Microbiome Diversity Research Articles

Health-Improving Effects of Polyphenols on the Human Intestinal Microbiota: A Review

Dietary polyphenols are garnering attention in the scientific community due to their potential health-beneficial properties and preventative effects against chronic diseases, viz. cardiovascular diseases, diabetes, obesity, and neurodegenerative diseases. Polyphenols are antioxidants that change microbial composition by suppressing pathogenic bacteria and stimulating beneficial bacteria. The interaction of polyphenols with dietary fibers affects their bioaccessibility in the upper and lower parts of the digestive tract. Dietary fibers, polyphenols, their conjugates, and their metabolites modulate microbiome population and diversity. Consuming polyphenol-rich dietary fibers such as pomegranate, cranberry, berries, and tea improves gut health. A complex relationship exists between polyphenol-rich diets and gut microbiota for functioning in human health. In this review, we provide an overview of the interactions of dietary polyphenols, fibers, and gut microbiota, improving the understanding of the functional properties of dietary polyphenols.

Impact of host physiology and external stressors on the bacterial community of Schmidtea mediterranea

Abstract To fully comprehend host-microorganism interactions, it is crucial to understand the composition and diversity of the microbiome, as well as the factors that shape these characteristics. We investigated microbiome variation using the freshwater planarian Schmidtea mediterranea, an invertebrate model in regeneration biology and (eco-)toxicology, by exposing the organisms to various controlled conditions. The microbiome composition exhibited high variability, with most of the bacteria belonging to the Betaproteobacteria. Among the diverse microbial communities, a few genera, such as Curvibacter, were consistently present, but exhibited significant alterations in response to changing conditions. The relative abundance of Curvibacter fluctuated during the regeneration process, initially increasing before returning to a composition similar to the beginning situation. After applying external stress, the relative abundance of Curvibacter and other genera decreased. Variation over time, between different origin laboratories and between individuals, showed that additional, yet to-be-identified, factors of variation are present. Taking all results together, our study provides a solid basis for future research focusing on bacterial functionality in planarians and other invertebrates.

Profiling the diversity of the village chicken faecal microbiota using 16S rRNA gene and metagenomic sequencing data to reveal patterns of gut microbiome signatures

IntroductionThe production environment of extensively raised village chickens necessitates their adaptability to low-resource systems. The gut microbiome plays a critical role in supporting this adaptability by influencing health and productivity. This study aimed to investigate the diversity and functional capacities of the faecal microbiome in village chickens from Limpopo and KwaZulu-Natal provinces of South Africa.MethodsUsing a combination of 16S rRNA gene sequencing and shotgun metagenomic sequencing technologies, we analysed 98 16S rRNA and 72 metagenomic datasets. Taxonomic profiles and functional gene annotations were derived, focusing on microbial diversity, antibiotic resistance genes (ARGs), and potential zoonotic pathogens.ResultsTaxonomic analysis showed that the predominant phyla in both provinces were Firmicutes, Bacteroidota, Proteobacteria, and Actinobacteria. At the genus level, Escherichia and Shigella were prevalent, with Escherichia coli and Shigella dysenteriae identified as major contributors to the gut microbiome. ARGs were identified, with MarA, PmrF, and AcrE detected in KwaZulu-Natal, and cpxA, mdtG, and TolA in Limpopo. These genes primarily mediate antibiotic efflux and alteration.DiscussionThe detection of zoonotic bacteria such as Escherichia coli and Streptococcus spp. highlights potential health risks to humans through the food chain, emphasizing the importance of improved household hygiene practices. This study underscores the role of the gut microbiome in village chicken health and adaptability, linking microbial diversity to production efficiency in low-resource settings. Targeted interventions and further research are crucial for mitigating zoonotic risks and enhancing sustainability in village chicken farming.

Multi‐omics reveals different signatures of obesity‐prone and obesity‐resistant mice

AbstractObesity‐prone (OP) and obesity‐resistant (OR) individuals demonstrate significant metabolic differences, potentially influenced by variations in the gut microbiome. However, the influence of host–microbiota interactions on obesity susceptibility remains unknown. We performed an integrative multi‐omics approach to explore microbial, metabolic, and genetic differences in high‐fat diet (HFD)‐fed OP and OR mice, with additional analyses of gut microbiota variations in humans. In OP mice, the dynamic gut microbiota was characterized by a stable presence of Longibaculum, while Kineothrix predominated in OR mice. We termed both as keystone bacteria. Beyond these, eight dominant bacterial genera were significantly associated with bile acid metabolites and amino acids. Three of these genera were also identified in OR humans and showed positive correlations with genes that may support intestinal barrier function. We identified 22 specific amino acid profiles as potential biomarkers for obesity susceptibility, along with significantly increased levels of ten non‐12‐OH bile acids in fecal of OR mice. In vivo, mouse experiments demonstrated that ursodeoxycholic and hyodeoxycholic acids could reduce HFD‐induced obesity. Additionally, the colon of OP mice displayed a higher presence of inflammatory cells. These findings suggest that host–microbiota interactions may contribute to phenotypic differences between OP and OR. Our study offers insights into crucial intestinal markers associated with obesity, providing a valuable resource for advancing the understanding of obesity‐prone and obesity‐resistant phenotypes.

Urinary bacteriophage cooperation with bacterial pathogens during human urinary tract infections supports lysogenic phage therapy.

Despite much promise in overcoming drug-resistant infections, clinical studies of bacteriophage antibacterial therapy have failed to show durable effectiveness. Although lysogeny plays an important role in bacterial physiology, its significance in diverse microbiomes remains unclear. Here, we tested the following hypotheses: 1) urinary microbiome phage populations switch to a higher relative proportion of temperate phages, and 2) the activity of the phage recombination machinery (integration/excision/transposition) is higher during human urinary tract infections (UTIs) than in non-infected urinary tracts. Using human urine, model organisms, mass spectrometry, gene expression analysis, and the phage phenotype prediction model BACPHLIP, the results corroborated our hypotheses at the functional protein and gene levels. From a human health perspective, these data suggest that temperate phages may facilitate bacterial infections rather than function as protective agents. These findings support the use of lysogenic phages as therapeutic Trojan Horses.

Exploring single cell microbial protein as a sustainable fishmeal alternative in yellowtail kingfish (Seriola lalandi) diets: impacts on health and gut microbiome

BackgroundWith the global expansion of aquaculture and the increasing demand for fish meal, identifying appropriate and sustainable alternative protein sources for aquafeeds has become essential. Single-cell protein (SCP), derived from methanotrophic bacteria, presents a promising alternative by converting methane into protein, potentially addressing both the need for alternative protein sources and reducing industrial greenhouse gas emissions. This study aimed to evaluate the effects of different levels of SCP inclusion (0%, 25%, 50%, and 75% fish meal replacement) on the health, gene expression, and gut microbiome of yellowtail kingfish (YTK, Seriola lalandi) following a 35-day growth trial.ResultsThe study found that SCP inclusion at the highest level of fishmeal replacement (75%) induced a mild inflammatory response in the hindgut of the fish. However, micromorphological assessments of the hindgut, serum biochemistry, and gene expression analyses revealed no significant detrimental effects from SCP replacement. Notably, there were indications of improved lipid digestibility with SCP. Furthermore, SCP inclusion significantly enhanced microbial richness and altered the composition of the gut microbiome, introducing beneficial bacterial taxa that may contribute to improved gut health and resilience.ConclusionsThis study highlights SCP as a viable and sustainable alternative to fish meal in YTK diets. The findings suggest that SCP can be included in YTK diets without adverse health effects at moderate levels and may even offer benefits in terms of lipid digestibility and gut microbiome diversity. These results contribute to the advancement of more sustainable aquaculture practices.

Biochar from crop residues mitigates N2O emissions and increases carbon content in tropical soils

AbstractThe application of biochar may offer a cost‐effective solution to decrease nitrous oxide (N2O) emissions in agriculture soils while having the potential to enhance soil carbon (C) accumulation. Biochar can be produced primarily from a range of agricultural and woody residual biomass, potentially resulting in biochar types with distinct properties. This study evaluated the effects of four different biochar types on soil N2O emissions, C storage, and diversity of the soil microbial community in a tropical environment. A greenhouse experiment with sugarcane plants was conducted with six treatments: soil only (CTR); soil + N fertilizer (NF); NF + sugarcane straw biochar (NF+SB); NF + sugarcane bagasse biochar (NF+BB); NF + Pinus residue biochar (NF+PB); and NF + eucalyptus residue biochar (NF+EB). Regardless of the origin of the feedstock, all biochar reduced the cumulative N2O emissions by 25% to 50% in comparison with the nitrogen‐fertilized treatment. Only NF+EB registered higher N2O emissions than NF+SB. The feedstock material also influenced the chemical properties of biochar, showing a negative correlation between oxidized functional groups and N2O emissions. Variations in the physicochemical properties of biochar did not affect soil C levels or microbial diversity, as all treatments with biochar presented similar results. All biochar types increased soil C levels, but only those derived from wood residues showed higher C content than CTR and NF. Despite biochar having no effects on overall soil microbiome diversity, the amendment tended to increase the abundance of Bacteroidetes and Proteobacteria, while suppressing the ammonia‐oxidizing phylum Thaumarchaeota. Biochar application had no significant effect on ammonium availability; however, it exhibited the capacity to retain nitrate. The application of biochar in tropical soils can therefore be considered a nature‐based solution to decrease N2O emissions and increase C levels without changing microbial diversity.

Microbial Changes Occurring During Oronasal Fistula Wound Healing

The oral microbiome is a complex community that matures with dental development and is recognized as a risk factor for systemic disease. Despite the oral cavity having a substantial microbial burden, healing of superficial oral wounds occurs quickly and with little scarring. By contrast, creation of an oro-nasal fistula (ONF), often occurring after surgery to correct a cleft palate, is a significant wound healing challenge. Methods: In this study, we characterized the changes in the oral microbiome of mice following a freshly inflicted wound in the oral palate that results in an open and unhealed ONF. Results: Creation of an ONF in mice significantly lowered oral microbiome alpha diversity, with concurrent blooms of Enterococcus faecalis, Staphylococcus lentus, and Staphylococcus xylosus in the oral cavity. Treatment with oral antibiotics one week before ONF infliction reduced microbiome alpha diversity and prevented E. faecalis, S. lentus, and S. xylosus blooms, but did not impact ONF healing. Conclusions: An ONF in the murine palate leads to a dysbiotic oral microbiome and a bloom of opportunistic pathogens that may prevent ONF healing. Delivery of therapeutics that accelerate ONF healing might restore oral microbiome diversity and inhibit blooms of opportunistic pathogens.

A Perspective on Lung Cancer and Lung Microbiome: Insight on Immunity.

Although the carcinogenic potential of microbes has long been recognized, their significance may have been underestimated. Currently, the connection between microbiota and cancer is under extensive research. The lung microbiota may serve as a proxy for the state of lung health based on its crucial role in preserving lung hemostasis. This review tried to outline the state of our understanding of the contribution of lung microbiome and lung cancer. A literature search was performed using PubMed, Google Scholar, and Scopus databases for recent research focusing on the development and possible pathogenesis of lung microbiome and lung cancer. Early research on lung cancer indicated that dysbiosis significantly impacted the development and spread of the tumor. As a result of these findings, the study of the lung microbiota as a possible therapeutic target and diagnostic marker has accelerated. Early-stage disease diagnostic biomarkers could be represented as microbiota profiles. Additionally, the microbiome is involved in anticancer therapy. There are limited studies on lung microbiota, and most microbiome studies commonly concentrate on the gut microbiota. A proper understanding of lung microbiota can have several potential therapeutic approaches. Therefore, more studies in this field may initiate remarkable advancements in microbiome-dependent treatment. Convincing data from studies on both humans and animals indicates that the microbiota might play a role in cancer initiation, influenced by internal and environmental factors of the host. Notably, the lung harbors its microbiome, as do lung cancers. In general view, it seems microbiome diversity in lung cancer patients is reduced. Meanwhile, some genera were increased in lung cancer patients in comparison with a noncancerous population (such as Streptococcus genus), and some of them were decreased (Granulicatella adiacens, G. adiacens). Furthermore, research on the microbiome-carcinogenesis relationship is still in its infancy, and much remains to be fully understood.

Alterations in gut microbiome in age- and diet-induced colorectal cancer (CRC) progression in a preclinical model.

223 Background: CRC is the third leading cause of cancer related deaths worldwide with age and diet among the strongest risk factors. Emerging evidence suggests gut microbiome plays important role in CRC and is highly impacted by the exposome primarily the food intake. Since diet and age plays an important role in gut microbiome diversity, the present study aimed to investigate the alterations in the gut microbiome in young versus old mice harboring CRC allografts and fed with different diets. Methods: Two cohorts of C57BL/6 including young (n = 9, age = 6 weeks) and old (n = 9, age = 20-24 months) mice were implanted with 1x10 6 MSI (microsatellite instable) CRC MC38 tumor cells. Mice in both cohorts were randomized into three different diet groups: normal diet (ND; standard chow), high-fat (HF) and calorie-restricted (CR: 30% reduction in total calories). Mice were housed individually under standard laboratory conditions. Mice fecal samples were collected and subjected to DNA isolation (ZymoBIOMICS-96 MagBead DNA Kit), followed by metagenomic shotgun and whole genome sequencing (ZymoBIOMICSe and Illumina NovaSeq, respectively). P ≤ 0.05 were considered as statistically significant. Results: Fecal microbiome analysis showed that old microbiome has higher alpha diversity compared to the young mice. No statistically significant differences in were found in microbiome diversities between the diet groups. Pairwise permanova results showed statistically significant differences between microbiomes of old vs. young groups ( P : 0.001), CR vs. HF groups ( P : 0.012) and HF vs. ND groups ( P : 0.021). ANCOM-BC analysis determined the differentiating features and microbial functional pathways in the young mice compared to the old mice group and in different diet groups with relative abundance differences of larger than log 10 2. Bacteroides thetaiotaomicron ( P : 1.43E-39) and Parabacteroides goldsteinii ( P : 2.20E-23) were enriched in young and old groups, respectively. Akkermansia muciniphila ( P : 0.008) was significantly enriched in ND compared to CR group. Lactococcus lactis ( P : 9.94E-160) and Lachnospiraceae bacterium A4 ( P : 4.95E-10) were significantly enriched in HF compared to ND diet groups and vice-versa, respectively. Among the functional pathways, CMP-legionaminate biosynthesis I ( P : 2.38E-13) and L-arginine biosynthesis IV (archaebacteria) ( P : 4.77E-11) were the most significantly enriched in young and old groups, respectively. Conclusions: Our findings highlight the differential diversity and microbial features of gut microbiome in age- and diet-induced CRC progression. Collectively, alteration in diet and age of the host lead to changes in gut microbiota which has a direct impact on activation of specific signaling pathways, metabolism and local and systemic immune responses, which may in turn affect chemosensitivity and outcome in CRC

Comparison of naturalization mouse model setups uncover distinct effects on intestinal mucosa depending on microbial experience

Abstract Introduction Concerns regarding the translational value of preclinical mouse models have been addressed by introducing various approaches of “naturalizing” research mice, which provide them with more diverse microbiomes and physiological immune responses. We have previously shown that “feralized” mice, i.e., inbred laboratory mice raised in a farmyard-like, microbe-rich environment exhibit a shifted gut microbiota, matured immunophenotype, and reduced severity of colorectal cancer. Similar studies occasionally involve co-housing with wild or pet-store-raised mice as microbial donors integrating species-specific commensals and pathogens. To what extent these different practices of microbial exposure are crucial for the resulting mouse phenotype remains unclear. Methods Here, we present the first side-by-side comparison of different methods to naturalize laboratory mice: co-housing with wild-caught house mice, feralization in a farmyard-like habitat only, or a combination of the two, with conventional clean laboratory mice as a reference. Results Independent of the method, the naturalized colon-mucosa microbiota was colonized by several Helicobacter species, and the colonic intestinal epithelial cells of naturalized mice displayed elevated expression of genes encoding antimicrobial peptides, mucus components, and reactive-oxygen-species-producing enzymes. They further showed significantly increased resident memory T cells in the colonic lamina propria and effector memory T cells in the mesenteric lymph nodes. The most pronounced changes of these parameters occurred in mice co-housed with wild-caught mice, while feralized mice displayed phenotypes that were intermediate between laboratory and co-housed mice. Conclusion These findings enhance our understanding of naturalization model setups and effects on the gut barrier and immune system, thereby aiding future decisions on the utilization of naturalized mouse models.

Dataset of shotgun metagenomic evaluation of Sorghum bicolor rhizosphere microbiome in soils preceded by Glycine max.

The dataset presents the microbial diversity, community structure, and functional potential of the rhizosphere microbiome associated with Sorghum bicolor in response to crop rotation involving a Glycine max precursor. Soil samples were collected from the rhizospheres of two Sorghum bicolor cultivars, Avenger and NS55, cultivated in soils previously used for Glycine max and cultivated in soils that have not previously been used for Glycine max cultivation, as follows: i) Sorghum bicolor Avenger (SA1, SA2, and SA3) cultivated in soils previously used for Glycine max, ii) Sorghum bicolor NS55 (SN1, SN2, and SN3) grown in soils that had been cultivated with Glycine max, iii) Sorghum bicolor Avenger (RA1, RA2, and RA3) cultivated in soils not previously used for Glycine max, iv) Sorghum bicolor NS55 (RN1, RN2, and RN3) grown in soils not previously cultivated with Glycine max. Thereafter, the shotgun sequencing was done to assess the microbial composition and functional genes from the extracted DNA. The effective metagenome after QC of the twelve samples include SA1 (99.72%), SA2 (99.50%), SA3 (99.68%), SN1 (99.75%), SN2 (99.76%), SN3 (99.70%), RA1 (99.72%), RA2 (99.77%), RN3 (99.72%), RN1 (99.67%), RN2 (99.68%), and RN3 (99.54%). Information from the metagenome sequences is accessible under the bioproject numbers PRJNA1166458 (SA1, SA2, and SA3), PRJNA1166463 (SN1, SN2, and SN3), PRJNA1166623 (RA1, RA2, and RA3), PRJNA1166627 (RN1, RN2 and RN3). Actinomycetota and Function unknown dominated the microbiomes across all cropping systems. The insights gained from this dataset hold promise for advancing sustainable agricultural practices, particularly through optimizing crop rotations, developing microbial bioinoculants, and enhancing soil health. Furthermore, the functional data and the function unknown from this dataset could enrich our understanding of microbial roles in nutrient cycling, plant growth promotion, and stress mitigation, which are critical for addressing challenges in food security and environmental sustainability.

A prospective multi-site translational study investigating the association of gut microbiome (GM) diversity with pathological complete response (pCR) after neoadjuvant treatment in early stage rectal and esophageal cancer.

TPS849 Background: The diversity of the GM is defined as the number and relative abundance distribution of distinct types of microorganisms colonizing within the gut. Studies have suggested that dysbiosis of the GM confers a predisposition to certain malignancies and impacts response to immunomodulating therapies. The influence of the GM diversity on the pathological response after neoadjuvant chemotherapy and radiotherapy is unclear. Some studies have suggested that the GM may offer predictive biomarkers for response to chemoradiation in rectal cancer. Other studies in early-stage rectal cancer patients indicated an association between GM diversity and pathological outcomes following neo-adjuvant therapy (NAT). We hypothesize that a more diverse GM constitution at baseline leads to an improved pathological response at the time of definitive surgery. Methods: We designed a cross-institutional translational study investigating the impact of the GM diversity on the efficacy of NAT in GI cancers by assessing its association with pathological response. The study population includes patients with early-stage rectal or esophageal cancer due to commence NAT (including chemotherapy and chemoradiation) who are planned for definitive surgery. Exclusion criteria includes prior allogenic tissue/solid organ transplantation and prior receipt of anti-cancer therapy. The study assessments include fecal sampling of the GM prior to NAT, upon completion and again six months post completion of therapy. Fecal samples are analysed by 16S RNA sequencing. Pathological response will be examined at time of surgery and patients will be classified as responders (complete pathological response) or non-responders. The primary endpoint of the study is to examine the association between the GM diversity and pathological response. Exploratory analysis will include the assessment of the association between cf-DNA and the GM diversity as well as an assessment of the association between cf-DNA at baseline and pCR. Species richness (Alpha Diversity) will be analysed using the Shannon diversity index and Jaccard similarity index will be used to calculate beta diversity. Following planned study recruitment, classification and clustering analysis will be performed with Principal Component Analysis (PCA) and Random Forest analysis. Logistic regression analysis adjusting for potential confounding factors will be employed to assess the primary endpoint of the association between GM and complete pCR in the final statistical analysis. Adjusted odds ratios (OR) and 95% confidence intervals will be presented. This trial accrued 11 patients between May 2023 and Sept 2024. Out of the 11 patients enrolled, 9 patients have undergone their planned surgery. We are expecting to have 30 patients accrued prior to Jan 2025.

Multi-omics analyses identify gut microbiota-fecal metabolites-brain-cognition pathways in the Alzheimer’s disease continuum

BackgroundGut microbiota dysbiosis is linked to Alzheimer’s disease (AD), but our understanding of the molecular and neuropathological bases underlying such association remains fragmentary.MethodsUsing 16S rDNA amplicon sequencing, untargeted metabolomics, and multi-modal magnetic resonance imaging, we examined group differences in gut microbiome, fecal metabolome, neuroimaging measures, and cognitive variables across 30 patients with AD, 75 individuals with mild cognitive impairment (MCI), and 61 healthy controls (HC). Furthermore, we assessed the associations between these multi-omics changes using correlation and mediation analyses.ResultsThere were significant group differences in gut microbial composition, which were driven by 8 microbial taxa (e.g., Staphylococcus and Bacillus) exhibiting a progressive increase in relative abundance from HC to MCI to AD, and 2 taxa (e.g., Anaerostipes) showing a gradual decrease. 26 fecal metabolites (e.g., Arachidonic, Adrenic, and Lithocholic acids) exhibited a progressive increase from HC to MCI to AD. We also observed progressive gray matter atrophy in broadly distributed gray matter regions and gradual micro-structural integrity damage in widespread white matter tracts along the AD continuum. Integration of these multi-omics changes revealed significant associations between microbiota, metabolites, neuroimaging, and cognition. More importantly, we identified two potential mediation pathways: (1) microbiota → metabolites → neuroimaging → cognition, and (2) microbiota → metabolites → cognition.ConclusionAside from elucidating the underlying mechanism whereby gut microbiota dysbiosis is linked to AD, our findings may contribute to groundwork for future interventions targeting the microbiota-metabolites-brain-cognition pathways as a therapeutic strategy in the AD continuum.

Synergism of 2′-FL and Lactobacillus plantarum 1.0642 on gut microbiome diversity and functionality in constipated mice: A metagenomic analysis

Synergism of 2′-FL and Lactobacillus plantarum 1.0642 on gut microbiome diversity and functionality in constipated mice: A metagenomic analysis

Oral microbiome alpha diversity and all-cause, cardiovascular, and non-cardiovascular mortality in US adults: Evidence from the NHANES 2009-2019

Knowledge about the association between oral microbiome diversity within individuals and cardiovascular disease (CVD) and non-CVD mortality is scarce. Besides, variation by sex and racial and ethnic groups, and the potential mediators of these associations remain unclear. We aimed to investigate the associations of oral microbiome alpha diversity with all-cause, CVD, and non-CVD mortality, and the interaction effects of sex and racial and ethnic groups and potential mediators in the associations. The National Health and Nutrition Examination Survey (NHANES) is a population-based observational study, conducted periodically in Mexican American, Other Hispanic, Non-Hispanic (NH) White, NH Black, and other racial/ethnic participants. We linked 2009-12 survey data of 8199 adults to the mortality data until 2019. By analyzing RNA gene sequences from oral rinse samples, microbiome alpha diversity within individuals was assessed using operational taxonomic unit (OTU) richness. Potential mediators included obesity, diabetes mellitus, dyslipidemia, hypertension, and periodontitis. Multivariable Cox proportional hazards regression and causal mediation analysis were used. Baseline mean±standard deviation (SD) age was 42.1±15.1 years. Over a median follow-up of 9.1 years, 405 all-cause mortality occurred (CVD, 105; non-CVD, 300). Each 1-SD increment in OTU richness was inversely associated with all-cause mortality (hazard ratio [HR] 0.92, 95% confidence interval [CI] 0.90-0.95), CVD mortality (HR, 0.92; 95% CI, 0.90-0.95), and non-CVD mortality (HR, 0.92; 95% CI, 0.90-0.95). With evidence of significant racial and ethnic groups-interaction (p <0.05), these associations were evident in Mexican American, NH White, and others racial/ethnic participants. None of the potential mediators significantly mediated the associations of OTU richness with all-cause, CVD, and non-CVD mortality. Lower oral microbiome alpha diversity is associated with higher risk for all-cause, CVD, and non-CVD mortality, and the associations are varied by racial and ethnic groups.

Why Didn't the Sifaka Cross the Road? Divergence of Propithecus edwardsi Gut Microbiomes Across Geographic Barriers in Ranomafana National Park, Madagascar.

This study uses a biogeographic framework to identify patterns of gut microbiome divergence in an endangered lemur species endemic to Madagascar's southeastern rainforests, the Milne-Edwards's sifaka (Propithecus edwardsi). Specifically, we tested the effects of (1) geographic barriers, (2) habitat disturbance, and (3) geographic distance on gut microbiome alpha and beta diversity. We selected 10 social groups from 4 sites in Ranomafana National Park with varied histories of selective logging. Sites were spaced between 4 and 17 km apart falling on either side of two parallel barriers to animal movement: the Namorona River and the RN25 highway. Using 16S rRNA metabarcoding, we found the greatest beta diversity differentiation to occur between social groups, with significant divisions on opposite sides of geographic barriers (road/river). Habitat disturbance had the most significant effect on alpha diversity, though, contrary to many other studies, disturbance was associated with higher microbial species richness. Without biomedical context, it is unclear whether microbiome differences observed herein are neutral, adaptive, or maladaptive. However, microbiome divergence associated with the road/river may be a symptom of reduced host gene flow, warranting further investigation and perhaps conservation action (e.g., construction of wildlife bridges). Finally, this work demonstrates that significant microbiome variation can accrue over small sampling areas, lending new insight into host-microbe-environmental interactions.

Microbiome characterization of two fresh pork cuts during production in a pork fabrication facility.

The goal of this study was to characterize the microbial profile of two different fresh pork cuts, bootjack (BJ) trim and tenderloin (TL), through a 16S rRNA sequencing workflow developed specifically for investigating low-biomass fresh meat within a commercial production schedule. Additionally, this study aimed to determine a baseline Salmonella prevalence and enumeration profile across these two fresh pork cuts. Results showed that microbiome diversity was different between the BJ and TL, and also differed significantly by processing date. The relative abundance of key bacterial genera associated with food safety and spoilage was also different between the two meat types. However, over the course of the production shift, changes in the meat microbiome were limited in both the BJ and TL. The crude prevalence and enumerated burden of Salmonella were lower than what has been previously reported in similar fresh pork cuts, and all of the Salmonella-positive samples occurred on just two processing windows of 1-2 days each. Taken together, the results of this study suggest that the microbial profile of two fresh pork cuts is significantly different even within the same plant at the same time points, and that day-to-day variability within the production process likely influences both the fresh pork microbiome and Salmonella profile of these two meat types.IMPORTANCEModern pork processing involves a series of processes that begin with the handling and transport of the live animals, proceed through harvest and fabrication, and end with the packaging and distribution of fresh pork to the consumer. Each step in this process can alter the microbial community of fresh pork and influence the meat's safety and shelf life. However, little is known about the microbial ecology of individual, unprocessed pork cuts and if the diversity of the meat microbiome remains consistent throughout a production schedule. Additionally, the crude prevalence and enumeration of Salmonella have not been well established for individual fresh pork cuts throughout a production schedule. A more thorough understanding of the microbial profile at different stages of pork production will help processors determine processing steps that impact the microbial characteristics of fresh pork. This insight will help processors implement targeted intervention strategies to enhance food safety and quality.

Microbiome metabolic capacity is buffered against phylotype losses by functional redundancy.

Diet can affect gut microbiome taxonomic composition and diversity, but its impacts on community-level functional capabilities are less clear. Host health and fitness are increasingly being linked to microbiome composition and further modeling of the relationship between microbiome taxonomic and metabolic functional capability is needed to inform these linkages. Invertebrate animal models like the omnivorous American cockroach are ideal for this inquiry because they are amenable to various diets and provide high replicates per treatment at low costs and thus enabling rigorous statistical analyses and hypothesis testing. Microbiome taxonomic composition is diet-labile and diversity was reduced after feeding on unbalanced diets (i.e., post-treatment), but the predicted functional capacities of the post-treatment microbiomes were less affected likely due to the resilience of several abundant taxa surviving the perturbation as well as many metabolic functions being shared by several taxa. These results suggest that both taxonomic and functional profiles should be considered when attempting to infer how perturbations are altering gut microbiome services and possible host outcomes.

P-2215. Intestinal microbiome and metabolome fluctuations in patients receiving intensive chemotherapy for AML: Results from a pilot, prospective observational study

Abstract Background Loss of a diverse intestinal microbiome, particularly through the depletion of anaerobic bacteria, is associated with poor outcomes in people undergoing treatment for leukemia. We present preliminary results from a pilot, prospective observational study characterizing longitudinal changes in the fecal microbiome and metabolome in patients undergoing intensive chemotherapy for newly diagnosed acute myeloid leukemia (AML). Methods We recruited 10 patients with newly diagnosed AML who were hospitalized for intensive chemotherapy. The subjects underwent daily serum and stool collections during the admission for induction chemotherapy and periodic serum and stool collections during subsequent admissions. Metabolome profiling was conducted by targeted GC- and LC-mass spectrometry of serum and stool specimens, and fecal microbiome composition was determined by Shotgun metagenomic sequencing. Clinical characteristics, including responses to chemotherapy and development of infections, were monitored. Results Metagenomic sequencing demonstrated marked variations in microbiome compositions between patients in our cohort. However, microbiome compositions and diversities remained stable within patients who maintained a higher prevalence of obligate anaerobes belonging to the Lachnospiraceae and Bacteroidaceae families. Moreover, despite stable microbiome compositions, we detected large fluctuations in fecal metabolite concentrations, particularly among secondary bile acids and conjugated and unconjugated bile acids, over the course of induction chemotherapy. Our results suggest that preservation of intestinal anaerobes enhances the stability of the microbiome over time, and the metabolic output of an individual’s microbiome is substantially impacted during cancer treatment. Conclusion Studying dynamics of the intestinal microbiome and metabolome during cancer therapy will help identify signals associated with microbiome diversity or disruption. We also plan to use broad targeted and untargeted platforms to identify metabolites in stool or serum that can be used as biomarkers to correlate with microbiome compositions and to identify patients who are at risk for adverse clinical outcomes associated with disrupted microbiomes. Disclosures All Authors: No reported disclosures