Alpha Abundance Research Articles

Baseline gut microbiome alpha diversity predicts chemotherapy-induced gastrointestinal symptoms in patients with breast cancer

Chemotherapy frequently causes debilitating gastrointestinal symptoms, which are inadequately managed by current treatments. Recent research indicates the gut microbiome plays a role in the pathogenesis of these symptoms. The current study aimed to identify pre-chemotherapy microbiome markers that predict gastrointestinal symptom severity after breast cancer chemotherapy. Fecal samples, blood, and gastrointestinal symptom scores were collected from 59 breast cancer patients before, during, and after chemotherapy. Lower pre-chemotherapy microbiome alpha diversity and abundance of specific microbes (e.g., Faecalibacterium) predicted greater chemotherapy-induced gastrointestinal symptoms. Notably, tumor and diet characteristics were associated with lower pre-chemotherapy alpha diversity. Lower baseline alpha diversity also predicted higher chemotherapy-induced microbiome disruption, which was positively associated with diarrhea symptoms. The results indicate certain cancer patients have lower microbiome diversity before chemotherapy, which is predictive of greater chemotherapy-induced gastrointestinal symptoms and a less resilient microbiome. These patients may be strong candidates for pre-chemotherapy microbiome-directed preventative interventions (e.g., diet change).

Gut Microbiota and Parkinson’s disease - a prospective analysis of the FINRISK 2002 Study

Abstract Background Parkinson’s disease (PD) is a neurodegenerative movement disorder with mainly unknown etiology. Constipation is a common symptom, and changes in gut microbiota may play role in PD pathogenesis. Previous studies exploring microbial associations to PD have been mostly cross-sectional, and the role of microorganisms in PD etiology remains unclear. Thus, we examined the association between microbiota features and incident PD in a prospective cohort design. Methods In the FINRISK 2002 Study, 7231 participants gave a stool sample that underwent shotgun metagenomic sequencing. Participants with missing stool sample, incomplete covariate data, pregnancy, antibiotic use, and prevalent cases were excluded (final n = 5562). Cox regression models, adjusted for age, sex, education, smoking, coffee consumption, diabetes, cardiovascular events, and constipation, were used to assess associations between incident PD and microbiota features, ie. alpha diversity (the number of different species present in a sample), beta diversity (the differences in microbial composition between individuals), and abundance of 381 core taxa (compositional detection rate of at least 0.1% and a prevalence of 1%). 120 incident cases of PD, identified through register linkage, occurred during a median follow-up of 17.8 years. Results In the multivariate models, PD incidence was not associated with the Shannon index, a measure on alpha diversity, (p-value 0.81), or with the ten first principal component axes in beta diversity analysis (p-values ranging between 0.49-0.91). In permutational analysis, PD did not explain differences in the composition of the gut microbiota (R2 <0.001, p-value 0.46)). None of the core species were associated with PD incidence (all FDR-corrected p-values > 0.05). Conclusions This prospective study showed no support for an association between gut microbiota features and incident PD. Key messages • Previous findings associating gut microbiota with PD may be due to the cross-sectional design, ie. PD affecting the gut microbiota. • Suggestions to screen gut bacteria to identify people at high risk of Parkinson’s disease are vastly premature as the scientific evidence is inconclusive.

Effect of fruits granola (Frugra®) consumption on blood pressure reduction and intestinal microbiome in patients undergoing hemodialysis

Cardiovascular diseases (CVDs) are a major cause of death in patients undergoing hemodialysis (HD). Blood pressure (BP) and uremic toxins are well-known risk factors for CVDs, which are influenced by diet. Dietary fiber supplementation in patients undergoing HD may reduce the risk of CVDs by improving lipid profiles and inflammatory status and lowering the levels of the uremic toxin indoxyl sulfate (IS). In this study, we investigated the relationship between the intestinal microbiota and risk factors for CVDs, such as BP and serum IS, in patients undergoing HD who consumed fruits granola (FGR). The study participants were selected from patients undergoing HD at the Izu Nagaoka Daiichi Clinic and consumed FGR for 2 months. Body composition and blood samples were tested at months 0, 1, 2 and fecal samples were collected at months 0 and 2 for intestinal microbiota analysis. FGR consumption decreased systolic and diastolic BP, estimated salt intake, and serum IS levels and improved the stool characteristics according to the Bristol Stool Form Scale (N = 24). Gut microbiota analysis showed an increase in the alpha diversity and abundance of Blautia and Neglecta. The abundance of lactic acid- and ethanol-producing bacteria also significantly increased, whereas the abundance of indole-producing bacteria significantly decreased. FGR consumption could be a useful tool for salt reduction, fiber supplementation, and improvement of the intestinal environment, thus contributing to improvement of BP and the reduction of other risk factors for CVDs in patients undergoing HD.

Tidal Impacts on Zooplankton Dynamics in a Major Ocean-Lagoon Channel: Insights from a 25-Hour Intensive Survey in the Cotonou Channel, Benin

This study investigates the effects of tidal cycles on the zooplankton community within the Cotonou Channel, an important waterway connecting the large Nokoué Lagoon to the Atlantic Ocean in Benin. From the determination of zooplankton composition from 25-hour samples collected in July 2020, alpha diversity indices and abundance were assessed, while relationships between biotic and abiotic parameters were analyzed through Pearson correlation, analysis of variance, and principal component analysis. A total of 66 zooplankton taxa were identified, with rotifers exhibiting the highest species richness (35 taxa), while copepods dominated in abundance (71%). Zooplankton abundance varied significantly, ranging from 2 to 95 ind L−1 depending on the tidal phase. A negative correlation was found between species richness (r = −0.51, p < 0.01) and increasing salinity (3–37), indicating that higher salinity reduced diversity (r = 0.06, p > 0.05). Resilient species like Synchaeta bicornis persisted despite salinity changes. The tidal cycle structurally altered the zooplankton community, with abundance and diversity peaking at different phases, notably higher at high tide (15 ind L−1.) These initial findings underscore the complex interactions between tidal dynamics and estuarine biodiversity, suggesting the need for further research across different tidal and seasonal conditions to inform effective management and conservation efforts.

Time-varying ambient air pollution exposure is associated with gut microbiome variation in the first 2 years of life

The infant gut microbiome matures greatly in the first year of life. Ambient air pollution (AAP) exposure is associated with the infant gut microbiome. However, whether time-varying AAP influences infant gut microbiome variation is rarely investigated. This study aimed to investigate the effects of PM2.5, PM10, and O3 on infant gut microbiome variation longitudinally. Demographic information, stool samples, and AAP exposure concentrations were collected at 6, 12, 24 months from infants. Gut microbiome was processed and analyzed using 16S rRNA V3-V4 gene regions. AAP exposure concentrations were calculated using the China High Air Pollutants (CHAP) database. Multiple pollutant models were used to assess the mixed effects of PM2.5, PM10, and O3 on infant gut microbiome variation. Infants’ gut microbiomes at 6, 12, 24 months old had significant differences in alpha diversity, beta diversity, and community composition. PM2.5 and O3 respectively explained 6.3% and 5.3% of the differences in community composition for 24-month-old infants. Single pollutant exposure and multiple pollutant exposure in different periods were both associated with alpha diversity indices and specific gut microbial phyla and genera. AAP was more associated with infant gut microbial alpha diversity indices, phyla variations, and genera variations at 12–24 months than 6–12 months. Multiple pollutant exposure in 0–2 lag months showed negative correlations with 12–24 months variation in Escherichia-Shigella (β = −0.854, 95%CI: 1.398 to −0.310) and Enterococcus (β = −0.979, 95%CI: 1.429 to −0.530). This study highlighted that time-varying PM2.5, PM10, and O3 synergistically influenced the variation of alpha diversity and abundance of gut microbial taxa in infants. Further research is needed to explore the effects and mechanisms of other environmental exposures on infant gut microbiome variation.

Compositional Metrics of Fast and Slow Alfvénic Solar Wind Emerging from Coronal Holes and Their Boundaries

We seek to understand the composition and variability of fast solar wind (FSW) and slow Alfvénic solar wind emerging from coronal holes (CHs). We leverage an opportune conjunction between Solar Orbiter and Parker Solar Probe (PSP) during PSP Encounter 11 to include compositional diagnostics from the Solar Orbiter Heavy Ion Sensor as these variations provide crucial insights into the origin and nature of the solar wind. We use potential field source surface and magnetohydrodynamic models to connect the observed plasma at PSP and Solar Orbiter to its origin footpoint in the photosphere and compare these results with the in situ measurements. A very clear signature of a heliospheric current sheet crossing as evidenced by enhancements in low first ionization potential (FIP) elements, ion charge state ratios, proton density, low Alfvénicity, and polarity estimates validates the combination of modeling, data, and mapping. We identify two FSW streams emerging from small equatorial CHs with low ion charge state ratios, low FIP bias, high Alfvénicity, and low footpoint brightness, yet anomalously low alpha particle abundance for both streams. We identify high-Alfvénicity slow solar wind emerging from the overexpanded boundary of a CH having intermediate alpha abundance, high Alfvénicity, and dips in ion charge state ratios corresponding to CH boundaries. Through this comprehensive analysis, we highlight the power of multi-instrument conjunction studies in assessing the sources of the solar wind.

The European livestock resistome.

Metagenomic sequencing has proven to be a powerful tool in the monitoring of antimicrobial resistance (AMR). Here, we provide a comparative analysis of the resistome from pigs, poultry, veal calves, turkey, and rainbow trout, for a total of 538 herds across nine European countries. We calculated the effects of per-farm management practices and antimicrobial usage (AMU) on the resistome in pigs, broilers, and veal calves. We also provide an in-depth study of the associations between bacterial diversity, resistome diversity, and AMR abundances as well as co-occurrence analysis of bacterial taxa and antimicrobial resistance genes (ARGs) and the universality of the latter. The resistomes of veal calves and pigs clustered together, as did those of avian origin, while the rainbow trout resistome was different. Moreover, we identified clear core resistomes for each specific food-producing animal species. We identified positive associations between bacterial alpha diversity and both resistome alpha diversity and abundance. Network analyses revealed very few taxa-ARG associations in pigs but a large number for the avian species. Using updated reference databases and optimized bioinformatics, previously reported significant associations between AMU, biosecurity, and AMR in pig and poultry farms were validated. AMU is an important driver for AMR; however, our integrated analyses suggest that factors contributing to increased bacterial diversity might also be associated with higher AMR load. We also found that dispersal limitations of ARGs are shaping livestock resistomes, and future efforts to fight AMR should continue to emphasize biosecurity measures.IMPORTANCEUnderstanding the occurrence, diversity, and drivers for antimicrobial resistance (AMR) is important to focus future control efforts. So far, almost all attempts to limit AMR in livestock have addressed antimicrobial consumption. We here performed an integrated analysis of the resistomes of five important farmed animal populations across Europe finding that the resistome and AMR levels are also shaped by factors related to bacterial diversity, as well as dispersal limitations. Thus, future studies and interventions aimed at reducing AMR should not only address antimicrobial usage but also consider other epidemiological and ecological factors.

Detailed chemical composition of the globular cluster Sextans A GC-1 on the outskirts of the Local Group

The chemical composition of globular clusters (GCs) across the Local Group provides information on chemical abundance trends. Studying GCs in isolated systems in particular provides us with important initial conditions plausibly unperturbed by mergers and tidal forces from the large Local Group spirals. We present a detailed chemical abundance analysis of Sextans A GC-1. The host galaxy, Sextans A, is a low-surface-brightness dwarf irregular galaxy located on the edge of the Local Group. We derive the dynamical mass of the GC together with the mass-to-light ratio and the abundances of the alpha , Fe-peak, and heavy elements. Abundance ratios were determined from the analysis of an optical integrated-light spectrum of Sextans A GC-1, obtained with UVES on the VLT. We apply non-local thermodynamic equilibrium (NLTE) corrections to Mg, Ca, Ti, Fe, and Ni. The GC appears to be younger and more metal-poor than the majority of the GCs of the Milky Way, with an age of 8.6pm 2.7 Gyr and $ Fe/H dex. The calculated dynamical mass is dyn odot $, which results in an atypically high value of the mass-to-light ratio, 4.35pm 1.40 M$_ odot $/L$_ V odot $. Sextans A GC-1 has varying alpha elements -- the Mg abundance is extremely low, Ca and Ti are solar-scaled or mildly enhanced, and Si is enhanced. The measured values are $ Mg/Fe Ca/Fe Ti/Fe and $ Si/Fe which makes the mean alpha abundance (excluding Mg) to be enhanced $ <Si,Ca,Ti>/Fe NLTE The Fe-peak elements are consistent with scaled-solar or slightly enhanced abundances: $ Cr/Fe Mn/Fe Sc/Fe and $ Ni/Fe The heavy elements measured are Ba, Cu, Zn, and Eu. Ba and Cu have sub-solar abundance ratios ($ Ba/Fe and $ Cu/Fe <-0.343$), while Zn and Eu are consistent with their upper limits being solar-scaled and enhanced, $ Zn/Fe <+0.171$ and $ Eu/Fe The composition of Sextans A GC-1 resembles the overall pattern and behaviour of GCs in the Local Group. The anomalous values are the mass-to-light ratio and the depleted abundance of Mg. There is no definite explanation for such an extreme abundance value. Variations in the initial mass function or the presence of an intermediate-mass black hole might explain the high mass-to-light ratio value.

The globular cluster VVV CL002 falling down to the hazardous Galactic centre

Context. The Galactic centre is hazardous for stellar clusters because of the strong tidal force in action there. It is believed that many clusters were destroyed there and contributed stars to the crowded stellar field of the bulge and the nuclear stellar cluster. However, the development of a realistic model to predict the long-term evolution of the complex inner Galaxy has proven difficult, and observations of surviving clusters in the central region would provide crucial insights into destruction processes. Aims. Among the known Galactic globular clusters, VVV CL002 is the closest to the centre, at 0.4 kpc, but has a very high transverse velocity of 400 km s−1. The nature of this cluster and its impact on Galactic astronomy need to be addressed with spectroscopic follow up. Methods. Here we report the first measurements of its radial velocity and chemical abundance based on near-infrared high-resolution spectroscopy. Results. We find that this cluster has a counter-rotating orbit constrained within 1.0 kpc of the centre, and as close as 0.2 kpc at the perigalacticon, confirming that the cluster is not a passerby from the halo but a genuine survivor enduring the harsh conditions of the tidal forces of the Galactic mill. In addition, its metallicity and α abundance ([α/Fe] ≃ +0.4 and [Fe/H] = −0.54) are similar to those of some globular clusters in the bulge. Recent studies suggest that stars with such α-enhanced stars were more common at 3–6 kpc from the centre around 10 Gyr ago. Conclusions. We infer that VVV CL002 was formed outside but is currently falling down to the centre, showcasing a real-time event that must have occurred to many clusters a long time ago.

Diazotrophic community in the sediments of Poyang Lake in response to water level fluctuations.

Water level fluctuations (WLFs) are typical characteristic of floodplain lakes and dominant forces regulating the structure and function of lacustrine ecosystems. The sediment diazotrophs play important roles in contributing bioavailable nitrogen to the aquatic environment. However, the relationship between the diazotrophic community and WLFs in floodplain lakes is unknown. In this paper, we carried out a comprehensive investigation on the alpha diversity, abundance, composition and co-occurrence network of the sediment diazotrophs during different water level phases in Poyang Lake. There were no regular variation patterns in the alpha diversity and abundance of the sediment diazotrophs with the water level phase transitions. The relative abundance of some diazotrophic phyla (including Alphaproteobacteria, Deltaproteobacteri, Euryarchaeota, and Firmicutes) and genera (including Geobacter, Deferrisoma, Desulfuromonas, Rivicola, Paraburkholderia, Methylophilus, Methanothrix, Methanobacterium, and Clostridium) was found to change with the water level phase transitions. The results of ANOSIM, PerMANOVA, and DCA at the OTU level showed that the diazotrophic community structure in the low water level phase was significantly different from that in the two high water level phases, while there was no significant difference between the two high water level phases. These results indicated that the diazotrophic community was affected by the declining water level in terms of the composition, while the rising water level contributed to the recoveries of the diazotrophic community. The diazotrophs co-occurrence network was disrupted by the declining water level, but it was strengthened by the rising water level. Moreover, redundancy analysis showed that the variation of the diazotrophic community composition was mostly related to sediment total nitrogen (TN) and total phosphorous (TP). Interestingly, the levels of sediment TN and TP were also found to vary with the water level phase transitions. Therefore, it might be speculated that the WLFs may influence the sediment TN and TP, and in turn influence the diazotrophic community composition. These data can contribute to broadening our understanding of the ecological impacts of WLFs and the nitrogen fixation process in floodplain lakes.

Gut diazotrophs in lagomorphs are associated with season but not altitude and host phylogeny.

Invertebrates such as termites feeding on nutrient-poor substrate receive essential nitrogen by biological nitrogen fixation of gut diazotrophs. However, the diversity and composition of gut diazotrophs of vertebrates such as Plateau pikas living in nutrient-poor Qinghai-Tibet Plateau remain unknown. To fill this knowledge gap, we studied gut diazotrophs of Plateau pikas (Ochotona curzoniae) and its related species, Daurian pikas (Ochotona daurica), Hares (Lepus europaeus) and Rabbits (Oryctolagus cuniculus) by high-throughput amplicon sequencing methods. We analyzed whether the gut diazotrophs of Plateau pikas are affected by season, altitude, and species, and explored the relationship between gut diazotrophs and whole gut microbiomes. Our study showed that Firmicutes, Spirochaetes, and Euryarchaeota were the dominant gut diazotrophs of Plateau pikas. The beta diversity of gut diazotrophs of Plateau pikas was significantly different from the other three lagomorphs, but the alpha diversity did not show a significant difference among the four lagomorphs. The gut diazotrophs of Plateau pikas were the most similarly to that of Rabbits, followed by Daurian pikas and Hares, which was inconsistent with gut microbiomes or animal phylogeny. The dominant gut diazotrophs of the four lagomorphs may reflect their living environment and dietary habits. Season significantly affected the alpha diversity and abundance of dominant gut diazotrophs. Altitude had no significant effect on the gut diazotrophs of Plateau pikas. In addition, the congruence between gut microbiomes and gut diazotrophs was low. Our results proved that the gut of Plateau pikas was rich in gut diazotrophs, which is of great significance for the study of ecology and evolution of lagomorphs.

Human gut microbiota from hepatitis B virus-infected individuals is associated with reduced triglyceride level in mice: faecal transplantation study

Background and aimsChronic hepatitis B virus (HBV) infection is associated with a reduced risk of dyslipidaemia. Using a human faecal microbiota transplantation (FMT), we compared changes in gut microbiota and lipid profiles in mice transplanted with human faeces from HBV-infected and non-infected individuals. Approach and resultsA total of 19 mice received human FMT from four HBV-infected individuals and were categorised into the HBV-positive mice group, while 20 mice received FMT from four HBV-non-infected individuals into the HBV-negative one. In the analysis of gut microbiota in FMT mice, we observed a robust increase in alpha diversity and abundance of Akkermansia muciniphila in HBV-positive mice, compared to that in HBV-negative. Functional inference analysis revealed that the pathways involved in glycerolipid metabolism were more enriched in HBV-positive mice. At 5 weeks of FMT, the reduced triglyceride (TG) level was predominantly observed in HBV-positive mice. ConclusionsAltered gut microbiota accompanied by HBV infection was associated with a robust increase in alpha diversity and butyrate producers, which resulted in a reduced level of TG at 5 weeks post-FMT. This indicates that the reduced risk of dyslipidaemia in chronic HBV infection may be due to the altered gut microbiota accompanied by HBV infection.

Abstract B074: A biobank of fecal immunochemical tests (FIT) to study gut microbiome-mediated cancer disparities

Abstract Introduction: Colorectal cancer (CRC) poses a disproportionate burden among certain Hispanic/Latino subgroups, such as Puerto Rican and Cuban individuals, and Black individuals. Causes of CRC disparities are poorly understood but are likely driven by social determinants of health (SDOH), which may directly and indirectly influence the gut microbiome (GM). In turn, the GM is increasingly implicated in colorectal carcinogenesis. Therefore, it is plausible that the GM may be targeted to reduce excess CRC burden among disproportionately affected populations. However, prior studies of the GM and CRC had limited inclusion of underserved populations and limited collection of SDOH data. Objective: To clearly define the role of the GM in CRC and other cancer disparities, we conducted a pilot study to establish a well-annotated cohort that includes longitudinally collected fecal specimens among diverse populations. Methods: We leveraged fecal immunochemical tests (FIT), a cost-effective method for CRC screening in patient populations with limited access to colonoscopy, in which the GM can be well characterized. Participants completed annual FIT testing following standard protocols as implemented in a Federally Qualified Health Center. FIT samples were processed and banked at Moffitt Cancer Center in -80ºC freezers. All participants completed stool and risk factor questionnaires capturing SDOH, medical history, diet, and lifestyle exposures. To further validate the FIT microbiome, we extracted DNA from 8 sets of triplicate FIT aliquots (200ul each) using the automated MagCore®️ DNA Kit and then performed shotgun sequencing to characterize the fecal microbiome. To test for quality of the data and to compare microbiome metrics (e.g., alpha diversity and microbial abundances) in replicate samples, we calculated intraclass correlation coefficients (ICCs) using linear mixed effects models. Results: In just one clinic, to date, more than N=79 individuals who are primarily Spanish speakers and persons from other racial/ethnic minority subgroups have been enrolled. The racial and ethnic distribution included 39% Mexican, 11% Black, 6% Puerto Rican, 9% Central or South American, and 5% Cuban individuals. Approximately, 59% of the consented population preferentially spoke Spanish and 14% tested positive on the FIT. In the pilot FIT testing samples, we found that the integrity of the DNA was high, with only a few (N=3 of 24) samples with insufficient DNA yield for shotgun metagenomic sequencing. ICCs were generally above ≥ 95% for alpha diversity metrics and abundance of species/genes indicating excellent handling and processing procedures for FIT microbiome extraction and sequencing. Conclusion: Our findings support the concept that FIT-based community screening programs offer exceptional opportunity for GM research in diverse, underrepresented populations. Our future studies will integrate the SDOH data and expand this cohort with the goal of contributing novel insights regarding associations of the GM with early pathogenesis of CRC across diverse populations. Citation Format: Doratha Byrd, Stephanie Hogue, Xuefeng Wang, Sugriva Forsyth, Martha Fuentes, Kathleen Egan, Tiffany Carson, Youngchul Kim, Jessica Islam, Cathy Meade, Clement Gwede. A biobank of fecal immunochemical tests (FIT) to study gut microbiome-mediated cancer disparities [abstract]. In: Proceedings of the 16th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2023 Sep 29-Oct 2;Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2023;32(12 Suppl):Abstract nr B074.

PSVIII-15 Saccharomyces Cerevisiae Fermentation Product Influences Indicators of Gut Health and Function in Healthy Adult Cats

Abstract Compared with other species, the gastrointestinal influences of dietary Saccharomyces cerevisiae fermentation product (SCFP) in cats are not well-characterized. In this study, SCFP (TruMune, Cargill, Inc.) was added to an extruded cat food to explore gut-related outcomes in healthy adult cats. Sixty-three cats (mean age = 6.3 ± 2.8 yr; mean BW = 4.4 ± 0.1 kg) were used in a randomized complete block design to evaluate a base diet without SCFP (CON) or supplemented with 150 mg/kg BW SCFP (TRUL) or 300 mg/kg BW SCFP (TRUH). All cats were fed CON during a 21-d adaptation period and subsequently fed their respective diet from d 0 to d 42. Fecal samples were collected at d 0, d 21 and d 42 for analysis of fecal characteristics, fermentation end-products and shotgun metagenomics. A 5-d total fecal collection was performed from d 35 to d 39 for analysis of apparent nutrient digestibility. Data were analyzed using R v.4.1.2. Non-metagenomic data were analyzed using linear and generalized linear mixed models with lme4 and emmeans packages and metagenomic data were analyzed using phyloseq, vegan, lme4, LinDA and emmeans packages. Differences P < 0.05 were considered significant and P < 0.10 as trends after FDR correction. Fecal pH was higher (P = 0.01) for SCFP-supplemented cats vs CON and exhibited a positive linear dose response (P < 0.05) at d 21 and d 42. Fecal score was higher (firmer; P = 0.05) for SCFP-supplemented cats vs CON at d 21 consistent with a linear decrease (P = 0.02) in the binary comparison of fecal moisture between CON vs SCFP-supplemented cats (P = 0.01) during total fecal collection. Fecal ammonia demonstrated a quadratic treatment dose response trend at d 21 (P = 0.09). Fecal butyrate decreased linearly with SCFP dose (P < 0.001) and was less (P < 0.05) for SCFP-supplemented than CON cats at d 21 and d 42. Total short-chain fatty acid (SCFA) decreased linearly (P = 0.08) with SCFP dose and was less (P = 0.05) for SCFP-supplemented than CON cats at d 21. Species level alpha diversity decreased for CON (P = 0.04) but did not change in the TRUL and TRUH groups. Shannon diversity tended to increase in TRUH (P = 0.08) among a subset of 25 butyrate producers identified by the presence of butyrate pathway enzymes. Differential abundance of butyrate producers showed Acidaminococcus timonensis; CAG-83 sp900545495 and Megasphaera elsdenii decreased while Butyricicoccus pullicaecorum and Lawsonibacter 1402 linearly increased over time for TRUH cats (P < 0.05). No differences in alpha diversity or abundance were detected for any other butyrate producing taxa in TRUH nor between CON and TRUL cats. These results suggest SCFP influences several gastrointestinal outcomes in adult cats including pathways associated with SCFA production, cross-feeding, and/or absorption.

Does the urinary microbiome profile change after treatment of bladder cancer?

We sought to investigate the change in the urinary microbiome profile after transurethral resection of bladder tumor (TURBT). Urine specimens were collected from consecutive patients with bladder cancer. Patients were divided into those with bladder tumors ("Tumor group": de novo tumors or recurrent/progressed after TURBT ± intravesical therapy) versus those without evidence of recurrence after treatment "No Recurrent Tumor group". Samples were analyzed using 16S rRNA sequencing. Alteration in the urinary microbiome was described in terms of alpha (diversity within a sample measured by Observed, Chao, Shannon, and Simpson indices), beta diversities (diversity among different samples measured by Brady Curtis Diversity index), and differential abundance of bacteria at the genus level. Analyses were adjusted for gender, method of preservation (frozen vs preservative), and method of collection (mid-stream vs. catheter). Sixty-eight samples were analyzed (42 in "Tumor" vs 26 in "No Recurrent Tumor" groups). The median age was 70years (IQR 64-74) and 85% were males. All patients in the "No Recurrent Tumor" group had non-muscle invasive bladder cancer and 85% received BCG compared to 69% and 43% for the "Tumor" group, respectively. There was no significant difference in alpha diversity (p > 0.05). Beta diversity was significantly different (p = 0.04). Veillonella and Bifidobacterium were more abundant in the "Tumor" group (> 2FC, p = 0.0002), while Escherichia-Shigella (> 2FC, p = 0.0002) and Helococcus (> 2FC, p = 0.0008) were more abundant in the "No Recurrent Tumor" group. Bladder cancer patients with no recurrence and/or progression exhibited a different urinary microbiome profile compared to those with tumors.

Variable microbiomes between mosquito lines are maintained across different environments.

The composition of the microbiome is shaped by both environment and host in most organisms, but in the mosquito Aedes aegypti the role of the host in shaping the microbiome is poorly understood. Previously, we had shown that four lines of Ae. aegypti harbored different microbiomes when reared in the same insectary under identical conditions. To determine whether these lines differed from each other across time and in different environments, we characterized the microbiome of the same four lines of Ae. aegypti reared in the original insectary and at another institution. While it was clear that the environment influenced the microbiomes of these lines, we did still observe distinct differences in the microbiome between lines within each insectary. Clear differences were observed in alpha diversity, beta diversity, and abundance of specific bacterial taxa. To determine if the line specific differences in the microbiome were maintained across environments, pair-wise differential abundances of taxa was compared between insectaries. Lines were most similar to other lines from the same insectary than to the same line reared in a different insectary. Additionally, relatively few differentially abundant taxa identified between pairs of lines were shared across insectaries, indicating that line specific properties of the microbiome are not conserved across environments, or that there were distinct microbiota within each insectary. Overall, these results demonstrate that mosquito lines under the same environmental conditions have different microbiomes across microbially- diverse environments and host by microbe interactions affecting microbiome composition and abundance is dependent on environmentally available bacteria.

High carbohydrate to protein ratio promotes changes in intestinal microbiota and host metabolism in rainbow trout (Oncorhynchus mykiss) fed plant-based diet

To ensure the sustainability of aquaculture, it is necessary to change the “menu” of carnivorous fish such as rainbow trout from a fish-based diet to one with plant-based ingredients. However, there is a major problem with the growth performance decrease of fish fed with a 100% plant-based diet due to the reduction in feed intake and feed efficiency. For the first time, we incorporated high levels of digestible carbohydrates (high-starch diet) in a 100% plant-based diet during a 12-week feeding trial in order to improve protein utilization for growth (protein sparing effect) and reduce nitrogen waste.We measured the changes in the intestinal microbiota, Short-Chain Fatty Acid (SCFA) levels and metabolic responses in liver. Dietary carbohydrates had a strong effect on alpha and beta diversity and abundance of 12 genera, including Ralstonia and Bacillus in digesta associated microbiota whereas mucosa associated microbiota was less affected. The change in microbial diversity might be linked to the change observed in SCFA production. High levels of Mycoplasma were observed in the intestinal mucosa. Overall, hepatic gene expression was significantly altered by the CHO/protein ratio. Up-regulation of genes involved in glucose metabolism (gcka, gckb, g6pcb2a), down-regulation of genes involved in lipid metabolism (hadh, acox3, srebp2a, and cyp51a) were associated with higher enzymatic activities (such as glucokinase or pyruvate kinase) and higher glycogen levels in the liver, suggesting adequate adaptation to diet. Interestingly, strong correlations were observed between abundances of certain bacterial OTUs and gene expression in the liver.The inclusion of digestible carbohydrates in combination with a 100% plant-based diet, could be a promising way to improve and reduce the use of plant proteins in rainbow trout. In addition, the relationship between intestinal microbiota and host metabolism needs further investigation to better understand fish nutrition.

Bacterial dysbiosis and epithelial status of the California sea lion (Zalophus californianus) in the Gulf of California.

Despite the high incidence of urogenital carcinoma (UGC) in California sea lions stranded along California, no UGC has been reported in other areas of their distribution; however, cell morphologies typical of premalignant states have been found. Risk factors for UGC include high of organochlorines and infection with a gammaherpesvirus, OtHV-1, but the importance of the bacteriome for epithelial status remains unknown. We characterized the genital bacteriome of adult female California sea lions along their distribution in the Gulf of California and examined whether the diversity and abundance of the bacteriome varied spatially, whether there were detectable differences in the bacteriome between healthy and altered epithelia, and whether the bacteriome was different in California sea lions infected with OtHV-1 or papillomavirus. We detected 2270 ASVs in the genital samples, of which 35 met the criteria for inclusion in the core bacteriome. Fusobacteriia and Clostridia were present in all samples, at high abundances, and Actinobacteria, Alphaproteobacteria, and Campylobacteria were also well-represented. Alpha diversity and abundance of the California sea lion genital bacteriome varied geographically. The abundance of bacterial ASVs varied depending on the genital epithelial status and inflammation, with differences driven by classes Fusobacteriia, Clostridia, Campylobacteria and Alphaproteobacteria. Alpha diversity and abundance were lowest in samples in which OtHV-1 was detected, and highest those with papillomavirus. Our study is the first investigation of how the bacteriome is related to epithelial status in a wild marine species prone to developing cancer.

Carbohydrate quality, fecal microbiota and cardiometabolic health in older adults: a cohort study

ABSTRACT The impact of carbohydrate quality, measured by the carbohydrate quality index (CQI), on gut microbiota and health has been scarcely investigated. The aim of this study was to cross-sectionally and longitudinally explore the relationships between CQI, fecal microbiota, and cardiometabolic risk factors in an elderly Mediterranean population at high cardiovascular risk. At baseline and 1-year, CQI was assessed from food frequency questionnaires data, cardiometabolic risk factors were measured, and fecal microbiota profiled from 16S sequencing. Multivariable-adjusted linear regression models were fitted to assess the associations between tertiles of baseline CQI, fecal microbiota, and cardiometabolic risk factors at baseline, and between tertiles of 1-year change in CQI, 1-year change in fecal microbiota and cardiometabolic risk factors. Cross-sectionally, higher CQI was positively associated with Shannon alpha diversity index, and abundance of genera Faecalibacterium and Christensenellaceae R7 group, and negatively associated with the abundance of Odoribacter, and uncultured Rhodospirillales genera. Some of these genera were associated with higher glycated hemoglobin and lower body mass index. In addition, we observed a positive association between CQI, and some pathways related with the metabolism of butyrate precursors and plants-origin molecules. Longitudinally, 1-year improvement in CQI was associated with a concurrent increase in the abundance of genera Butyrivibrio. Increased abundance of this genera was associated with 1-year improvement in insulin status. These observations suggest that a better quality of carbohydrate intake is associated with improved metabolic health, and this improvement could be modulated by greater alpha diversity and abundance of specific genera linked to beneficial metabolic outcomes.

Soil fungal community is more sensitive than bacterial to mining and reforestation in a tropical rainforest

AbstractMining is a major threat for tropical rainforests as it induces rapid land degradation. Reforestation of mined areas is important to mitigate degradation and biodiversity losses. Microbial diversity, which serve as a good indicator of environmental perturbations, is crucial for reforestation and ecosystem functioning. Yet, limited information is available on how it is influenced by mining. We investigated the bacterial and fungal taxonomic alpha (richness and abundance) and beta diversities (Bray–Curtis dissimilarities (BCD)), root traits and nutrients among mined, undisturbed, and reforested soils in a tropical rainforest in Hainan Island (China). Soil organic matter (SOM) content was highly associated with bacterial and fungal abundances, fungal species richness, and BCD. Mining‐led vegetation removal largely reduced the SOM, and it decreased bacterial and fungal abundances, fungal species richness, and BCD. After using mined soil to plant multiple fast‐growing tree species, the root traits functioned at the levels of an original secondary forest, and it quickly recovered SOM. This process restored bacterial and fungal abundance, fungal species richness, and BCD to originally undisturbed levels. We further conclude that (i) soil fungal diversity in tropical rainforest is more sensitive to mining and reforestation than bacterial diversity. This could be attributed to largely reduced/increased SOM resulting from loss/gain in vegetation during mining/reforestation, respectively. (ii) Reduced SOM, after mining and removal of vegetation, has profound negative influences on tropical rainforest. (iii) Use of mined soil as a post‐mining substrate along with fast‐growing tree species ensures the recovery of SOM during reforestation, which alleviates the negative impacts of mining on tropical rainforests.