Higher Alpha Diversity Research Articles

Insights into the Gut Microbiota of the Freshwater Crab Sinopotamon planum across Three Seasons and Its Associations with the Surrounding Aquatic Microbiota

Gut microbiota is closely related to the health of the host and its adaptation to environmental changes. Sinopotamon planum is a species of freshwater crab that lives in the water for three seasons and plays a key role in freshwater ecosystems as a benthic macroinvertebrate, an important indicator of aquatic ecological health. In this study, we sequenced 60 gut microbial samples of S. planum and nine microbial samples from the surrounding water in spring, summer, and autumn based on the 16S rRNA gene. The results showed that gut microbiota had the highest alpha diversity in summer, which may be related to increased adaptability in summer. Firmicutes, Proteobacteria, and Bacteroidota were the most dominant phyla of gut microbiota across three seasons, with Candidatus Hepatoplasma and Candidatus Bacilloplasma being the main genera. These main phyla and genera may be key to maintaining a stable function of the intestinal environment. Firmicutes was the phylum with the highest relative abundance, which is probably related to the carnivorous behaviour of S. planum. The abundant C. Hepatoplasma may be related to the starvation of S. planum in the wild. In both gut and water microbiota, beta diversity analyses showed significant differences across seasons. Comparative analysis of gut microbes and surrounding water microbes showed significant differences in microbial diversity and composition between gut and surrounding water. In conclusion, the structure of the gut microbial community of S. planum differed significantly between the studied seasons, but the water microbial community around S. planum was less variable and significantly different from the gut microbes. The seasonal differences in gut microbes are more likely the result of self-internal adaptation to changes in water temperature and food resources between seasons.

Distinct cervical tissue-adherent and luminal microbiome communities correlate with mucosal host gene expression and protein levels in Kenyan sex workers

BackgroundThe majority of studies characterizing female genital tract microbiota have focused on luminal organisms, while the presence and impact of tissue-adherent ectocervical microbiota remain incompletely understood. Studies of luminal and tissue-associated bacteria in the gastrointestinal tract suggest that these communities may have distinct roles in health and disease. Here, we performed a multi-omics characterization of paired luminal and tissue samples collected from a cohort of Kenyan female sex workers.ResultsWe identified a tissue-adherent bacterial microbiome, with a higher alpha diversity than the luminal microbiome, in which dominant genera overall included Gardnerella and Lactobacillus, followed by Prevotella, Atopobium, and Sneathia. About half of the L. iners-dominated luminal samples had a corresponding Gardnerella-dominated tissue microbiome. Broadly, the tissue-adherent microbiome was associated with fewer differentially expressed host genes than the luminal microbiome. Gene set enrichment analysis revealed that L. crispatus-dominated tissue-adherent communities were associated with protein translation and antimicrobial activity, whereas a highly diverse microbial community was associated with epithelial remodeling and pro-inflammatory pathways. Tissue-adherent communities dominated by L. iners and Gardnerella were associated with lower host transcriptional activity. Tissue-adherent microbiomes dominated by Lactobacillus and Gardnerella correlated with host protein profiles associated with epithelial barrier stability, although with a more pro-inflammatory profile for the Gardnerella-dominated microbiome group. Tissue samples with a highly diverse composition had a protein profile representing cell proliferation and pro-inflammatory activity.ConclusionWe identified ectocervical tissue-adherent bacterial communities in all study participants of a female sex worker cohort. These communities were distinct from cervicovaginal luminal microbiota in a significant proportion of individuals. We further revealed that bacterial communities at both sites correlated with distinct host gene expression and protein levels. The tissue-adherent bacterial community could possibly act as a reservoir that seed the lumen with less optimal, non-Lactobacillus, bacteria.1vNfGdLTcr4_vB6d-MCta-Video

Dominant bacterial taxa drive microbiome differences of juvenile Pacific oysters of the same age and variable sizes

Oyster aquaculture is a growing industry that depends on production of fast-growing, healthy larvae and juveniles (spat) to be sold to farmers. Despite nearly identical genetics and environmental conditions in the early life stages of oysters, larvae and spat sizes can vary drastically. As the microbiome can influence the health and size of marine invertebrates, we analyzed the microbiomes of differently-sized juvenile Pacific oyster (Crassostrea gigas) spat of the same age to examine the relationship of their microbiomes with size variation. We used 16S sequencing of 128 animals (n = 60 large, n = 68 small) to characterize the microbiomes of each size class, comparing alpha diversity, beta diversity, and differentially abundant taxa between size classes. We observed that small spat had higher alpha diversity using measures that considered only richness, but there was no difference in alpha diversity between the two size classes using measures that incorporate compositional metrics. Additionally, large and small spat had distinct microbiomes, the separation of which was driven by more dominant bacterial taxa. Taxa that were differentially abundant in large oysters were also more abundant overall, and many appear to have roles in nutrient absorption and energy acquisition. The results of this study provide insight into how the microbiome of C. gigas may affect the early development of the animal, which can inform hatchery and nursery practices.

Sex-Specific Effects on Total Body Fat Gain with 4-Week Daily Dosing of Raspberry Ketone [4-(4-Hydroxyphenyl)-2-butanone] and Ketogenic Diet in Mice

Background: Raspberry ketone (RK: [4-(4-Hydroxyphenyl)-2-butanone]) is a dietary supplement marketed for weight control. RK is structurally unrelated to the ketone bodies elevated with a ketogenic diet (KD). This study aims to determine whether RK oral supplementation with KD improves the weight loss outcomes in high-fat diet (HFD; 45% fat)-fed mice. Methods: Male and female C57BL/6J mice were HFD-fed for 9 weeks and switched to KD (80% fat) or a control diet (CD; 10% fat) or continued with the HFD for 4 weeks. Coincident with the diet switch, each diet group received oral RK (200 mg/kg/day) or a vehicle. Results: In male KD-fed mice, oral RK reduced body weight by ~6% (KD_Veh: -9.2 ± 1% vs. KD_RK: -15.1 ± 1%) and fat composition by ~18% (KD_Veh: -16.0 ± 4% vs. KD_RK: -34.2 ± 5%). HFD and KD feeding induced glucose intolerance in both male and female mice. Oral RK decreased the glucose area under the curve in female mice by ~6% (KD_Veh: 44,877 ± 957 vs. KD_RK: 42,040 ± 675 mg*min/dl). KD also had gut microbiota alterations with higher alpha diversity in males and more beta diversity with RK. These findings suggest sex-specific weight loss effects with RK and KD in mice.

Effects of nitrogen addition and plant litter manipulation on soil fungal and bacterial communities in a semiarid sandy land.

The plant and soil microbial communities are influenced by variability in environmental conditions (e.g., nitrogen addition); however, it is unclear how long-term nitrogen addition and litter manipulation affect soil microbial communities in a semiarid sandy grassland. Therefore, we simulated the impact of N addition and litter manipulation (litter removal, litter doubling) on plant and soil microbial communities in Horqin grassland, northern China through an experiment from 2014 to 2019. Our results revealed that in the case of non-nitrogen (N0), litter manipulation significantly reduced vegetation coverage (V) (p < 0.05); soil bacterial communities have higher alpha diversity than that of the fungi, and the beta diversity of soil fungi was higher than that of the bacteria; soil microbial alpha diversity was significantly decreased by nitrogen addition (N10) (p < 0.05); N addition and litter manipulation had significantly interactive influences on soil microbial beta diversity, and litter manipulation (C0 and C2) had significantly decreased soil microbial beta diversity (p < 0.05) in the case of nitrogen addition (N10) (p < 0.05). Moreover, bacteria were mostly dominated by the universal phyla Proteobacteria, Actinobacteria, and Acidobacteria, and fungi were only dominated by Ascomycota. Furthermore, the correlation analysis, redundancy analysis (RDA), and variation partitioning analysis indicated that the soil fungi community was more apt to be influenced by plant community diversity. Our results provide evidence that plant and soil microbial community respond differently to the treatments of the 6-year N addition and litter manipulation in a semiarid sandy land.

Control factors of soil diazotrophic community assembly and nitrogen fixation rate across eastern China

Biological nitrogen (N) fixation is an essential N input into terrestrial ecosystems and plays a critical role in global N cycling. However, the driving factors of the diazotrophic community composition and soil N fixation rate at the regional scale remain largely unclear, especially in different land-use types. Here, we explored the environmental adaptation of diazotrophic communities and controlling factors of N fixation in maize, rice, and forest soils across eastern China. Results showed that the diversity, composition, and co-occurrence network differed significantly among these habitats, with a relatively higher alpha diversity and network complexity in rice fields. The mean annual precipitation plays a predominant role in shaping diazotrophic community composition. Dispersal limitation, belonging to stochastic processes, contributed most to diazotrophic community assembly in terrestrial ecosystems. Habitat niche breadth analysis indicated that the environmental adaptation of diazotrophic communities was highest in rice fields, followed by forest and maize fields. The overall N fixation rate was higher in rice fields, followed by maize and forest soils. Structural equation modeling revealed that the N fixation rate was mainly affected by soil properties in maize and forest soils. In contrast, the N fixation rate was more influenced by diazotrophic community composition and climatic factors in rice habitats. Our results revealed that the environmental adaptation of the diazotrophic communities and controlling factors of the N fixation function were different among maize, rice, and forest ecosystems. These findings will help us understand and predict the N bioavailability in different ecosystem types under climate changes.

Abstract P1-04-02: Gut microbiome diversity correlates with tumor PD-L1 status in metastatic triple negative breast cancer (mTNBC): correlative analysis of gut microbiome and tumoral biomarkers

Abstract Background: Greater gut microbiome diversity is observed in patients with a clinical response to immune checkpoint inhibitor (ICI) therapy in solid tumors and in preclinical models targeting the gut microbiome is a promising strategy to improve ICI efficacy. The investigation of the immunomodulatory effects of the gut microbiome and tumor biology is in its infancy and whether interindividual microbiome variations correlate with tumor biology in breast cancer is unknown. Here we report a correlative analysis of gut microbiome diversity with tumor biomarkers: PD-L1, tumor immune cell density, tumor infiltrating lymphocytes (TILs), MutSig3, and interferon (IFN) gene signatures in a cohort of mTNBC patients treated with olaparib and durvalumab of the Adaptive Multi-Drug Treatment of Evolving Cancers (AMTEC) trial (NCT03801369). Methods: AMTEC participants undergo a baseline biopsy (bx) and fecal sample collection, then start olaparib monotherapy on a 28-day cycle. Following the first cycle, an on-treatment (on-tx) bx and fecal sample are collected, then as part of enrollment to Arm 1, durvalumab is added to the treatment regimen. Ten patients with stool collections and tissue biopsies were used in this analysis, eight had paired pre- and on-tx collections. At interim-analysis, participants were categorized as responders (PR/SD) or non-responders (PD). Gut microbiome composition in fecal samples collected pre- and on-olaparib monotherapy was assessed by 16S rRNA sequencing and alpha diversity was quantified by observed diversity, Fisher, Inverse Simpson, Pielou, and Shannon indices. Response, PDL1 expression (Positive CPS &amp;gt;1), multiplex immunohistochemistry (mIHC) immune cell density and immune cell signature, TILs, RNA signatures including interferon (INF) family signatures, and mutational significance (MutSig3) were correlated to alpha diversity by T-test. Results: Average baseline alpha diversity of the fecal microbiome did not vary based on response (6 non-responses and 4 responses). However, in the on-tx samples, Fisher (CB: mean = 21.81, std. dev. = 3.6; PD: mean = 17.04, std. dev. = 2.3; p=0.048) and Observed alpha diversity (CB: mean = 260, std. dev. = 38.8; PD: mean = 209, std. dev. = 25.8; p = 0.049) were higher in responders. Average baseline alpha diversity of the gut microbiome as measured across all examined indices was significantly lower in participants with PD-L1 expressing tumors (p &amp;lt; 0.05 for each, T-test). Among on-tx samples, there was a trend toward lower alpha diversity in PD-L1 expressing tumors, but PD-L1 expression did not correlate with clinical response. There was a notable trend toward greater alpha diversity in on-tx bx and high TILs. Alpha diversity did not differ by immune cell densities by mIHC (CD8+ T cell, B cell, and regulatory T cells), hypo-inflamed/pro-inflammatory signature, IFN gene signature, nor MutSig3 score. Conclusion: Our preliminary data reveal that higher alpha diversity following olaparib monotherapy correlated with response to therapy with combination olaparib and durvalumab and correlated with tumor PD-L1 status. Whether gut microbiome features represent a meaningful biomarker for ICI treatment of mTNBC warrants further study. Enrollment to stage 2 of AMTEC Arm 1 is ongoing. Citation Format: Brie Chun, Shaun Goodyear, Travis Rice-Stitt, Lisa Karstens, Erin Dahl, Allen Li, Evthokia Hobbs, Mitri Zahi. Gut microbiome diversity correlates with tumor PD-L1 status in metastatic triple negative breast cancer (mTNBC): correlative analysis of gut microbiome and tumoral biomarkers [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P1-04-02.

Abstract MP02: Gut Microbiome Alteration and Structural Brain Features Among Healthy Japanese Men

Introduction: Growing evidence supports the bidirectional brain-gut microbiome interaction that contributes to brain health. However, no prior study has assessed the association between gut microbiomes and structural brain features in a healthy general population. Hypothesis: We assess the hypothesis that the gut microbiome composition is associated with structural brain features in healthy humans. Methods: Healthy Japanese men (n=623) aged 40-79 years participated in the examination of the Shiga Epidemiological Study of Subclinical Atherosclerosis II (SESSA II) between 2010 and 2014. Gut microbiota composition including diversity was assessed using 16S rRNA sequencing with DNA extracted from stool samples, and brain volumes (i.e., total brain volume, white matter, gray matter, and hippocampus) and white matter lesion volume (WMLV, reflecting Cerebral small vessel disease) were quantified using brain magnetic resonance imaging (MRI). We performed principal coordinate analysis (PCoA), multivariable-adjusted linear regression models, and linear discriminant analysis (LDA) by measuring effect size (Lefse). Results: Higher alpha diversity was associated with lower brain volumes of gray matter, white matter, and hippocampus (FDR adjusted Q &lt;0.01). For beta diversity, weighted unifrac Bray-Curtis distances measured by PCoA showed lower and higher groups formed distinct clusters in white and gray matter volumes. Multivariable linear regression and LDA analysis suggested that higher amount of the genera Lachnospiraceae butyrate-producing bacteria were associated with greater gray and white matter volume (see Figure). Conclusions: In conclusion, the gut microbiome was associated with the brain gray and white matter structural alterations in healthy Japanese adult men. Persons with higher amount of Lachnospiraceae butyrate-producing bacteria had higher gray and white matter volumes compared to those with lower amount of the bacteria.

Comparative analysis of the vaginal microbiome of healthy and polycystic ovary syndrome women: a large cross-sectional study

Research questionWhat are the different features of the vaginal microbiome (VMB) between patients with polycystic ovary syndrome (PCOS) and healthy women? DesignA cross-sectional study was conducted at a single academic university-affiliated centre. A total of 1446 participants were recruited (PCOS group, n =713, control group, n = 733). Vaginal swabs were analysed using 16S rRNA gene sequencing. The diversity and composition of the microbiome were compared between the PCOS group and the control group. Microbial interaction networks and functional prediction were investigated. ResultsThe PCOS group had a higher alpha diversity than the control group (Shannon P = 0.03, Simpson P = 0.02), and higher intra-group variability was observed in PCOS group (P < 2.2E-16). At the genus level, the proportion of Lactobacillus decreased (85.1% versus 89.3%, false discovery rate [FDR] = 0.02), whereas the proportion of Gardnerella vaginalis and Ureaplasma increased in the PCOS group (5.1% versus 3.3%, FDR = 0.006; 1.2% versus 0.6%, FDR = 0.002, respectively). Lactobacillus acidophilus, Prevotella buccalis and G. vaginalis were identified as the main differential species. L. acidophilus was positively correlated with serum levels of anti-Müllerian hormone (AMH), and triglyceride (P = 2.01E-05, P = 0.004, respectively). P. buccalis was negatively correlated with serum levels of AMH and testosterone (P = 0.002, P = 0.003, respectively). G. vaginalis was positively correlated with serum levels of AMH, oestradiol and progesterone (P = 0.004, P = 0.005, P = 0.03, respectively). The VMB interaction network indicated that Lactobacillus crispus, Prevotella timonensis, and P. buccalis could be key drivers in the PCOS group. Overall, 55 predicted genes were found to be differentially abundant between PCOS and the control (FDRs < 0.25). ConclusionsThe PCOS group had a higher diversity of vaginal microbiome and showed an enhanced level of heterogeneity. The proportion of Lactobacillus in the PCOS group decreased, whereas the proportions of Gardnerella and Ureaplasma increased. These results warrant further research that can validate the correlation between PCOS and VMB.

Preterm Prelabor Rupture of Membranes Linked to Vaginal Bacteriome of Pregnant Females in the Early Second Trimester: a Case-Cohort Design.

Preterm prelabor rupture of membranes (PPROM) is a major cause of spontaneous preterm birth (sPTB), one of the greatest challenges facing obstetrics with complicated pathogenesis. This case-cohort study investigated the association between vaginal bacteriome of singleton pregnant females in the early second trimester and PPROM. The study included 35,255 and 180 pregnant females with PPROM as cases and term-birth without prelabor rupture of membranes (TWPROM) and term prelabor rupture of membranes (TPROM) pregnant females as controls, respectively. Using 16S rRNA sequencing, the vaginal microbiome traits were analyzed. Females with PPROM had higher alpha and beta diversity (P < 0.05) than TWPROM and TPROM. The presence of L. mulieris was associated with a decreased risk of PPROM (adjusted odds ratio [aOR] = 0.35; 95% confidence interval [CI]: 0.17-0.72) compared with TWPROM. Meanwhile, the presence of Megasphaera genus (aOR = 2.27; 95% CI: 1.09-4.70), Faecalibacterium genus (aOR = 3.29; 95% CI: 1.52-7.13), Bifidobacterium genus (aOR = 3.26; 95% CI: 1.47-7.24), Xanthomonadales genus (aOR = 2.76; 95% CI: 1.27-6.01), Gammaproteobacteria class (aOR = 2.36; 95% CI: 1.09-5.14), and Alphaproteobacteria class (aOR = 2.45; 95% CI: 1.14-5.26) was associated with an increased risk of PPROM compared with TWPROM. Our results indicated that the risk of PPROM can decrease with vaginal L. mulieris but increase with high alpha or beta diversity, and several vaginal bacteria in pregnant females may be involved in the occurrence of PPROM.

Microbiome in paired root apices and periapical lesions and its association with clinical signs in persistent apical periodontitis using next-generation sequencing.

To assess and compare the microbiome of paired root apices and periapical lesions from cases with failed endodontic treatment and to associate the microbiome and bacterial metabolic pathways in both sites with asymptomatic apical periodontitis (AAP) and symptomatic apical periodontitis (SAP), using next-generation sequencing (NGS). Matched root apices and periapical lesions of patients with failed root canal treatments were surgically extracted. Specimens were cryopulverized, bacterial DNA was extracted and the V3-V4 hypervariable regions of the 16 S rRNA gene were amplified and sequenced using the Illumina Miseq platform. Diversity and community composition were studied in the paired samples, as well as in AAP and SAP cases. Diversity indices were compared in each case by means of the Wilcoxon matched-pairs signed rank and Mann-Whitney U tests. Differences in the community composition were explored with multivariate statistical analysis and Linear discriminant analysis Effect Size (LEfSe). Bacterial functional study was performed through the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis. Twenty-one paired apices and lesions were successfully sequenced and analysed, identifying a total of 21 phyla and 600 genera. A higher alpha-diversity was observed in the periapical lesions, although no global differences in the community composition between the two sites were found (p=.87), the most prevalent genera being Fusobacterium, Porphyromonas and Streptococcus. Prevotella, Clostridiales_vadinBB60_group, Bosea, Phreatobacter, Afipia and Xanthobacteriaceae_unclassified were enriched in SAP samples, while Pseudopropionibacterium, Campylobacter and Peptoniphilus were significantly more abundant in AAP cases (p < .05). Metabolic pathways involved in the amino acid metabolism or degradation and flagellum assembly were more abundant in SAP samples, whereas glucose metabolism-related pathways were associated with AAP. The bacterial community composition was similar in the apices and periapical lesions. The microbiome was different in AAP and SAP samples, gram-negative bacteria showing higher relative abundances in SAP cases. An association was observed between amino acid degradation and flagellum assembly pathways, and the development of tenderness to percussion or palpation.

Diversity and Composition of Caddisflies (Insecta: Trichoptera) along an Elevation Gradient in Southeastern Mexico

We analyzed the alpha and beta components of male Trichoptera diversity along an altitudinal gradient ranging from 136 to 2432 m a.s.l. by studying five assemblages of adult male caddisflies in five streams of the Sierra de Juárez, Oaxaca, Mexico. Samples were collected with light traps in the “nortes” (February) and rainy (October) seasons of 2016, recording air temperature and relative humidity. The assemblages showed an abundance pattern clearly associated with the rainy season, and a high dissimilarity in their species composition. Species richness and abundance were significantly higher at lower altitudinal levels. The highest alpha diversity was recorded in the Flor de Azahar stream; beta diversity increased with altitude and made an important contribution to gamma diversity. These results suggest that temporal and altitudinal variations affect environmental variables, which influence the structure of Trichoptera assemblages. Temperature was the primary factor determining spatial and temporal distribution patterns of caddisfly assemblages in the study area. However, in the rainy season, this factor explained a smaller proportion of the observed changes. Therefore, it is necessary to evaluate other environmental variables and explore other ecosystems to provide additional evidence on the factors affecting the diversity patterns of the Trichoptera in the Sierra de Juárez.

Effects of submerged macrophytes (Elodea nuttallii) on water quality and microbial communities of largemouth bass (Micropterus salmoides) ponds.

Traditional aquaculture ponds are one of the most vulnerable ecosystems; thus, ecological aquaculture is increasingly valued for its beneficial ecological properties and ecosystem services. However, little is known about ecological aquaculture of largemouth bass with submerged vegetation. Here, we designed three ecological ponds of cultured largemouth bass with submerged macrophytes (the EM group) and three ponds with traditional aquaculture (the M group) to reveal the response of water quality, and phytoplankton and bacterial communities, to submerged macrophyte bioremediation during a 90-day culture period. We observed that Cyanobacterial outbreak occurred in the M group ponds from day 7 to the end of the experiment; however, there were no Cyanobacterial blooms in the EM group ponds throughout the culture period. Compared with the M group ponds, the EM group ponds, which had submerged hydrophytes, had significantly decreased concentrations of TP, TN, and CODMn, but significantly increased DO concentrations throughout the experimental period. Moreover, ecological aquaculture with submerged macrophytes showed strong effects on the phytoplankton and bacterial community compositions. In particular, the M group ponds had higher phytoplankton density and mainly included Cyanobacteria, whereas the EM group had lower phytoplankton density and mainly included Chlorophyta. Moreover, higher alpha diversity, as determined by Ace and Simpson index values, was detected for bacterial communities in the EM group ponds. Furthermore, PCoA clearly grouped the bacterial communities according to the two culture modes throughout the culture period. These results indicate that ecological aquaculture with submerged macrophytes can improve water quality, control Cyanobacterial blooms, and affect the diversity and composition of bacterial communities. These valuable effects seem to be beneficial and consistent to maintaining aquaculture ecosystem stability.

Effects of weight loss and feeding specially formulated diets on the body composition, blood metabolite profiles, voluntary physical activity, and fecal metabolites and microbiota of obese dogs.

Canine obesity negatively influences health and well-being, but can be managed by altering diet composition and caloric intake. Restricted feeding, dietary intervention, and consequent weight loss may be used to improve health and modify gastrointestinal microbiota. In this study, we aimed to determine the effects of restricted feeding of specially formulated foods on weight loss, body composition, voluntary physical activity, serum hormones and oxidative stress markers, and fecal metabolites and microbiota populations of obese dogs. Twenty-four obese dogs [body weight (BW) = 15.2 ± 1.7 kg; body condition score (BCS) = 8.7 ± 0.4; muscle condition score (MCS) = 3.5 ± 0.3; age = 7.2 ± 1.6 yr] were used in a 24-wk study. A control (OR) food was fed during a 4-wk baseline to identify intake needed to maintain BW. After baseline, dogs were allotted to one of two diets: OR or test (FT), and then fed to lose 1.5% BW/wk. Food intake, BW, BCS, and MCS were measured, blood and fecal samples were collected, DEXA scans were performed, and voluntary physical activity was measured over time. Microbiota data were evaluated using QIIME2 and change from baseline data from other measures were evaluated using the Mixed Models procedure of SAS, with P < 0.05 being significant. Restricted feeding led to reduced BW, BCS, fat mass, and blood cholesterol, triglyceride, glucose, and leptin concentrations, and increased MCS and lean body mass percentage. Blood cholesterol reduction was greater in dogs fed FT vs. OR. Fecal metabolites and bacterial alpha-diversity were affected by diet and weight loss. Dogs fed FT had greater reductions in fecal short-chain fatty acid, branched-chain fatty acid, and ammonia concentrations than those fed OR. Dogs fed OR had a higher alpha-diversity than those fed FT. Weight loss increased alpha-diversity (weeks 16, 20, and 24 > weeks 0 and 4). Beta-diversity showed separation between dietary groups and between week 0 and all other time points after week 8. Weight loss increased fecal Allobaculum and Ruminococcus torques. Weight loss also increased fecal Bifidobacterium, Faecalibaculum, and Parasutterella, but were greater in dogs fed OR. Weight loss decreased fecal Collinsella, Turicibacter, Blautia, Ruminococcus gnavus, Faecalibacterium, and Peptoclostridium, but were greater in dogs fed OR. In summary, restricted feeding promoted safe weight and fat loss, reduced blood lipid and leptin concentrations, and altered fecal microbiota of obese dogs.

Особенности микробиома кишечника при некротизирующим энтероколите у недоношенных новорожденных и доношенных новорожденных с врожденными пороками сердца по данным метагеномного секвенирования

Necrotizing enterocolitis (NEC) is a serious disease that predominantly affects premature infants with a birth weight of less than 1500 g. Newborns with ductus-dependent congenital heart disease (CHD) are also at risk of developing NEC, which is associated with impaired mesenteric perfusion and hypoxemia. Objective. To identify features of the intestinal microbiome composition of preterm neonates and full-term neonates with ductusdependent CHD, depending on the development of NEC. Patients and methods. A prospective observation of neonates and a retrospective “case-control” analysis (1:1 ratio) of the intestinal microbiome composition depending on the development of NEC were performed. In neonates with NEC, specimens were collected at the onset of NEC (±2 days), in patients without NEC – on the day of life, corresponding to the onset of the disease in newborns with NEC (±3 days) matched by gestational age. The intestinal composition was analyzed in 31 preterm newborns with stage IB–III NEC (subgroup N1 with early-onset NEC (days 1–7 of life) (n = 19); subgroup N2 with late-onset NEC (days 13–34 of life) (n = 12)), as well as in 31 preterm neonates without NEC (subgroup C1 of patients with specimens collected on days 2–7 of life (n = 19), subgroup C2 of patients with specimens collected on days 11–36 of life (n = 12)). Also, an analysis of the microbiome composition was performed in 14 full-term newborns with ductus-dependent CHD who developed NEC (group H1), and 14 full-term newborns with ductus-dependent CHD without NEC (group H2). Fecal specimens were collected from diapers into sterile tubes and stored at -40°C. Analysis of the intestinal microbiome was performed on Illumina MiSeq by prokaryotic 16S rRNA sequencing of amplicons with primers F515/R806 to the V4 16S rRNA variable region. A Naive Bayes classifier trained on the NCBI 16S RefSeq database was used for ASV taxonomic classification. Results. NEC stages of preterm neonates: IB – 5 children, IIA – 19, IIB – 4, III – 3. Stages of NEC in newborns with ductusdependent congenital heart disease: IB – 3 children; IIA – 11. There were no statistically significant differences in the Shannon alpha diversity index between groups (N1 and C1, N2 and C2, H1 and H2). Neonates with antibiotic exposure (ABT) at specimen collection had different beta diversity (PERMANOVA F-value: 24.534; R-squared: 0.21997; p = 0.001) and had a higher alpha diversity (Shannon index: 2.0 (0.8–2.8) vs. 1.2 (0.8–1.5), p = 0.004), primarily due to representatives of opportunistic flora. Analysis of the intestinal microbiome did not reveal bacteria, which could be interpreted as a universal marker for the development of NEC, but some features were identified. Among neonates from the “early” groups (N1 and C1), the dominant genera were more often Staphylococcus, Serratia, and Corynebacterium. Neonates with early-onset NEC (N1) had a significantly lower relative abundance of Enterococcus, Lacticaseibacillus, Clostridium, Fusobacterium, Limosilactobacillus, Agrococcus, Alkalibacterium, Ancrocorticia, Blautia, Brachybacterium, Brevibacterium, Carnobacterium, Citricoccus, Flaviflexus, Garicola, Lactococcus, Microbacterium, Phocaeicola, Propionimicrobium, Ruoffia, Stenotrophomonas compared to subgroup C1. Preterm neonates with late-onset NEC (N2) had a lower relative abundance of Bifidobacterium (p = 0.027) and Streptococcus (p = 0.037) than the comparison subgroup (C2) had. Neonates with late-onset NEC (N2) had a significantly higher relative abundance of Enterococcus than in early-onset NEC (N1) (7.83 (0.09–46.15) % vs. 0 (0–0.18) % resp., p = 0.0004), no differences were found between the comparison subgroups (C2 and C1). Preterm neonates with a longer NEC duration (n = 16, nil per os 20 (16–27) days) compared to children with a shorter duration (nil per os 10 (9.5–11) days) had several pathobionts/pathogens in fecal specimens at the NEC onset: Alkalibacterium, Brevibacterium, Flaviflexus and Ruo (Facklamia). Full-term neonates with ductus-dependent CHD and NEC (H1) had a higher relative abundance of Staphylococcus (p = 0.029), Serratia ( p = 0.011; OR = 14 (95% CI 1.43–137.3)), Pelomonas ( Roseateles) (p = 0.017), Methylobacterium (p = 0.017), and Nitrincola (p = 0.017) than neonates with CHD without NEC (H2). Conclusion. Intestinal dysbiosis may act as a predisposing background for the development of NEC, but not its main cause. The dysbiosis by antibiotic exposure is not a sufficient factor for NEC development; the mother's health, fetal development status, and the early postnatal period play a significant role. Early correction of antibiotic-induced dysbiosis may be a reasonable approach to preventing NEC. Probiotics, prebiotics, postbiotics/metabolites, live biotherapeutic products, and phages may be potential microbiome-modulating agents in neonates. Key words: necrotizing enterocolitis, ductus-dependent congenital heart disease, metagenomics, 16S rRNA sequencing, intestinal microbiome

Systematic Review of Human and Animal Evidence on the Role of Buckwheat Consumption on Gastrointestinal Health.

Buckwheat is a commonly cultivated crop with growing evidence that it is beneficial to gastrointestinal (GI) health. This systematic review summarizes the role of buckwheat in modifying GI health outcomes and microbiomes. Four medical databases and Google Scholar were systematically searched. Clinical trials, observational studies, animal in vivo, and in vitro studies with human and animal GI-derived samples were included. There were 32 studies (one randomized controlled trial [RCT], one non-randomized trial, 3 observational, 9 in vitro, and 18 animal in vivo studies) included. In preclinical studies, buckwheat extracts were observed to have cytotoxic potential against human-derived GI cancer cell lines. Animals fed with buckwheat had lower GI mucosal inflammation, higher alpha diversity in the GI microbiome, and higher levels of fecal short-chain fatty acids. Human evidence studies and clinical trials were limited and predominantly of moderate risk of bias. The majority of in vitro studies with GI-derived samples and in vivo studies were reliable without restrictions in study design. In vivo and in vitro studies show that buckwheat may have potential GI benefits due to its anti-oxidant and anti-inflammatory potential; however, human evidence remains limited, and its impact on health in humans remains to be elucidated in future trials.

Assessing the drivers of gut microbiome composition in wild redfronted lemurs via longitudinal metacommunity analysis

The gut microbiome influences host’s immunity, development, and metabolism and participates in the gut–brain axis, thus impacting the health of the host. It is a dynamic community varying between individuals and within individuals at different time points. Hence, determining the factors causing this variability may elucidate their impact on host’s health. However, understanding the drivers of variation has proven difficult particularly as multiple interactions occur simultaneously in the gut microbiome. We investigated the factors shaping the gut microbiome by applying the metacommunity concept where the gut microbiome is considered as a microbial community shaped by the interactions within the community, with the host and microbial communities outside the host, this through a longitudinal study in a wild primate. Focal behavioral data were collected for 1 year in four groups of redfronted lemurs to determine individual social and feeding behaviors. In addition, regular fecal samples were collected to assess bacteria, protozoa, and helminths through marker gene analysis and to measure fecal glucocorticoid metabolite (fGCM) concentrations to investigate the impact of physiological stress on the gut microbiome. Higher consumption of leaves and elevated fGCM concentrations correlated with higher alpha diversity, which also differed among groups. The major drivers of variation in beta diversity were group membership, precipitation and fGCM concentrations. We found positive and negative associations between bacterial genera and almost all studied factors. Correlations between bacterial indicator networks and social networks indicate transmission of bacteria between interacting individuals. We detected that processes occurring inside the gut environment are shaping the gut microbiome. Host associated factors such as, HPA axis, dietary changes, and fluctuations in water availability had a greater impact than interactions within the microbial community. The interplay with microbial communities outside the host also shape the gut microbiome through the exchange of bacteria through social relationships between individuals and the acquisition of microorganisms from environmental water sources.

Single Night Surveys of Moth Communities Can Serve as Ultra-Rapid Biodiversity Assessments.

Biodiversity conservation decisions are typically based on limited data and resources. For this reason, there is great interest in surveying taxa that may allow for a rapid assessment of the biodiversity at a site. Numerous taxa have been proposed and utilized for rapid assessments that allow for such a survey in a matter of weeks or less. Herein, we test the idea that nocturnal moths have many of the characteristics that make them ideal for such surveys, such as relative ease of identification, strong ecological association with specific plant species and habitats, high alpha diversity, extended seasonal activity, and ease of trapping. We demonstrate that even in a few hours of sampling during single night surveys, moth communities are predictive of regional forest types at sampling sites in New Jersey. We sampled moths in five different forest habitats in New Jersey, USA: Pine Barrens, Upland Deciduous Forest, Palustrine Deciduous Forest, Maritime Forest, and Ruderal/Disturbed Forests, at four sites per forest type. Non-metric multidimensional scaling (NMDS) analyses revealed that moth communities differ significantly across these four forest types (p &lt; 0.01). We used Analysis of Similarity (ANOSIM) R tests to quantify the degree of differentiation among moth communities, and found that Tortricidae (R = 0.657) and Geometridae (R = 0.637) predict forest communities nearly as well as the total moth diversity (R = 0.668). Uncommon species (R = 0.665) were better predictors than common species (R = 0.500). Host plant generalists (R = 0.654) were better predictors than specialists (0.538), which was a surprising find.

Lower Genital Tract Microbiome in Early Pregnancy in the Eastern European Population.

It is known that the features of the cervicovaginal microbiome can depend on ethnicity, which might be caused by genetic factors, as well as differences in diet and lifestyle. There is no research on the cervicovaginal microbiome of Eastern European women during early pregnancy. We evaluated the cervical and cervicovaginal microbiome of women with first-trimester pregnancy (n = 22), further delivered at term, using the 16S rRNA sequencing method. The predominant bacterial species in both groups was Lactobacillus iners, followed by Prevotella copri, Ileibacterium valens, Gardnerella vaginalis and Muribaculum intestinale in the cervical samples, and Gardnerella vaginalis, Prevotella copri, Bifidobacterium longum, Ileibacterium valens and Muribaculum intestinale in the cervicovaginal samples. The cervical microbiome had higher alpha diversity; a higher abundance of Muribaculum intestinale, Aquabacterium parvum and Methyloversatilis universalis; and a lower abundance of Psychrobacillus psychrodurans. The Lactobacillus iners-dominated microbiome (CST III) was the predominant type of cervical and cervicovaginal microbiome in early pregnancy in the majority of the women. The presence of soil and animal bacteria in the cervicovaginal microbiome can be explained by the rural origin of patients.

New perspectives on soil animal trophic ecology through the lens of C and N stable isotope ratios of oribatid mites

Knowledge of the trophic ecology of soil animals is important for understanding their high alpha diversity as well as their functional role in soil food webs and systems. In the last 20 years, the analysis of natural variations in stable isotope ratios (15N/14N, 13C/12C) has revolutionized our view on soil animal trophic ecology. Here, we review the state of the art of the trophic ecology of a highly abundant and diverse soil animal taxon, oribatid mites (Oribatida), investigated by stable isotope analyses. The review is based on 25 papers reporting stable isotope data of 292 oribatid mite taxa from 30 different sites. Four main findings emerged. (1) Oribatid mites cluster into six trophic groups, i.e. moss feeders, lichen feeders, primary decomposers, fungal feeders/secondary decomposers, predators/scavengers and marine algal feeders, plus one additional group, which incorporates CaCO3 in their cuticle for defence but still belongs to the fungal feeders/secondary decomposers group. (2) Of the 292 species studied 43.7% were classified as fungal feeders/secondary decomposers, 27.0% as primary decomposers and 15.7% as predators/scavengers, only few species include CaCO3 into their skeleton (6.1%), feed on lichens (4.9%), mosses (2.1%) or marine algae (0.7%). (3) In about one-third of the species studied the trophic niche was constant or varied little between sites or habitats, but in two-thirds of the species their trophic niche varied between habitats, with some species even shifting trophic levels, indicating trophic plasticity. (4) When aggregated at higher taxonomic level oribatid mite species clustered in only three instead of six trophic groups. This indicates that species within the same high level taxon often belong to different trophic groups, for example because feeding habits evolved convergently. Therefore, to accurately reflect the trophic ecology of oribatid mites their stable isotope signatures need to be analysed at species level. However, stable isotope analyses also have limitations, e.g. feeding on bacteria and fungi cannot be separated, and the same is true for feeding on ectomycorrhizal and arbuscular mycorrhizal fungi. Other methods such as fatty acid, amino acid and molecular gut content analyses as well as microbiome analyses may complement stable isotope studies and resolve oribatid mite trophic niche differentiation at a higher resolution. This will contribute to a better understanding of the local coexistence of large numbers of species in soil. Finally, we provide perspectives on how to integrate microarthropods into soil food webs using stable isotope and other methods allowing deeper insight into their trophic structure.