World Microbiome Day 2021

The collection of bacteria, fungi, and other microbes that form microbiota play an important role in both human and environmental health. In recognition of World Microbiome Day, we have curated a Collection of articles, news and commentary to celebrate the diversity of microbiome research published at Communications Biology, and highlight exciting new avenues for the field.

While reforestation efforts are important in limiting the progression of climate change, tree stems are known to emit the potent greenhouse gas, methane. Luke Jeffrey and colleagues recently discovered that methanotrophic bacteria colonize the bark of the common lowland tree, Melaleuca quinquenervia, and significantly reduce its methane emissions. Their results expand the known pool of habitats for methanotrophic bacteria and suggest that these bark-dwelling taxa may be a future target for limiting methane emissions from trees.

Denise Akob is a Research Microbiologist for the United State Geological Survey (USGS), based at the Geology, Energy & Minerals Science Center in Reston, VA. Dr. Akob received her Ph.D. in 2008 from Florida State University and completed a postdoctoral research fellowship at Friedrich Schiller University Jena before starting her independent research career with the USGS in 2012. In this Q&A, Dr. Akob tells us about her current work, experiences in federal research, and the best bacterial taxa.

Helen Vuong is a postdoctoral fellow in the Hsiao lab at the University of California, Los Angeles, where she is currently funded by a K99 Pathway to Independence Award from the National Institutes of Health. In this Q&A, Dr. Vuong tells us about her current work and the importance of tailoring scientific educational experiences to students. Dr. Vuong also shares tips on how to better support young parents in STEM.

Dr. César de la Fuente is a Presidential Assistant Professor at the University of Pennsylvania. He leads a Machine Biology group developing computational tools to expand the antibiotic arsenal, engineer the microbiome and study and control brain function and behavior. His work has been recognized by the Langer Prize, ACS Kavli Emerging Leader in Chemistry award, ACS Infectious Diseases Young Investigator Award, STAT News, GEN, and the MIT Technology Review. We asked Dr. de la Fuente about his research and journey of the field as part of our series on early-career researchers.

Caroline Palmer proposes the concept of coral holobiont damage thresholds to stimulate research into coral health and immunity as tropical reefs are increasingly threatened by climate change. This framework may be used to develop targeted approaches to coral reef restoration, management and conservation.

Fackelmann et al. study the gut microbial composition of spiny rats across tropical forests in Panama with varying levels of protection and fragmentation in order to disentangle the relative influences of habitat fragmentation and anthropogenic disturbance on wildlife gut microbiomes. They find that habitat fragmentation on its own did not affect the gut microbiome, but the microbiomes of individuals inhabiting forest fragments affected by anthropogenic disturbance displayed a shift in community composition and structure, and were more likely to have microbiota associated with domesticated animals and their pathogens.

Ben Harvey et al. use the gradient provided by a natural CO₂ seep off Shikine Island, Japan and lab microcosm experiments to determine how ocean acidification promotes turf algal habitat conditions that create stabilizing feedback loops and hysteresis capable of locking turf systems in place. These results further our understanding of feedback loops initiated by ocean acidification, and can assist in the management of coastal habitats.

Corinaldesi et al. investigated the biological responses to microplastic contamination of the red coral Corallium rubrum, a genus with near global distribution. Microplastics caused feeding impairment, tissue damage, altered gene expression, oxidative DNA damage and microbiome alteration. Such diverse deleterious effects may be generalizable to other habitat-forming suspension and filter feeders given the burgeoning levels of microplastic contamination across the world’s oceans.

Manupriyam Dubey et al. use experimental systems with naturally derived soil microbiomes in liquid suspensions and encapsulated beads to compare community dynamics in well-connected and poorly connected environments. While their results show that microbial growth does not vary between conditions, they report that low connectivity led to reduced microbial diversity and suggest that these reductions in microbial diversity may be due to increased negative interspecific interactions.

William King, Caylon Yates, and colleagues utilize a 23-year-old common garden experiment to investigate how microbial filtering acts across root branching order. Their results demonstrate that roots of different orders have different microbial assemblages, and point to lower order roots as the main point of microbial interaction with fine roots.

Ian Ware et al. use reciprocal plant population by soil location feedback experiments to show how the soil microbiomes of the narrowleaf cottonwood are influenced by genetic and environmental variation, and how these factors affect foliar phenology. They find a landscape-level feedback between tree populations and their associated soil microbial counterparts. This study contributes to the understanding of the interplay between soil, climate, plant and microbial populations with climate warming.

MacKnight et al. compared the phenotypic and microbial responses of seven Caribbean coral species with diverse life-history strategies after exposure to white plague disease. The different species exhibited a spectrum of disease susceptibility and associated mortality that corresponded with their tolerances to microbial change, indicating that coral disease and microbial dysbiosis may ultimately shape reef ecosystems.

Silvia Acinas et al. report the Malaspina Gene Database, a gene catalogue from deep ocean microbes and the Malaspina Deep Metagenome-Assembled Genomes (MAGs) which is made publicly available. The analysis of the metabolic pathways within these MAGs sheds light on the composition and of the strategies these microbes use to survive the deep ocean microbiome.

Chrats Melkonian and colleagues use metagenomics and transcriptomics to study microbial dynamics in a 15-year old bioreactor. In contrast to what is expected in a system where benzene is the primary carbon and energy source, relatively few members of the microbial community can degrade this compound. The results have implications for understanding interdependencies within such a community.

Alneberg et al. conduct metagenomics binning of water samples collected over major environmental gradients in the Baltic Sea. They use machine-learning to predict the placement of genome clusters along niche gradients based on the content of functional genes.

Pedro R. Frade et al. analyze published bacterial data and environmental data from the eReefs platform to study bacterioplankton community dynamics across the Great Barrier Reef. They identify communities within inshore and outershelf reefs that are susceptible to nutrient and temperature changes, highlighting the importance of understanding microbial ecosystems dynamics informing reef health.

Yuya Sato et al. present de novo RNA sequencing of microbial communities from two activated sludge bioreactors that differ in their heavy-oil degradation performance. They find that the higher performing bioreactor showed higher expression of nitrification genes, even though nitrifiers represent a small minority of the community.

Michael Ochsenkühn et al. look at the microbial and metabolic composition of coral surfaces and the surrounding seawater. They find that the metabolites found on the surface of the coral create a concentration gradient that influences the surrounding microbiome.

Araujo et al. investigate the soil microbiome across four major vegetation zones of the Brazilian Cerrado and find that protist taxon richness increases towards the tree-dominated climax vegetation. Their findings suggest that increased microbiome complexity might enhance system stability towards climax vegetation.

Simone Rampelli, Silvia Turroni and colleagues report ancient bacterial profiles of fecal sediments from four stratigraphic units of El Salt Middle Paleolithic site in Spain. The results of this study suggest a core human gut microbiome that could have been shared by Neanderthals and modern humans, and would pre-date the split between these two lineages.

Tahliyah S. Mims et al. investigate the influence of the gut mycobiome abundance and composition on host metabolism. Using mice from four different commercial suppliers they find that the gut mycobiome is shaped by diet, and that abundance and composition correlate with key metabolic features. In particular they find that Thermomyces and Saccharomyces species most strongly associate with weight gain.

Kim et al. show that several Streptococcus species improve the structure and barrier function of human skin. They find that Streptococcus-secreted spermidine accelerates the recovery of skin structure and barrier function by increasing collagen and lipid synthesis in aged cells. This study suggests the role of skin microbiome for anti-aging.

Diener, Hoge et al. show that a third of mice exhibit tolerance to a high dose of the β-lactam antibiotic cefoperazone, independent of antibiotic treatment duration or dietary phytochemical amendment. They find that non-responder microbiota upregulates antimicrobial tolerance genes and downregulates central metabolism without altering community composition or diversity, providing insights into the mechanisms of community-wide antibiotic tolerance.

Travis Sims and Molly El Alam et al. show that diversity of gut microbiota is associated with a favorable response to chemoradiation for cervical cancer and use flow cytometry to show that patients with high microbiome diversity had increased tumor infiltration of CD4+ lymphocytes as well as activated subsets of CD4 cells expressing ki67+ and CD69+ throughout radiation therapy. These results reveal how modulation of the gut microbiota could potentially be used to improve treatment efficacy and outcome.

Using a multi-omics platform, Mesnage et al present an extensive dataset that reports the effects of low-dose pesticides frequently detected in food on Sprague-Dawley rats. This study suggests potential metabolic biomarkers that may predict health risks from exposure to chemical pollutants.

Here, the authors designed a lipopeptide, Pam-3, based on an eight-amino acid carboxyl-terminal fragment of human β-defensin 1 with prominent antimicrobial activity against multidrug-resistant ESKAPE pathogens and antibiofilm properties. They show in mouse models, that Pam-3 selectively reduced acute intestinal Salmonella and established Citrobacter infections, without compromising the core microbiota.

Rong Xu, Renfei Lu, Tao Zhang, Qunfu Wu, and colleagues perform a longitudinal analysis of throat and gut microbiomes on adult COVID-19 patients. They find initially lower bacterial diversity in COVID-19 patients, but demonstrate a restoration of microbiome diversity throughout disease progression for patients with mild forms of the disease.

Through metagenomics and metatranscriptomics analyses, Calusinska et al. investigate the adaptation of the gut microbiome of the termite Cortaritermes sp. to a diet of Miscanthus grass. This work is a starting point for the identification of lignocellulose-degradation enzymes for potential biotechnology applications.

Chen et al. show that hippuric acid (HA), which is a diet-derived phenolic acid, inhibits bone resorption and increases bone mass in wild type mice, but not in G-protein coupled receptor (GPR109A) knockout mice. This study suggests that GPR109A mediates the effects of HA on inhibiting bone resorption during skeletal development.

Lv et al. associate the gut mycobiota with clinical features and the bacterial microbiota by comparing COVID-19 patients to those infected with H1N1 and healthy controls. They find that gut mycobiota dysbiosis occurs in both COVID-19 patients and those infected with H1N1 and that it does not improve until patients no longer require medical attention, providing insights into a better healthcare guideline.

Xing Wang et al. report a 1.2 Gb complete genome assembly of the earthworm Amynthas corticis and demonstrate that it is a triploid species. Gene family evolution, proteomic iTRAQ analysis, and 16 S rDNA sequencing demonstrate the evolution of adaptive defensive functions relative to other species in Annelida.

Yu et al. demonstrates the role of RSPO4, a Wnt signaling agonist, in liver fibrogenesis and its impact on the gut microbiome. By knocking out RSPO4 gene in fibrotic-liver rat model, they show that it relieved liver fibrosis in rats and restored the microflora composition, highlighting its potential in liver fibrosis treatment.

Jacob Rasmussen et al. use metagenomic analyses to examine the diversity of Mycoplasma species among three commonly-fished species of salmonids. Their results establish a phylogeny of candidate salmonid related Mycoplasma species and suggest a mutualistic relationship between these microbial species and salmon hosts.

Ericsson et al. show that different vendors (suppliers of mouse strains) harbor distinct microbiomes, which drive distinct behavioral phenotypes when the genetics are fixed. They specifically focus on changes relating to exploratory and anxiety-related behavior, physiological phenotypic parameters, glucose metabolism, and blood leukocytes. They conclude by emphasizing that supplier-origin fecal microbiomes represent potential sources of poor experimental reproducibility and suggest means to optimize experimentation with mice and their microbiomes.

Trabjerg et al. show that the activity of carnitine palmitoyl transferase 1 (CPT1) and lipid metabolism are associated with the disease progression of the SOD1 G93A mouse model mimicking a motor neuron disease Amyotrophic lateral sclerosis (ALS). This study suggests CPT1 as a potential therapeutic target in treating ALS.

Daisley et al. show that antibiotic treatment with oxytetracycline impairs the gut microbiota and immune system of honey bees, and reduces capped brood counts. They also show that supplementation with lactobacilli during antibiotic recovery can reverse the harmful effects of the antibiotic treatment. Their findings offer a simple microbial-based solution that aims to reduce honey bee disease burden, environmental pollution by xenobiotics, and spread of antimicrobial resistance.

Ishida et al. investigated genome-wide associations between 1068 healthy Japanese adults and their gut microbiota. They find that five loci account for a small variation of the human gut microbiota composition and that six genera are heritable. This study suggests that human gut microbiota composition is likely to be affected by multiple genetic loci.

Osakunor et al. show that infection of Zimbabwean preschool-aged children with Schistosoma haematobium correlates with abundance changes in Pseudomonas, Stenotrophomonas, Derxia, Thalassospira, Aspergillus, Tricholoma, Periglandula, and Azospirillum. This study provides a microbiome and resistome dataset of African preschool-aged children.

Kevin Neil et al. quantified horizontal gene transfer rates for 13 conjugative plasmids in the mouse gut microbiota to identify those that might be useful for developing microbiome editing technologies. They find that the Incl-family plasmid TP114 has a nearly 100% transfer efficiency in the mouse gut.

Feng et al. show that colonization of mice with Pediococcus acidilactici strain BT36 reduces chromate accumulation in the liver, which is associated with changes in expression of a Cr(VI)-resistance gene in the gut microbiota. This study suggests that BT36 regulates the gut microbiota in response to chrome exposure, protecting mice against chromate toxicity.

Hans Jonsson et al. report the metagenomic reconstruction of the genome of a potentially immune modulatory segmented filamentous bacteria (SFB) from a human ileostomy sample. They demonstrate that the genome clusters closely with SFB genomes from other species. They also detect the unique SFB variant in human faecal metagenomics datasets.

Aluthge et al. evaluated the establishment of human fecal bacterial communities in human microbiota-associated (HMA) piglet and mouse models under identical dietary conditions. They find that human fecal bacterial communities from mature microbiotas establish more successfully in the HMA porcine model than mice, suggesting the broader applicability of the piglet model for human microbiome studies.

Feng et al. show that oxidized fish oil exacerbates alcoholic liver injury in mice by enhancing intestinal dysbiosis, barrier dysfunction, and hepatic inflammation that is mediated by gut-derived endotoxin. This study suggests that n-3 polyunsaturated fatty acids enriched in fish oil should be kept from oxidation to exert their health benefits.

Kanakaraju Kaliannan et al. show that converting omega-6 polyunsaturated fatty acids (n-6 PUFA) to omega-3 polyunsaturated fatty acids (n-3 PUFA) improves overall metabolism in mice, lowering risks for liver cancer. This study suggests the importance of keeping the tissue level of n-3 PUFA comparable to that of n-6 PUFA in preventing metabolic diseases.

Juan Feng et al. show that hawk tea extract reduces cholesterol by suppressing Niemann-Pick C1 like 1-mediated free cholesterol uptake and decreasing the production of very low-density lipoprotein through hepatocyte nuclear factor 4 alpha. This study suggests a therapeutic potential of hawk tea extract for hypercholesterolemia.

Zhen Zhang, Chao Ran et al. show that whether or not polysaccharides injure the liver depends on their ability to keep endotoxin-bearing bacteria at bay and induce antimicrobial peptide (AMP) expression in zebrafish. They suggest polysaccharides can protect the liver only when AMPs are induced through HIF1α.

Monica Tulstrup et al. show that antibiotic treatment of female rats during pregnancy leads to altered intestinal colonization in early life and lower body weight in adulthood. They find that this effect correlates with lower feed intake and increased expression of satiety hormone at weaning.

Simone Rampelli, Kathrin Guenther, and their colleagues discover correlations between pre-obese children’s low-diverse, dysbiotic microbiome configurations and their unhealthy diets. This study suggests that diet interventions may promote healthy adulthood by modulating the intestinal microbiota.

Nathan Dumont-Leblond et al. present a protocol for lung microbiota analysis, including all steps from patient recruitment to bioinformatics. The data show how methodological variation, such as use of different DNA extraction kits, can impact the results and represent an important step toward methods standardization in the pulmonary microbiome field.

Jurburg et al. explored the discrepancies between reported and actual availability of archived 16S rRNA sequencing data in the microbial literature. They identify that only a small portion of archived datasets can be reliably accessed and used by researchers.

Shashank Gupta, Martin Mortensen et al. compare the diagnostic efficiency of culturing and amplicon sequencing for studying the human microbiome. They show that amplicon sequencing identifies a greater number of species per sample, and can be implemented in clinical settings.