May 22, 2020

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We’ve got a decently sized digest today with a lot of environmental microbe papers, including descriptions of novel species. There is also the Cell paper (highlighted) from Peter Turnbaugh’s group on ketogenic diets and the gut microbiome, which has been getting a lot of press. For new bioinformatic and other techniques, we have a new R package to predict functional profiles in Tax4Fun2, an assessment of phylogenetic rooting methods for bacteria, and a description of fiber intervention used in undergraduate classes for active learning.

 Have a great weekend!

Events

Today is the last day of the Virtual Microbiome Summit.

Pregnancy and early life

Women’s multisite microbial modulation during pregnancy – Luiz G. Sparvoli – Microbial Pathogenesis

Multi-site human microbiome

Review: Bi-Directional Interactions Between Microbiota and Ionizing Radiation in Head and Neck and Pelvic Radiotherapy-Clinical Relevance – Nidhya Teresa Joseph – International Journal of Radiation Biology

Human oral microbiome

Defining the oral microbiome by whole-genome sequencing and resistome analysis: the complexity of the healthy picture – Elisabetta Caselli – BMC Microbiology

Human gut microbiome

Ketogenic diets alter the gut microbiome resulting in decreased intestinal Th17 cells – Qi Yan Ang – Cell

Preprint: Host genetic and environmental factors shape the human gut resistome – Caroline I. Le Roy – bioRxiv

MinION Sequencing of colorectal cancer tumour microbiomes—A comparison with amplicon-based and RNA-Sequencing – William S. Taylor – PLOS One (Originally posted to the Digest as a pre-print, now published)

Animal experiments

Broilers divergently selected for digestibility differ for their digestive microbial ecosystems – Marion Borey – PLOS One

Dietary Isomalto/Malto‐Polysaccharides Increase Fecal Bulk and Microbial Fermentation in Mice – Rima H. Mistry – Molecular Nutrition and Food Research

Longitudinal Effects of Dietary Oxidized Lipids on the Gut Microbiome and Mycobiome in Pigs – Folagbayi Arowolo – FASEB Journal

Animal microbiome

Single-cell amplicon sequencing reveals community structures and transmission trends of protist-associated bacteria in a termite host – Michael E. Stephens – PLOS One

Plant, root, and soil microbiome

Xylella fastidiosa subsp. pauca and olive produced lipids moderate the switch adhesive versus non-adhesive state and viceversa – Valeria Scala – PLOS One

Mitochondrial genome sequence of Phytophthora sansomeana and comparative analysis of Phytophthora mitochondrial genomes – Guohong Cai – PLOS One

nirS-type denitrifying bacterial communities in relation to soil physicochemical conditions and soil depths of two montane riparian meadows in North China. – Xiaoli Han – Environmental Science and Pollution Research

Tissue-Specific Dynamics in the Endophytic Bacterial Communities in Arctic Pioneer Plant Oxyria digyna – Cindy Given – Frontiers in Plant Science

Effects of Cultured Root and Soil Microbial Communities on the Disease of Nicotiana tabacum Caused by Phytophthora nicotianae – Tianbo Liu – Frontiers in Microbiology

Novel putative rhizobial species with different symbiovars nodulate Lotus creticus and their differential preference to distinctive soil properties – M Rejili – FEMS Microbiology Letters

Water, air, and extremophile microbiome

The microbiome of alpine snow algae shows a specific inter-kingdom connectivity and algae-bacteria interactions with supportive capacities – Lisa Krug – ISME Journal

Variation of near surface atmosphere microbial communities at an urban and a suburban site in Philadelphia, PA, USA – JD Stewart – Science of the Total Environment

Pilot-scale petroleum refinery wastewaters treatment systems: performance and microbial communities’ analysis – Fatma Karray – Process Safety and Environmental Protection

Adverse effects of levofloxacin and oxytetracycline on aquatic microbial communities – Zhigao Zhou – Science of the Total Environment

Application of microbial network analysis to discriminate environmental heterogeneity in Fildes Peninsula, Antarctica – Qian Liu – Marine Pollution Bulletin

Tools for successful proliferation: diverse strategies of nutrient acquisition by a benthic cyanobacterium – HS Tee – ISME Journal

Metabolic diversity and co-occurrence of multiple Ferrovum species at an acid mine drainage site – Christen L. Grettenberger – BMC Microbiology

Halocatena pleomorpha gen. nov. sp. nov., an extremely halophilic archaeon of family Halobacteriaceae isolated from saltpan soil – Ashish Verma – IJSEM

Unveiling Cultivable and Uncultivable Halophilic Bacteria Inhabiting Marakkanam Saltpan, India and Their Potential for Biotechnological Applications – Jojy John – Geomicrobiology Journal

Flavobacterium profundi sp. nov., isolated from a deep-sea seamount – Qian Wang – IJSEM

Food microbiology

Molecular epidemiology, genetic diversity and antimicrobial resistance of Staphylococcus aureus isolated from chicken and pig carcasses, and carcass handlers – Onyinye J. Okorie-Kanu – PLOS One

Traditional milk transformation schemes in Côte d’Ivoire and their impact on the prevalence of Streptococcus bovis complex bacteria in dairy products – Aimé R Sanhoun – PLOS One

Comparison of Microbial Communities and Amino Acid Metabolites in Different Traditional Fermentation Starters Used during the Fermentation of Hong Qu Glutinous Rice Wine – Zhang-Cheng Liang – Food Research International

Preprint: Monitoring the microbiome for food safety and quality using deep shotgun sequencing – Kristen L. Beck – bioRxiv

Viruses

Are pangolins the intermediate host of the 2019 novel coronavirus (SARS-CoV-2)? – Ping Liu – PLOS Pathogens

Vector competence of Aedes aegypti from New Caledonia for the four recent circulating dengue virus serotypes – Olivia O’Connor – PLOS Neglected Tropical Diseases

Bioinformatics

Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences – Franziska Wemheuer – Environmental Microbiome

Techniques

Assessing the accuracy of phylogenetic rooting methods on prokaryotic gene families – Taylor Wade – PLOS One

Science education techniques: Fiber Force: A Fiber Diet Intervention in an Advanced Course-Based Undergraduate Research Experience (CURE) Course – Julia Massimelli Sewall – Journal of Microbiology & Biology Education

Science and art

This photographer creates prints with algae.

Non-microbiology picks:

Herd of fuzzy green “glacier mice” baffles scientists.

May 21, 2020

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There is a wide range of interesting articles and topics in today’s digest.
For example, an article by McGenity et al. discusses education, and how to communicate the importance of microbes and the microbiome to the general population. There is a discussion by Xi et al. on how specific oligosaccharide molecules such as stachyose (found in human milk and various vegetables) can modulate the intestinal microbiota and thereby influence the immune system in early life, and a discussion on how the iminosugar drug Miglustat might be repurposed as a Covid-19 therapy. Gradilla-Hernandez et al discuss the use of a simulated gut system to model the interactions and relative growth of gut microbial strains under different conditions, using differential neural network approaches.
I find it fascinating to think of the gut microbiome as an ecological system, and the papers on tryptophan and on the interactions between rotavirus and gut bacteria, mediated by host glycans, speak to this.
Development of any microbiome-based therapeutics will need to consider formulation, delivery, and release/engraftment of the product, and the paper by Chang et al. discusses the development of oral formulations for Akkermansia muciniphila.
One significant mechanism by which the microbiome affects human health is via the products of bacterial metabolism. Johnson et al. discuss how the production of sphingolipids by gut bacteria can affect host sphingolipid and ceramide levels and utilization, and the review by Weersma et al. discusses the field of “pharmacomicrobiomics”, whereby bacterial metabolism can influence the fate of drugs doses to patients, increasing the magnitude of differences in patient-to-patient response. The microbiome has also been implicated in many chronic human health conditions, and the paper by Matenchuk et al. discusses the influence of gut bacteria on circadian rhythms and sleep patterns. Finally, Burberry et al. discuss the interplay between anti-inflammatory gut bacteria and the effects of the C9orf72 mutation which contributes to ALS/Lou Gehrig’s disease and frontotemporal dementia.

General Microbiome
Tryptophan as a Central Hub for Host/Microbial Symbiosis
M Borghi et al.
International Journal of Tryptophan Research, 2020

Host–microbiome interactions: the aryl hydrocarbon receptor as a critical node in tryptophan metabolites to brain signaling
N Ma et al.
Gut Microbes, 2020

Visualizing the invisible: class excursions to ignite children’s enthusiasm for microbes
TJ McGenity at al.
Microbial Biotechnology, 2020

Pregnancy and early life
Stachyose increases intestinal barrier through Akkermansia muciniphila and reduces gut inflammation in germ-free mice after human fecal transplantation
M Xi et al.
Food Research International, 2020

Extremophile Microbiomes
Preprint:
Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys
J Hou et al.

Covid-19
Preprint:
Neutralizing antibody and soluble ACE2 inhibition of a replication-competent VSV-SARS-CoV-2 and a clinical isolate of SARS-CoV-2.
JB Case et al.

Preprint:
Repurposing of Miglustat to inhibit the coronavirus Severe Acquired Respiratory Syndrome SARS-CoV-2
S Rajasekharan et al.

Animal Microbiome
Preprint:
Effects of parity, blood progesterone, and non-steroidal anti-inflammatory treatment on the dynamics of the uterine microbiota of healthy postpartum dairy cows
OB Pascottini et al.

Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance
M-Y Xue et al.
Microbiome 2020

Techniques
Applying Differential Neural Networks to Characterize Microbial Interactions in an Ex Vivo Gastrointestinal Gut Simulator
MS Gradilla-Hernández et al. 
Processes, 2020

Oral Microbiome
Longitudinal Study of Oral Microbiome Variation in Twins
M Freire et al.
Scientific Reports, 2020

Antimicrobial peptide GH12 prevents dental caries by regulating dental plaque microbiota
W Jiang et al.
Applied and Environmental Microbiology 2020

Microbes in built environments
Taxonomic and functional profiling of nitrifying biofilms in freshwater, brackish and marine RAS biofilters
J Hüpeden et al.
Aquacultural Engineering, 2020

Human vaginal microbiome
Preprint: Structure and regulation of the cervicovaginal microbiome in a cohort of Afro-Caribbean women
O Roachford et al.
Microbiome, 2020

Phages and Viruses
Rotavirus infection induces glycan availability to promote ileum-specific changes in the microbiome aiding rotavirus virulence
M Engevik et al.,
Gut Microbes, 2020

Pharmacological interventions
Preprint:
The Changes of Gut Microbiota in Drug-Naïve First-Episode MDD Patients Under Treatment by SSRIs
Y Shen et al.
BMC Psychiatry 2020

Interaction between drugs and the gut microbiome
RK Weersma at al.
Gut, 2020

The Therapeutic Optimization of the Gut Microbiota in Diabetes Management
P Davidson et al.
ADCES in Practice, 2020

Improved viability of Akkermansia muciniphila by encapsulation in spray dried succinate-grafted alginate doped with epigallocatechin-3-gallate
Y Chang et al.

Gut Microbiome
The probiotic L. casei LC-XCAL™ improves metabolic health in a diet-induced obesity mouse model without altering the microbiome
CJ Walsh et al.
Gut Microbes, 2020

Patients infected with Mycobacterium africanum versus Mycobacterium tuberculosis possess distinct intestinal microbiota
S Namasivayam et al.
PLOS Neglected Tropical Diseases, 2020

Sphingolipids produced by gut bacteria enter host metabolic pathways impacting ceramide levels
E Johnson et al.,
Nature Communications 2020

Sleep, Circadian Rhythm, and Gut Microbiota
BA Matenchuk et al.
Sleep Medicine Reviews, 2020

C9orf72 suppresses systemic and neural inflammation induced by gut bacteria
A Burberry et al.
Nature, 2020

Market Analyses
Market Report:
Human Microbiome Market Insights & Deep Analysis, Future Scenario Till 2025 | Enterome …
News Distinct

Market Report:
COVID-19 Impact on Human Microbiome Sequencing Technology Market Research Report …
3rd Watch News

Market Report:
Pre, pro- and microbiotics and your business
Natural Products INSIDER

Market Report:
Microbiome Sequencing Services Market Types, Applications And Competitors 2019-2025 …
openPR (press release)

Market Report:
PGR decision provides much-needed clarity in fast-growing microbiome space
IAM (blog)

Market Report:
Human Microbiome Market Research Report 2020 By Size, Share, Trends, Analysis and Forecast …
Cole of Duty

Market Report:
Human Microbiome Market size, historical growth, analysis, opportunities and forecast to 2026 …
Surfacing Magazine

May 20, 2020

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Greetings from Pittsburgh, PA!

Television and movies are a welcome distraction from the current global pandemic. For this digest, I’d like to highlight two articles. The article by Sajjad et al. investigates the possibility of resurrection of ancient microbes present in the natural frozen world and is a perfect pair for the monster-of-the-week X-Files episode “Ice.” The second highlighted article focuses on the microbiome present on two ancient Slavonic parchment codices and how this data can be used to provide additional historical context. Maybe Harrison Ford can team up with Piñar et al. to create a fourth movie in the Indiana Jones Franchise based on their work?

Happy reading, everyone!

General microbiome

Effect of a novel synbiotic on Streptococcus mutans – Bijle et al. – Nature Scientific Reports

Culturomics‐based genomics sheds light on the ecology of the new haloarchaeal genus Halosegnis – Durán‐Viseras et al. – Environmental Microbiology

Review: Ecological features of the persistence of Vibrio cholerae: retrospective analysis and actual state of the problem – Menshikova et al. – Jounral of microbiology, epidemiology, and immunobiology

Metagenome-assembled genomes reveal unique metabolic adaptations of a basal marine Thaumarchaeota lineage – Reji and Francis – ISME Journal

Homoplastic single nucleotide polymorphisms contributed to phenotypic diversity in Mycobacterium tuberculosis – Tantivitayakul et al. – Nature Scientific Reports

Plant, root, and soil microbiome

Impacts of forest conversion to plantations on the soil carbon and nitrogen dynamics, and microbial communities – Wang et al. – Soil Biology and Biochemistry

Water and extremophile microbiome

Novel yeast taxa from the cold: description of Cryolevonia giraudoae sp. nov. and Camptobasidium gelus sp. nov. – de Garcia et al. – International Journal of Systematic and Evolutionary Microbiology

Remote sensing reveals Antarctic green snow algae as important terrestrial carbon sink – Gray et al. – Nature Communications

Review: Resurrection of inactive microbes and resistome present in the natural frozen world: Reality or myth? – Sajjad et al. – Science of the Total Environment

Built environment

Decoding the biological information contained in two ancient Slavonic parchment codices: an added historical value – Piñar et al. – Environmental Microbiology

Bioinformatics

Preprint: Efficiently processing amplicon sequencing data for microbial ecology with dadasnake, a DADA2 implementation in Snakemake – Weißbecker et al. – bioRxiv

Techniques

Editorial: Visualizing the invisible: class excursions to ignite children’s enthusiasm for microbes – McGenity et al. – Microbial Biotechnology

Discovery of thermophilic Bacillales using reduced-representation genotyping for identification – Talamantes-Becerra et al. – BMC Microbiology

May 19, 2020

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Good afternoon from sunny South Wales!

Today’s digest has a lot of great papers, with something for just about everyone. We’ll start off with a bang, and highlight a great paper in which Rajasekaran and collegaues challenge the current dogma that human intervertebral discs are sterile using a 16S rRNA sequencing approach.

We then have an interesting, or perhaps concerning paper looking at the prevalence of underreported parasites in laboratory zebrafish populations. A must read for anybody using zebrafish models. We also have plenty of papers concerning plant and water microbiomes, including a rather huge report on ocean systems.

Finally, with the current health climate, what better paper peruse than the contribution of Qureshi et al. who have demonstrated that gender neutral bathrooms are more rapidly colonised than single gender bathrooms. If recent anecdotal news articles are to be believed (although they seldom are) it’s usually the men letting the side down. You’ve got to wash those hands!

I hope everyone is staying safe, and enjoys today’s post!

COVID-19

Preprint: Identification of five antiviral compounds from the Pandemic Response Box targeting SARS-CoV-2 – Holwerda et al.

General microbiome

Longitudinal Study of Oral Microbiome Variation in Twins – Freire et al. – Sci Rep

Human nearly-sterile sites

Human intervertebral discs harbour a unique microbiome and dysbiosis determines health and disease – Rajasekaran et al. – European Spine Journal

Human gut microbiome

Early signs of gut microbiome aging: biomarkers of inflammation, metabolism, and macromolecular damage in young adulthood – Gaydosh et al. – The Journals of Gerontology

Animal experiments

Behavioural effects of the common brain-infecting parasite Pseudoloma neurophilia in laboratory zebrafish (Danio rerio) – Midttun et al. – Sci Rep

Lactobacillus plantarum FRT10 alleviated high-fat diet–induced obesity in mice through regulating the PPARα signal pathway and gut microbiota – Cai et al. – Applied Microbial and Cell Physiology

Animal microbiome

Factors affecting the microbiome of Ixodes scapularis and Amblyomma americanum – Brinkerhoff et al. – PLoS ONE

Preprint: Distinct Microbial Assemblages Associated with Genetic Selection for High- and Low- Muscle Yield in Rainbow Trout – Walker et al.

Whole-genome sequences of an abortive Bacillus safensis strain isolated from a mare’s uterus – Little, Hillhouse and Lawhorn – Genome Sequences

Plant, root, and soil microbiome

Preprint: A fungal member of the microbial phyllosphere antagonizes infection of Arabidopsis thaliana by the oomycete pathogen Albugo laibachii via a putative secreted hydrolase – Eitzen et al.

Preprint: Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts – Higdon et al.

Fungal communities and their association with nitrogen-fixing bacteria affect early decomposition of Norway spruce deadwood – Gómez-Brandón et al. – Sci Rep

Fruitbody chemistry underlies the structure of endofungal bacterial communities across fungal guilds and phylogenetic groups – Pent, Bahram and Põldmaa – ISME J

Endophytic fungal community in grape is correlated to foliar age and domestication – Fan et al. – Annals of Microbiology

Water and extremophile microbiome

Microbial genomics of the global ocean system – Joye and Kostka – Coloqium Report

How do microbiota associated with an invasive seaweed vary across scales? – Bonthond et al. – Molecular Ecology

Preprint: Differences in the microbiota of native and non-indigenous gelatinous zooplankton organisms in a low saline environment – Jaspers et al.

Built environment

Gender‐neutral bathroom surfaces recolonized by microbes more quickly than single gender bathrooms – Qureshi, Kedo and Berthrong – Letters in Applied Microbiology

Food microbiology

Dynamic distribution of gut microbiota in meat rabbits at different growth stages and relationship with average daily gain (ADG) – Fang et al. – BMC Microbiology

Techniques

Preprint: Evaluation of Methods to Optimise Shotgun Metagenomic Sequencing-Based Analysis of the Microbiome of Milk – Feehily et al.

May 18, 2020

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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!

COVID-19

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.

Fungi

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

Methods

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

Metagenomics

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

Transcriptomics

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 18, 2020

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Good morning everyone. Today’s microbiome digest is very short specifically the human gut microbiome section. I have included only one study in this section which shows no association of gut microbiome and fecal calprotectin levels with enteropathy in preterm infants. Additionally, I have covered several interesting reviews and research articles to explore the role of the gut microbiome in Type 1 diabetes and Hashimoto’s thyroiditis, ameliorates ulcerative colitis, aging process, regulation of energy metabolism and oxidative stress. I hope you will enjoy today’s feed.

General microbiome

Fungal communities and their association with nitrogen-fixing bacteria affect early decomposition of Norway spruce deadwood – María Gómez-Brandón – Scientific Reports

Review: Gut microbiota and metabolites in the pathogenesis of endocrine disease – Fenneman AC – Biochemical Society Transactions

Review: Role of the Phytochemical Compounds like Modulators on Gut Microbiota and Oxidative Stress – Yordan Martínez – Current Pharmaceutical Design

Human gut microbiome

Faecal calprotectin and gut microbiota do not predict enteropathy in very preterm infants – Florence Campeotto – Acta Paediatrica

Animal microbiome / Animal experiments

Lizhong decoction ameliorates ulcerative colitis in mice via modulating gut microbiota and its metabolites – Junfeng Zou – Applied microbial and cell physiology

Age-related compositional changes and correlations of gut microbiome, serum metabolome, and immune factor in rats – Xia Zhang – GeroScience

The Beneficial Effects of Lippia Citriodora Extract on Diet‐Induced Obesity in Mice are Associated with the Modulation in the Gut Microbiota Composition – Patricia Diez‐Echave – Molecular Nutrition and Food Research

The gut microbiota attenuates muscle wasting by regulating energy metabolism in chemotherapy-induced malnutrition rats – Haitao Chen – Cancer Chemotherapy and Pharmacology

Slc26a3 deletion alters pH‐microclimate, mucin biosynthesis, microbiome composition and increases Tnfα expression in murine colon – A. Kini – Acta Physiologica

Tibet plateau probiotic mitigates chromate toxicity in mice by alleviating oxidative stress in gut microbiota – Pengya Feng – Communications Biology

Antimicrobial peptide GH12 prevents dental caries by regulating dental plaque microbiota – Wentao Jiang – Microbial Ecology

Methods

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

Review: Metaproteomics: A strategy to study the taxonomy and functionality of the gut microbiota – Yuqiu Wang – Journal of Proteomics

Microbes in news

DOE scientists identify microbial link in gut-memory connection

May 17, 2020

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Hello from the Sonoran Desert! It is a sunny Sunday over Tucson, Az! I find that Sundays are the best to explore new ideas and concepts, and I especially love to take the time to read a good opinion piece or parse few review papers. In today’s digest, you’ll find a fascinating review on the Tara Ocean expedition and how it changed our understanding of marine microbial communities. If you’re more interested in the human-associated microbiome, fear not! There is also great pieces on the gut microbiota in athletes and on the interaction of oral and lung microbiome in the context of lung diseases.

If like me, you are a computational biologist thinking about microbiome data all day, you should enjoy reading today’s non microbiology pick, a great perspective paper discussing the FAIR (Findable, Accessible, Interoperable and Reusable) data principle and what are the current hurdles that limit open data reuse.

Have a great Sunday!

Pregnancy and early life

Review: The impact of maternal and early life malnutrition on health: a diet-microbe perspective – Andrew J. Forgie et al. – BMC Medicine

Multi-site human microbiome

Perspective: Microbial Diagnostics for Cancer: A Step Forward but Not Prime Time Yet –  Cynthia L. Sears et al. – Cancer Cell

Human respiratory microbiome

Review: Oral-lung microbiome interactions in lung diseases –  Manoj J. Mammen et al. – Periodontology

Human gut microbiome

Review: The athletic gut microbiota – Alex E. Mohr et al. – Journal of the International Society of Sports Nutrition

Colorectal cancer occurrence and treatment based on changes in intestinal flora – Huifang Si et al. –  Seminars in cancer Biology

Animal experiments 

Microbial communities modulating brain functioning and behaviors in zebrafish: A mechanistic approach – Larica Mohanta et al. –  Microbial Pathogenesis

Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance – Ming-Yuan Xue et al. – Microbiome

Preprint: Rumen protozoa shape microbiome composition and metabolic output of fermentation – Ronnie Solomon et al. – bioRxiv

Animal microbiome (for animals in the wild)

Changes in the gut microbiota during Asian particolored bat (Vespertilio sinensis) development – Zhongwei Yin et al. – Microbiology

After the bite: bacterial transmission from grey seals (Halichoerus grypus) to harbour porpoises (Phocoena phocoena) – Maarten J. Gilbert et al. – Royal Society open science

Exploration of the virome of the European brown shrimp (Crangon crangon) – Benigna Van Eynde et al. – Journal of General Virology

Plant, root, and soil microbiome

Opinion: The Role of Rhizosphere Bacteriophages in Plant Health – Akbar Adjie Pratama et al. – Trends in Microbiology

Analyzing bacterial community in pit mud of Yibin Baijiu in China using high throughput sequencing –  Li Chen et al. – PeerJ

Shifts of bacterial community structure and function in long-term soybean monoculture – Fengjuan Pan et al. – Archives of Agronomy and Soil Science

Bacterial Diversity in Peat Soils of Forest Ecosystems and Oil Palm Plantation – N. A. Kusai et al. – Soil Biology

Space Is More Important than Season when Shaping Soil Microbial Communities at a Large Spatial Scale – Kaoping Zhang et al. – mSystems

Effects of cadmium perturbation on the microbial community structure and heavy metal resistome of a tropical agricultural soil – Lateef B. Salam et al. – Bioresources and Bioprocessing

Competition for iron drives phytopathogen control by natural rhizosphere microbiomes – Shaohua Gu et al. – Nature Microbiology

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

Review: Tara Oceans: towards global ocean ecosystems biology – Shinichi Sunagawa et al. – Nature Reviews Microbiology

Review: Microbial genomics amidst the Arctic crisis – Arwyn Edwards et al. – Microbial genomics

Exceptional but vulnerable microbial diversity in coral reef animal surface microbiomes – Marlène Chiarello et al. – Proceedings of the royal society biological sciences

Bioinformatics

A powerful microbial group association test based on the higher criticism analysis for sparse microbial association signals – Hyunwook Koh et al. – Microbiome

Review: A practical guide to amplicon and metagenomic analysis of microbiome data – Yong-Xin Liu et al. – Protein Cell

TAMA: improved metagenomic sequence classification through meta-analysis – Mikang Sim et al. – BMC Bioinformatics

nf-rnaSeqMetagen: A nextflow metagenomics pipeline for identifying and characterizing microbial sequences from RNA-seq data – Phelelani T. Mpangase et al. – Medicine in Microecology

My non-microbiology pick

Perspective: FAIR Data Sharing: The Roles of Common Data Elements and Harmonization – R.D.Kush et al. – Journal of Biomedical Informatics

May 16th, 2020

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Good morning!

A few nice studies today, with highlights being utilising Streptomyces endophytes to aid in plant growth, a review on the gut-brain-axis with a focus on psychiatry, and a bioinformatics study looking into the role of pathogenic E.coli in cancer. Enjoy!

COVID-19

The coding capacity of SARS-CoV-2 Y.Finkel/O. Mizrahi et al. bioXriv.

Human vaginal microbiome

The study of host-bacterial relationships and immune function in different vaginal environments (Study in progress) A. berard et al. Journal of Obstetrics and Gynaecology Canada.

Human gut microbiome

Relationship between the composition of the digestive microbiota and the concentrations of opportunistic pathogens in intensive care patients. C. Fontaine et al. bioXriv.

Animal microbiome

Evaluation of fecal Lactobacillus populations in dogs with idiopathic epilepsy: a pilot study. Karen R. Muñana et al. Animal microbiome.

Plant, root and soil microbiome

Streptomyces endophytes promotes the growth of Arabidopsis thaliana S. F Worsley et al. bioXriv.

Water and extremophile microbiome

Deciphering a marine bone degrading microbiome reveals a complex community effort E. Borchert et al. bioRxiv.

Prebiotics

Human microbiome and homeostasis: insights into the key role of prebiotics, probiotics and symbiotics. B. Salehi et al. Critical Reviews in Food Science and Nutrition.

Probiotics and the Microbiota-Gut-Brain Axis: Focus on Psychiatry. Mörkl S. Current Nutrition Reports.

Bioinformatics

Novel Discoveries Targeting Pathogenic Gut Microbes and New Therapies in Pancreatic Cancer: Does Pathogenic E. coli Infection Cause Pancreatic Cancer Progression Modulated by TUBB/Rho/ROCK Signaling Pathway? A Bioinformatic Analysis. W. Luo et al. BioMed Research international.

May 15th, 2020

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We have got a balanced mix for folks today of human, animal, plant, and free-living microbiome research. In particular I want to highlight the work of Inagaki et al., who tracked gut microbiome dynamics within Japanese termites (Reticulitermes speratus) during dispersal and colony formation. They observed a rapid increase then decrease of gut protozoa coinciding with larval hatching of a pioneering termite pair’s first brood; a pattern they call a ‘gut microbial pulse’ (what a wonderfully evocative term!). This is a neat example of how host-associated microbiomes might play a integral role in the ecology of free-living organisms.

General microbiome

Dynamic metabolic adaptation can promote species coexistence in competitive communities– Leonardo Pacciani-Mori et al. – PLOS Computational Biology

The role of the microbiota in periodontal disease – Mike A. Curtis et al. – Periodontology 2000

Human respiratory microbiome

Oral‐lung microbiome interactions in lung diseases– Manoj J. Mammen et al. – Periodontology 2000

Human nearly-sterile sites

Microbiome and Schizophrenia: Current Evidence and Future Challenges – Thiago Macedo e Cordeiro et al. – Current Behavioural Neuroscience Reports

Human gut microbiome

Patients infected with Mycobacterium africanum versus Mycobacterium tuberculosis possess distinct intestinal microbiota – Sivaranjani Namasivayam et al. – PLOS Neglected Tropical Diseases

A systematic machine learning and data type comparison yields metagenomic predictors of infant age, sex, breastfeeding, antibiotic usage, country of origin, and delivery type – Alan Le Goallec et al. – PLOS Computational Biology

The role of small intestinal bacterial overgrowth and false positive diagnosis of lactose intolerance in southwest Hungary — A retrospective observational study – Péter Varjú et al. – PLOS One

The Bacterial Gut Microbiota of Adult Patients Infected, Colonized or Noncolonized by Clostridioides difficile – Monique J.T Crobach et al. – Microorganisms

Animal experiments

Effect of age and the individual on the gastrointestinal bacteriome of ponies fed a high-starch diet– Philippa K. Morrison et al. – PLOS One

Animal microbiome

Gut microbial pulse provides nutrition for parental provisioning in incipient termite colonies – Tatsuya Inagaki et al. – Behavioural Ecology and Sociology

The role of the gut microbiome in mediating standard metabolic rate after dietary shifts in the viviparous cockroach, Diploptera punctata – Paul A. Ayayee et al. – Journal of Experimental Biology

Plant, root, and soil microbiome

Genome reconstruction of the non-culturable spinach downy mildew Peronospora effusa by metagenome filtering – Joël Klein et al. – PlOS One

Unraveling the Microbiota of Natural Black cv. Kalamata Fermented Olives through 16S and ITS Metataxonomic Analysis – Maria Kazou et al. – Microorganisms

Quantifying Plant-Borne Carbon Assimilation by Root-Associating Bacteria – Spenser Waller et al. – Microorganisms

Water and extremophile microbiome

Community-level signatures of ecological succession in natural bacterial communities – Alberto Pascual-Garcia & Thomas Bell – Nature Communications

Instigation of indigenous thermophilic bacterial consortia for enhanced oil recovery from high temperature oil reservoirs – Leha Sharma et al. – PLOS One

Microplastics affect sedimentary microbial communities and nitrogen cycling – Meredith E. Seeley et al. – Nature Communications

Peatland Microbial Community Composition Is Driven by a Natural Climate Gradient – James Seward et al. – Environmental Microbiology

Techniques

Confocal Raman microscopy to identify bacteria in oral subgingival biofilm models – Lukas Simon Kriem et al. – PLOS One

 

Probiotics to precision probiotics

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

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

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

Problems with top-down approach

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

Bottom up approach

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

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

Challenges with bottom-up approach

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

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

Precision probiotics strategies

The big aim

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

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

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