Members Of Microbiome Research Articles

Carbohydrate-active enzymes from Akkermansia muciniphila break down mucin O-glycans to completion

Akkermansia muciniphila is a human microbial symbiont residing in the mucosal layer of the large intestine. Its main carbon source is the highly heterogeneous mucin glycoprotein, and it uses an array of carbohydrate-active enzymes and sulfatases to access this complex energy source. Here we describe the biochemical characterization of 54 glycoside hydrolases, 11 sulfatases and 1 polysaccharide lyase from A. muciniphila to provide a holistic understanding of their carbohydrate-degrading activities. This was achieved using a variety of liquid chromatography techniques, mass spectrometry, enzyme kinetics and thin-layer chromatography. These results are supported with A. muciniphila growth and whole-cell assays. We find that these enzymes can act synergistically to degrade the O-glycans on the mucin polypeptide to completion, down to the core N-acetylgalactosaime. In addition, these enzymes can break down human breast milk oligosaccharide, ganglioside and globoside glycan structures, showing their capacity to target a variety of host glycans. These data provide a resource to understand the full degradative capability of the gut microbiome member A. muciniphila.

BT1549 coordinates the in vitro IL-10 inducing activity of Bacteroides thetaiotaomicron.

Intestinal homeostasis requires the establishment of peaceful interactions between the gut microbiome and the intestinal immune system. Members of the gut microbiome, like the symbiont Bacteroides thetaiotaomicron, actively induce anti-inflammatory immune responses to maintain mutualistic relationships with the host. Despite the importance of such interactions, the specific microbial factors responsible remain largely unknown. Here, we show that B. thetaiotaomicron, which stimulates Toll-like receptor 2 (TLR2) to drive IL-10 production, can stimulate TLR2 independently of TLR1 or TLR6, the two known TLR that can form heterodimers with TLR2 to mediate TLR2-dependent responses. Furthermore, we show that IL-10 induction is likely mediated by a protease-resistant or non-proteogenic factor, and that this requires gene BT1549, a predicted secreted lipoprotein and peptidase. Collectively, our work provides insight into the molecular dialog through which B. thetaiotaomicron coordinates anti-inflammatory immune responses. This knowledge may facilitate future strategies to promote such responses for therapeutic purposes.

Gut phages and their interactions with bacterial and mammalian hosts.

The mammalian gut microbiome is a dense and diverse community of microorganisms that reside in the distal gastrointestinal tract. In recent decades, the bacterial members of the gut microbiome have been the subject of intense research. Less well studied is the large community of bacteriophages that reside in the gut, which number in the billions of viral particles per gram of feces, and consist of considerable unknown viral "dark matter." This community of gut-residing bacteriophages, called the gut "phageome," plays a central role in the gut microbiome through predation and transformation of native gut bacteria, and through interactions with their mammalian hosts. In this review, we will summarize what is known about the composition and origins of the gut phageome, as well as its role in microbiome homeostasis and host health. Furthermore, we will outline the interactions of gut phages with their bacterial and mammalian hosts, and plot a course for the mechanistic study of these systems.

P0149 Deep functional analysis of a defined sulphide-reducing diet (4-SURE diet) as a novel therapy for ulcerative colitis (UC) demonstrates all specific luminal micro environmental objectives were achieved

Abstract Background As a dietary approach to reducing inflammation in ulcerative colitis (UC), the 4-SURE diet was designed to correct pathogenic alterations of excessive protein fermentation and hydrogen sulphide (H2S) production in the distal colon. Specific dietary objectives were achieved (Day et al,J Nutr 2022;152:1690) but it is uncertain whether mechanistic objectives could be achieved with 8 weeks of diet. Therefore, we aimed to perform a deep functional analysis (microbial and metabolomic) of the faeces. Methods Faecal samples of 28 adults with mild-moderately active UC were collected at week 0 and 8 of diet intervention, subsampled and stored at−80 °C. Shotgun metagenomic sequencing was used to identify genes involved in H2S metabolism. Metagenomic reads were trimmed, reads mapping to the human genome removed. Gene identification was performed using Diamond v2.1.9 for alignment against a database of genes involved in global sulphur cycling. Gas-chromatography mass-spectrometry was used to characterise volatile organic compounds (VOCs) with specific analysis of products of protein fermentation. Microbiota capacity to produce H2S was assessed by anaerobic incubation of homogenates followed by spectrophotometric determination of total H2S production. Results Majority of microbiome members belonged to the Bacteroidota and Bacillota phyla, with no significant difference in bacterial diversity determined between time points (p=0.16). However, using a Random Forest Classifier, known H2S producers, Odoribacter and Peptostreptococcaceae, were identified as the most important taxa in discriminating between pre and post-diet samples, with abundances markedly lower after diet intervention. A shift in microbiota metagenomic profiles putatively involved in H2S metabolism was identified post-diet, with differences (p<0.05, Wilcoxon signed-rank with Benjamini-Hochberg correction) in 12 of 23 analysed genes involved in H2S cycling determined, including iscS, cysK (Fig), metC, luxS, asrC and sseA. 173 faecal VOCs were identified across all samples. Indole (a specific marker of protein fermentation) decreased from 0.42 [-0.25,0.61] at week 0 to -0.28 [-0.77,0.48] at week 8 (p=0.007, FDR correction; Fig). Faecal H2S reduced from median 2.61 (interquartile range 2–4.96)µmol to 1.41 (0.81-2.27)µmol of H2S/g stool (wet weight)(p=0.002)(Fig). Conclusion Deep functional analysis of the faeces demonstrated the micro-environmental objectives of the 4-SURE diet successfully reduced protein fermentation, changed microbial community sulphur-metabolic gene profile and reduced H2S production ex vivo. Applying functional analysis to a diet study is novel, highlighting exemplar framework for including biomarkers of pathogenic relevance in analysis of therapeutic diets.

Vintage and terroir are the strongest determinants of grapevine carposphere microbiome in the viticultural zone of Drama, Greece.

The role of microbial terroir for enhancing the geographical origin of wines is well appreciated. Still, we lack a good understanding of the assembly mechanisms driving carposphere grapevine microbiota. We investigated the role of cultivar, vintage, terroir units (TUs) and vineyard geographic location on the composition of the carpospheric microbiota of three important cultivars in the viticultural zone of Drama, Greece using amplicon sequencing. Our strategy to define TUs based on georeferencing analysis allowed us to disentangle the effects of TU and vineyards geographic location, considered as a lumped factor in most studies to date. We hypothesized that: (i) these factors contribute differently on the assembly of the carposphere microbiome and that (ii) fungal and bacterial communities follow different assembly mechanisms. Vintage and TU were the stronger determinants of the carposphere fungal and bacterial communities, although the latter showed weaker response. The stronger effect of TU over vineyard geography and cultivar reinforces the role of microbial terroir in viticulture. We identified fungi (Cladosporium, Aureobasidium, Alternaria) and bacteria (Pseudomonas, Methylobacterium, Sphingomonadaceae) as main members of the core microbiome. These microorganisms were associated with specific cultivars and TUs, a feature that could be pursued towards a new microbiome-modulated paradigm of viticulture.

In vitro evolution of ciprofloxacin resistance in Neisseria commensals and derived mutation population dynamics in natural Neisseria populations.

Commensal Neisseria are members of a healthy human oropharyngeal microbiome; however, they also serve as a reservoir of antimicrobial resistance for their pathogenic relatives. Despite their known importance as sources of novel genetic variation for pathogens, we still do not understand the full suite of resistance mutations commensal species can harbor. Here, we use in vitro selection to assess the mutations that emerge in response to ciprofloxacin selection in commensal Neisseria by passaging 4 replicates of 4 different species in the presence of a selective antibiotic gradient for 20 days; then categorized derived mutations with whole genome sequencing. 10/16 selected cells lines across the 4 species evolved ciprofloxacin resistance (≥ 1 ug/ml); with resistance-contributing mutations primarily emerging in DNA gyrase subunit A and B (gyrA and gyrB), topoisomerase IV subunits C and E (parC and parE), and the multiple transferable efflux pump repressor (mtrR). Of note, these derived mutations appeared in the same loci responsible for ciprofloxacin reduced susceptibility in the pathogenic Neisseria, suggesting conserved mechanisms of resistance across the genus. Additionally, we tested for zoliflodacin cross-resistance in evolved strain lines and found 6 lineages with elevated zoliflodacin minimum inhibitory concentrations. Finally, to interrogate the likelihood of experimentally derived mutations emerging and contributing to resistance in natural Neisseria, we used a population-based approach and identified GyrA 91I as a substitution circulating within commensal Neisseria populations and ParC 85C in a single gonococcal isolate. A small cluster of gonococcal isolates shared commensal alleles at parE, suggesting recent cross-species recombination events.

Aeromonas isolation reveals this genus's contribution to antimicrobial resistance fluxes across the wastewater-treated water-river interface.

Aeromonas spp. are common members of water and wastewater microbiomes, but some are listed as opportunistic pathogens and are often reported to carry antimicrobial resistance (AMR) genes. We aimed to assess the performance of isolation media for capturing their distribution and their role in AMR dissemination into aquatic environments. We investigated the abundance, diversity, and AMR profile of Aeromonas isolates from wastewater and receiving water bodies at five municipal wastewater treatment plants in Denmark using three isolation media. This was then compared with the diversity estimated from community-wide 16S rRNA gene amplicon sequencing and resistance patterns inferred from high-throughput qPCR of resistance genes. Isolates from ampicillin sheep blood agar were the most phylogenetically diverse, but the overall Aeromonas recovery on the three media was similarly good and matched the dominant amplicon sequence variants. While the dominant phylotypes were ubiquitous, some types were only detected in treated wastewater and the receiving rivers. The resistance prevalence was moderate and mostly to beta-lactams and tetracyclines. Isolates resistant to piperacilin-tazobactam, cefepime, and tetracycline downstream of the plants were linked to wastewater origin. Overall, our work demonstrates Aeromonas and Aeromonas-mediated AMR fluxes at the wastewater/environment interfaces and provides methodological bases for monitoring aeromonads in wastewater and surface waters.

Mosquitoes Reared in Nearby Insectaries at the Same Institution Have Significantly Divergent Microbiomes.

The microbiome influences critical aspects of mosquito biology and variations in microbial composition can impact the outcomes of laboratory studies. To investigate how biotic and abiotic conditions in an insectary affect the composition of the mosquito microbiome, a single cohort of Aedes aegypti eggs was divided into three batches and transferred to three different climate-controlled insectaries within the Liverpool School of Tropical Medicine. The bacterial microbiome composition was compared as mosquitoes developed, the microbiome of the mosquitoes' food sources was characterised, environmental conditions over time in each insectary were measured, and mosquito development and survival were recorded. While developmental success was similar across all three insectaries, differences in microbiome composition were observed between mosquitoes from each insectary. Environmental conditions and bacterial input via food sources varied between insectaries, potentially contributing to the observed differences in microbiome composition. At both adult and larval stages, specific members of the mosquito microbiome were associated with particular insectaries; the insectary with less stable and cooler conditions resulted in a slower pupation rate and higher diversity of the larval microbiome. These findings underscore that even minor inconsistencies in rearing conditions can affect the composition of the mosquito microbiome, which may influence experimental outcomes.

Façade eluates affect active and total soil microbiome

The application of biocides in building materials has become a prevalent practice to mitigate the growth of microorganisms such as algae, fungi, and bacteria on the façades. These can leach out from the material and reach the nearby soil environment. This study aimed to characterize the effect of façade eluates generated within different leaching experiments on total and metabolic active soil microbial community composition and functions. Façade eluates were produced by immersion testing DIN EN 16105 and a natural weathering experiment. Afterward, soil microcosms were treated with the respective façade eluate and incubated for 29 days. Subsequently, the active and total soil microbial community compositions were investigated.Fungal internal transcribed spacer region gene and bacterial 16S rRNA gene were sequenced for active (bromodeoxyuridine labeled DNA) microbial community and total community. Façade eluates reduced total bacterial and fungal gene copy numbers. Overall, active bacterial and fungal richness was reduced and altered in community composition in comparison to the total richness and composition, respectively. Façade eluates retrieved of façade samples without biocides did alter the soil microbial communities to the same extent as façade eluates with biocides. Additionally, members of the active microbiome that benefit from the presence of façade eluates and omitted ones could be identified. Our result demonstrated that façade eluates affect active and total soil microbial community composition and function regardless of the leaching procedure and biocides addition.

The microbiome's influence on the neurobiology of opioid addiction and brain connectivity.

Opioids are the most effective and potent analgesics available for acute pain management. With no viable alternative for treating chronic or post operative pain, it is not surprising that over 10 million people misuse opioids. This study explores the developmental influence of the microbiome on resistance to opioid addictive behavior and functional connectivity. Female germ free reared (GFR) mice were compared to wild-type (WT) mice, before and after conventionalization using conditioned place preference (CPP) with oxycodone (OXY) exposure. Functional connectivity data were collected providing site-specific analysis for over 140 different brain areas. GFR mice showed significant reduction in CPP after OXY exposure. When GFR mice are conventionalized CPP reward behavior mirrors WT mice. Functional connectivity data shows significant differences across several brain regions e.g., thalamus, hippocampus, and sensory cortices between GFR and WT before and after conventionalization. Prior to conventionalization GFR mice showed hyperconnectivity that became less organized and more global after conventionalization. Sequencing of the fecal microbiome of the GFR mice before conventionalization showed an absence of normal murine gut microbiome members, but the presence of Corynebacterium, Staphylococcus, Paenibacillus, and Turicibacter. The implications suggest the microbiome has a direct impact on the development of reward seeking behavior. With the widespread number of opioid receptors found in the gut, studying the interaction between the microbiota and substance use disorder may lead to a better understanding of the mechanisms that lead to the development of addiction as well as potential treatments.

Salivary features of periodontitis and gingivitis in type 2 diabetes mellitus

Type 2 diabetes mellitus (T2DM) is associated with cellular abnormalities, tissue and organ dysfunctions, and periodontitis. This investigation examined the relationship between the oral microbiome and salivary biomarkers in T2DM patients with or without periodontitis. This cohort (35–80 years) included systemically healthy non-periodontitis (NP; n = 31), T2DM without periodontitis (DWoP; n = 32) and T2DM with periodontitis (DWP; n = 29). The oral microbiome [Operational Taxonomic Units (OTUs)] (16 s rRNA sequencing) and targeted host salivary biomarkers (immunoassays) were assessed. We identified 47 OTUs that were significantly different in abundance between NP samples and any disease subset or between disease subgroups. The most unique microbiome patterns were observed in the DWP group. Differences in genera/species abundance were also observed when T2DM patients were stratified by extent of periodontal inflammation and disease (i.e., generalized versus localized gingivitis/periodontitis). Salivary biomarkers showed significant elevations in MMP-8, MMP-9, resistin, IL-1β, IL-6, IFNα, and BAFF (THFSR13b) comparing generalized to localized periodontitis. Salivary analytes showed significant positive correlations with specific microbiome members, predominantly in DWP patients. Odds ratio analyses reinforced that a panel of biologic markers (IL-6, MMP-8) and bacteria (e.g., Bacteroidetes, Fusobacteria, Spirochaetes) discriminated the severity and extent of periodontal disease in this diabetic population.

The Gut Microbiomes of Wild Rodents within Forested Environments in Sarawak, Borneo

The gut microbiota of rodents is shaped by highly diverse bacterial communities. Within the gut environment, there are core gut bacteria that are responsible for facilitating essential bodily processes while maintaining the health of the host rodents. Currently, research on the gut microbiota of wild rodents in Borneo remains limited, especially those encompassing the potential influence of environmental factors. Through the Next-Generation Sequencing (NGS) performed using Oxford Nanopore Technologies, a total of 1052 bacterial genera were detected from 16 rodent individuals of six rodent species. These bacteria were found to be prevalent in the gut microbiota of wild rodents in forested regions. Several bacterial families of importance belonging to the phylum Bacillota were identified, including Lachnospiraceae (18%), Lactobacillaceae (20%) and Oscillospiraceae (19%). They were found to have a high relative abundance when compared with other bacterial families. The diversity of gut microbes among individual rodents showed no significant differences. However, the gut microbiome composition of wild rodents appears to have been influenced by the host species and their life stages. The outcome of this study allows for a better understanding of the prevailing core microbiome members shared across multiple wild rodent individuals within forested areas.

In vitro biofilm formation only partially predicts beneficial Pseudomonas fluorescens protection against rhizosphere pathogens.

Plant roots form associations with both beneficial and pathogenic soil microorganisms. While members of the rhizosphere microbiome can protect against pathogens, the mechanisms are poorly understood. We hypothesized that the ability to form a robust biofilm on the root surface is necessary for the exclusion of pathogens; however, it is not known if the same biofilm formation components required in vitro are necessary in vivo. Pseudomonas fluorescens WCS365 is a beneficial strain that is phylogenetically closely related to an opportunistic pathogen P. fluorescens N2C3 and confers robust protection against P. fluorescens N2C3 in the rhizosphere. We used this plant-mutualist-pathogen model to screen collections of P. fluorescens WCS365 increased attachment mutants (iam) and surface attachment defective (sad) transposon insertion mutants that form increased or decreased levels of biofilm on an abiotic surface, respectively. We found that while the P. fluorescens WCS365 mutants had altered biofilm formation in vitro, only a subset of these mutants, including those involved in large adhesion protein (Lap) biosynthesis, flagellin biosynthesis and O-antigen biosynthesis, lost protection against P. fluorescens N2C3. We found that the inability of P. fluorescens WCS365 mutants to grow in planta, and the inability to suppress pathogen growth, both partially contributed to loss of plant protection. We did not find a correlation between the extent of biofilm formed in vitro and pathogen protection in planta indicating that biofilm formation on abiotic surfaces may not fully predict pathogen exclusion in planta. Collectively, our work provides insights into mechanisms of biofilm formation and host colonization that shape the outcomes of host-microbe-pathogen interactions.

Eukaryotic composition across seasons and social groups in the gut microbiota of wild baboons.

Animals coexist with complex microbiota, including bacteria, viruses, and eukaryotes (e.g., fungi, protists, and helminths). While the composition of bacterial and viral components of animal microbiota are increasingly well understood, eukaryotic composition remains neglected. Here we characterized eukaryotic diversity in the microbiomes in wild baboons and tested the degree to which eukaryotic community composition was predicted by host social group membership, sex, age, and season of sample collection. We analyzed a total of 75 fecal samples collected between 2012 and 2014 from 73 wild baboons in the Amboseli ecosystem in Kenya. DNA from these samples was subjected to shotgun metagenomic sequencing, revealing members of the kingdoms Protista, Chromista, and Fungi in 90.7%, 46.7%, and 20.3% of samples, respectively. Social group membership explained 11.2% of the global diversity in gut eukaryotic species composition, but we did not detect statistically significant effect of season, host age, and host sex. Across samples, the most prevalent protists were Entamoeba coli (74.66% of samples), Enteromonas hominis (53.33% of samples), and Blastocystis subtype 3 (38.66% of samples), while the most prevalent fungi included Pichia manshurica (14.66% of samples), and Ogataea naganishii (6.66% of samples). Protista, Chromista, and Fungi are common members of the gut microbiome of wild baboons. More work on eukaryotic members of primate gut microbiota is essential for primate health monitoring and management strategies.

Affinity of Malassezia and Other Yeasts for Pulmonary Lipids

Pulmonary surfactant, the primary substance lining the epithelium of the human Lower Respiratory Tract (LRT), is rich in lipids, with dipalmitoyl-phosphatidylcholine (DPPC) being the most abundant. Although surfactants are known to have antifungal activity against some yeast species, the significant presence of species like Malassezia restricta in the lung mycobiome suggests that these yeasts may exhibit some level of lipo-tolerance or even lipo-affinity for pulmonary lipids. This study explored the affinity and tolerance of yeasts, identified as significant members of the lung microbiome, to pulmonary lipids through culture-based methods. Eleven species from the genera Malassezia, Candida (including the new genera Nakaseomyces and Meyerozyma), and Cryptococcus were tested for their growth on media containing pulmonary lipids such as DPPC and commercial porcine surfactant and in other culture medium that contain non-pulmonary lipids such as glycerol monostearate and tweens. The yeasts’ lipo-affinity or lipo-tolerance was assessed based on their growth on these lipids compared to standard media, specifically Modified Leeming Notman Agar (MLNA) for Malassezia species and Sabouraud Dextrose Agar (SDA) for the other genera. The addition of DPPC or surfactant to the media enhanced the growth of most Malassezia yeasts and some Cryptococcus species. C. parapsilosis, Meyerozyma guilliermondii and Cryptococcus neoformans s.s. showed similar growth to that on the standard media, while the other yeasts primarily demonstrated lipo-tolerance without lipo-affinity for these compounds. To our knowledge, this is the first report on the influence of pulmonary lipids on the in vitro growth of Malassezia spp. and other yeast members of the lung mycobiome. Some yeasts, such as Malassezia restricta, commonly found in the lower respiratory tract (LRT), exhibit specific affinity for lung lipids like DPPC and commercial porcine surfactant. This finding suggests that lung lipids may play a significant role in shaping the LRT mycobiome.

A framework for understanding collective microbiome metabolism.

Microbiome metabolism underlies numerous vital ecosystem functions. Individual microbiome members often perform partial catabolism of substrates or do not express all of the metabolic functions required for growth. Microbiome members can complement each other by exchanging metabolic intermediates and cellular building blocks to achieve a collective metabolism. We currently lack a mechanistic framework to explain why microbiome members adopt partial metabolism and how metabolic functions are distributed among them. Here we argue that natural selection for proteome efficiency-that is, performing essential metabolic fluxes at a minimal protein investment-explains partial metabolism of microbiome members, which underpins the collective metabolism of microbiomes. Using the carbon cycle as an example, we discuss motifs of collective metabolism, the conditions under which these motifs increase the proteome efficiency of individuals and the metabolic interactions they result in. In summary, we propose a mechanistic framework for how collective metabolic functions emerge from selection on individuals.

Structure and identification of the native PLP synthase complex from Methanosarcina acetivorans lysate.

Many protein-protein interactions behave differently in biochemically purified forms as compared to their in vivo states. As such, determining native protein structures may elucidate structural states previously unknown for even well-characterized proteins. Here, we apply the bottom-up structural proteomics method, cryoID, toward a model methanogenic archaeon. While they are keystone organisms in the global carbon cycle and active members of the human microbiome, there is a general lack of characterization of methanogen enzyme structure and function. Through the cryoID approach, we successfully reconstructed and identified the native Methanosarcina acetivorans pyridoxal 5'-phosphate (PLP) synthase (PdxS) complex directly from cryogenic electron microscopy (cryo-EM) images of fractionated cellular lysate. We found that the native PdxS complex exists as a homo-dodecamer of PdxS subunits, and the previously proposed supracomplex containing both the synthase (PdxS) and glutaminase (PdxT) was not observed in cellular lysate. Our structure shows that the native PdxS monomer fashions a single 8α/8β TIM-barrel domain, surrounded by seven additional helices to mediate solvent and interface contacts. A density is present at the active site in the cryo-EM map and is interpreted as ribose 5-phosphate. In addition to being the first reconstruction of the PdxS enzyme from a heterogeneous cellular sample, our results reveal a departure from previously published archaeal PdxS crystal structures, lacking the 37-amino-acid insertion present in these prior cases. This study demonstrates the potential of applying the cryoID workflow to capture native structural states at atomic resolution for archaeal systems, for which traditional biochemical sample preparation is nontrivial.IMPORTANCEArchaea are one of the three domains of life, classified as a phylogenetically distinct lineage. There is a paucity of known enzyme structures from organisms of this domain, and this is often exacerbated by characteristically difficult growth conditions and a lack of readily available molecular biology toolkits to study proteins in archaeal cells. As a result, there is a gap in knowledge concerning the mechanisms governing archaeal protein behavior and their impacts on both the environment and human health; case in point, the synthesis of the widely utilized cofactor pyridoxal 5'-phosphate (PLP; a vitamer of vitamin B6, which humans cannot produce). By leveraging the power of single-particle cryo-EM and map-to-primary sequence identification, we determine the native structure of PLP synthase from cellular lysate. Our workflow allows the (i) rapid examination of new or less characterized systems with minimal sample requirements and (ii) discovery of structural states inaccessible by recombinant expression.

The Parkinson’s disease drug entacapone disrupts gut microbiome homeostasis via iron sequestration

Many human-targeted drugs alter the gut microbiome, leading to implications for host health. However, the mechanisms underlying these effects are not well known. Here we combined quantitative microbiome profiling, long-read metagenomics, stable isotope probing and single-cell chemical imaging to investigate the impact of two widely prescribed drugs on the gut microbiome. Physiologically relevant concentrations of entacapone, a treatment for Parkinson’s disease, or loxapine succinate, used to treat schizophrenia, were incubated ex vivo with human faecal samples. Both drugs significantly impact microbial activity, more so than microbial abundance. Mechanistically, entacapone can complex and deplete available iron resulting in gut microbiome composition and function changes. Microbial growth can be rescued by replenishing levels of microbiota-accessible iron. Further, entacapone-induced iron starvation selected for iron-scavenging gut microbiome members encoding antimicrobial resistance and virulence genes. These findings reveal the impact of two under-investigated drugs on whole microbiomes and identify metal sequestration as a mechanism of drug-induced microbiome disturbance.

Extracellular Phosphate Modulation and Polyphosphate Accumulation by Corynebacterium matruchotii and Streptococcus mutans.

(1) Background: An alternative and understudied microbial mechanism that may influence demineralization is the microbially mediated ion exchange of Ca2+ and orthophosphate (Pi), which alters the saturation state of the mineral species within the surface enamel. There is a need to examine the ability of members of the oral microbiome to modulate Ca2+ and Pi, which control mineral solubility, in order to effectively evaluate mineralization therapies to improve oral health. (2) Methods: Pi uptake was measured using an ascorbic acid assay during a BHI liquid culture growth of Corynebacterium matruchotii and Streptococcus mutans for up to 20 h. The initial and endpoint medium Ca2+ levels were measured using ICP-OES. Bacterial cells were examined at different growth stages using DAPI/polyP binding emission at 525 nm to detect the presence of internalized macromolecules of polyphosphates (polyP) that could drive Pi uptake. (3) Results: C. matruchotii (p = 0.0061) substantially accumulated Pi (3.84 mmol/L), with a concomitant formation of polyP. In contrast, S. mutans did not take up Pi or accumulate polyP. No significant Ca2+ drawdown in the media was observed in either strain. (4) Conclusions: This study suggests that when examining the future efficacy of prevention technologies to improve, in vitro assays may consider including specific oral bacteria capable of substantial Pi uptake.

Bacterial and fungal components of the microbiome have distinct roles in Hawaiian drosophila reproduction.

The microbiome provides numerous physiological benefits for host animals. The role of bacterial members of microbiomes to host physiology is well-documented. However, much less is known about the contributions and interactions of fungal members, even though fungi are integral components of many microbiomes, including those of humans and insects. Here, we used antibacterial and antifungal drugs to manipulate the gut microbiome of a Hawaiian picture-wing Drosophila species, Drosophila grimshawi, and identified distinct effects for each treatment on microbiome community stability, reproduction, and lipid metabolism. Female oogenesis, fecundity, and mating drive were significantly diminished with antifungal treatment. In contrast, male fecundity was affected by antibacterial but not antifungal treatment. For males and females, simultaneous treatment with both antibacterial and antifungal drugs resulted in severely reduced fecundity and changes in fatty acid levels and composition. Microbial transplants using frass harvested from control flies partially restored microbiome composition and female fecundity. Overall, our results reveal that antibacterial and antifungal treatments have distinct effects on host fecundity, mating behavior, and lipid metabolism, and that interkingdom interactions contribute to microbial community stability and reproduction.