriasis – Nanna Fyhrquist – Nature Communications

Human reproductive tract microbiome

Review: Maternal microbiome and the hypertensive disorder of pregnancy, preeclampsia – Kalie F Beckers – American Journal of Physiology Heart and Circulatory Physiology

Animal microbiome / Animal experiments

Changes in Microbiota and Development of Nonspecific Inflammation of Genitals in Female C57Bl/6 Mice after Aerosol Infection with Mycobacterium tuberculosis – S. I. Kayukova – Bulletin of Experimental Biology and Medicine

Land-use change has host-specific influences on avian gut microbiomes – Priscilla A. San Juan – The ISME Journal

Host genetic effects upon the early gut microbiota in a bovine model with graduated spectrum of genetic variation – Peixin Fan – The ISME Journal

Host determinants of among-species variation in microbiome composition in drosophilid flies – Karen L. Adair – The ISME Journal

Faecal microbiome sequences in relation to the egg-laying performance of hens using amplicon-based metagenomic association analysis – A. A. Elokil – Animal

Of microbes and mange: consistent changes in the skin microbiome of three canid species infected with Sarcoptes scabiei mites – Alexandra L. DeCandia – Parasites & Vectors

Commensal gut microbiota can modulate adaptive immune responses in chickens vaccinated with whole inactivated avian influenza virus subtype H9N2 – AlexanderYitbarek – Vaccine

Bioinformatics

CSMD: A computational subtraction-based microbiome discovery pipeline for species-level characterization of clinical metagenomic samples – Yu Liu – Bioinformatics

Microbiome news

MICROBE TALK: THE ROLE OF MICROBES IN CANCER

EcoBiome Innovation Center Launches MyEcoBiome™ Personal Soil Health Test

By: Puck deRoos

Please join me in welcoming our new contributor Puck deRoos. She will be writing short articles about the latest microbiome papers. I am so excited to have you on the team! – Elisabeth Bik

New research has highlighted a potential system that can specifically target pathogenic bacteria without disturbing the rest of the microbial community¹.  

Currently, the ways to treat pathogenic bacterial infections are non-specific and may have unintentional longer lasting effects because they often alter the composition of the gut microbiome. The rise of multi-drug resistant bacteria has shown the limitations of general broad-spectrum antibiotics², while phage-based therapy has been associated with  a smaller but similar rise in phage resistant bacteria³,.  Stool transplants have shown promising results in treatment of particular intestinal conditions, but are not suitable for many other diseases. In addition, they completely alter the patients gut microbiome, which may have unknown long-term effects⁴. 

The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) Cas-9 (CRISPR ASsociated protein-9) system is able to target specific microbial species, and cause cell death due to double stranded breaks in the microbial DNA. In a recent paper published in Nature Communications, researchers have developed a method to specifically target microbial pathogens using a cis-conjugative CRISPR system where all the necessary machinery is encoded within one plasmid, or bacterial DNA sequence.

The cis-conjugative plasmid system has much higher rate of conjugation, which is how bacteria transfer genetic material between different cells, than its trans-conjugative counterpart, which has the CRISPR and conjugative sequences on different plasmids. One of the reasons the cis-conjugative system is more effective is that it is able to continue to work throughout multiple conjugations, so its effect increases exponentially throughout time. In contrast,  the trans system only works once. 

The rates of conjugation were measured from host bacteria Escherichia coli to bacterial recipient Salmonella enterica. The rate for the cis system continually increased and reached a maximum of 1 X 10^-2 at 24hour, while the trans system maxed out early at ~1 X 10^-3 but decreased to ~1 X 10^-5 at 24hours. These results showed a ~1000-fold increase in the rates of the new cis-conjugative system compared to previous trans-conjugative system. 

This new tool for targeting specific bacteria can be extremely useful within the human microbiome. Most microbial communities in our body exists as a biofilm, a community of different microorganisms that stick together on a surface. The new cis-conjugative system developed by researchers at Schulich School of Medicine and Dentistry has up to a potential 100% effective rate of conjugation with bacteria grown in a biofilm. The same cis system in a regular bacterial assay or filter based assay shows a ~500 to 1000-fold decrease in the rate of conjugation, increasing the systems usefulness in regards to the microbiome. 

In conclusion, this new method of specifically delivering a CRISPR-Cas-9 system to pathogenic bacteria without disrupting the composition of the entire microbial community is an exciting new direction for the targeted  treatment of microbial infections. 

1. Hamilton TA et al. Efficient inter-species conjugative transfer of a CRISPR nuclease for targeted bacterial killing. Nature Communications. 10, 4544 (2019). https://doi.org/10.1038/s41467-019-12448-3

2. Theuretzbacher, U. Antibiotic innovation for future public health needs. Clin. Microbiol. Infect. 23, 713–717 (2017). 

3. Chatain-Ly, M. H. The factors affecting effectiveness of treatment in phages therapy. Front. Microbiol. 5, 51 (2014). 

4. Khanna, S. et al. Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease. Microbiome 5, 55 (2017). 

Good Morning! Highlights of today’s digest include investigation about early childhood microbiota assembly in mother-infant participants from the Tsimane indigenous population from Amazon and with findings suggesting that socioeconomic changes may be altering interactions of highly abundant members of the microbiota in the host. Results from a gut-brain axis rat model showed possibility of novel biomarkers development for stress response based on abundance of genes in microbiomes. Finally, another study is aiming to access biologically active small molecules with antibacterial activity derived from human microbiota by sequencing of metagenomes and the use of computational and synthetic biology methods.

Pregnancy and early life
Prenatal and postnatal contributions of the maternal microbiome on offspring programming – Jasarevic and Bale – Frontiers in Neuroendocrinology

Multi-site human microbiome
*Microbiota Assembly, Structure, and Dynamics Among Tsimane Horticulturalists of the Bolivian Amazon – Sprockett et al. – bioRxiv

Human vaginal microbiome
Oncogenic Virome Benefits from the Different Vaginal Microbiome-Immune Axes – Campisciano et al. – MDPI Microorganisms

Non-optimal vaginal microbiota after azithromycin treatment for Chlamydia trachomatis infection – Tamarelle et al. – The Journal of Infectious Diseases

Human nearly-sterile sites
Targeted High-Throughput Sequencing Identifies Predominantly Fungal Pathogens in Patients with Clinically Infectious, Culture-Negative Endophthalmitis in South India – Gandhi et al. – MDPI Microorganisms

Human gut microbiome
Review: Synthetic ecology of the human gut microbiota – Vrancken et al. – Nature Reviews Microbiology

Review: The interaction between gut microbiome and nutrients on development of human disease through epigenetic mechanisms – Ho-Sun Lee – Genomics & Informatics

Adaptation of Syntenic Xyloglucan Utilization Loci of Human Gut Bacteroidetes to Polysaccharide Side Chain Diversity – Dejean et al. – Applied and Environmental Microbiology

Pre‐and post‐serial metagenomic analysis of gut microbiota as a prognostic factor in patients undergoing haematopoietic stem cell transplantation – Kusakabe et al. – British Journal of Haematology

Animal experiments
Experimental evidence for adaptation to species-specific gut microbiota in house mice – Moeller et al. – mSphere

Low‐calcium diet in mice leads to reduced gut colonization by Enterococcus faecium – Top et al. – MicrobiologyOpen

Letrozole treatment of pubertal female mice results in activational effects on reproduction, metabolism and the gut microbiome – Arroyo et al. – PLOS ONE

Transplanting Fecal Virus-Like Particles Reduces High-Fat Diet-Induced Small Intestinal Bacterial Overgrowth in Mice – Lin et al. – Frontiers in Cellular and Infection Microbiology

*Metabolome and microbiome profiling of a stress-sensitive rat model of gut-brain axis dysfunction – Bassett et al. – Nature Scientific Reports

Animal microbiome
The composition and stability of the faecal microbiota of Merino sheep – Al Mamun et al. – Journal of Applied Microbiology

Faecal microbiota and functional capacity associated with weaning weight in meat rabbits – Fang et al. – Microbial Biotechnology

Review: Feline Virome—A Review of Novel Enteric Viruses Detected in Cats – Martino et al. – MDPI Viruses

Phylogeography and ecological niche shape the cichlid fish gut microbiota in Central American and African lakes – Baldo et al. – Frontiers in Microbiology

Plant, root and soil microbiome
Biocontrol activities of rhizobacteria associated with apple, apricot and kiwi rhizosphere against bacterial canker caused by Clavibacter michiganensis – Gautam et al. – Indian Phytopathology

Distinct Drivers of Core and Accessory Components of Soil Microbial Community Functional Diversity under Environmental Changes – Zhang et al. – mSystems

Antarctic tundra soil metagenome as useful natural resources of cold-active lignocelluolytic enzymes – Oh et al. – Journal of Microbiology

Microbial communities in bioswale soils and their relationships to soil properties, plant species, and plant physiology – Brodsky et al. – Frontiers in Microbiology

Soil prokaryotes associated with decreasing pathogen density during anaerobic soil disinfestation – Lee et al. – bioRxiv

Water and extremophile microbiome
Bacterial Communities of Microbial Mats of the White Sea Supralittoral and of the Littoral of the Lakes Separated from the Sea – Burganskaya et al. – Microbiology

Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom – Bhatnagar et al. – bioRxiv

Bioinformatics
*A metagenomic strategy for harnessing the chemical repertoire of the human microbiome – Sugimoto et al. – Science

Techniques
Protocol: Open-Source Software Tools, Databases, and Resources for Single-Cell and Single-Cell-Type Metabolomics – Biswapriya B. Misra – Single Cell Metabolism

An Entropy-Based Graph Construction Method for Representing and Clustering Biological Data – Ariza-Jimenez et al. – Latin American Conference on Biomedical Engineering

Microbes in the news
Artificial gut aims to expose the elusive microbiome – Anne McGovern – MIT PHYS.ORG