Shannon Index Research Articles

Seasonal changes of ammonia-oxidizing bacterial communities during tropical forest restoration

In this study, we used a high-throughput sequencing technology to survey the dry-wet seasonal change characteristics of soil ammonia-oxidizing bacteria (AOB) communities in the three restoration stages [i.e., Mallotus paniculatus community (early stage), Millettia leptobotrya community (middle stage), and Syzygium oblatum community (later stage)] of Xishuangbanna tropical forest ecosystems. We analyzed the effects of soil physicochemical characteristics on AOB community composition and diversity during tropical forest restoration. The results showed that tropical forest restoration significantly affected the relative abundance of dominant AOB phyla and their dry-wet seasonal variation. The maximum relative abundance of Proteobacteria (71.3%) was found in the early recovery stage, while that of Actinobacteria was found in the late recovery stage (1.0%). The abundances of Proteobacteria and Actinobacteria had the maximum ranges of dry-wet seasonal variation in the early and late stages, respectively. The abundance of dominant AOB genera and its dry-wet seasonal variation varied across tropical forest restoration stages. The maximum average relative abundance of Nitrosospira and Nitrosomonas in the late recovery stage was 66.2% and 1.5%, respectively. In contrast, the abundance of Nitrosovibrio reached its maximum (25.6%) in the early recovery stage. The maximum dry-wet seasonal variation in relative abundance of Nitrosospira and Nitrosomonas occurred in the early recovery stage, while that of Nitrosovibrio occurred in the middle recovery stage. The Chao1, Shannon, and Simpson diversity indices of AOB communities increased along the restoration stages, which were significantly higher in the wet season than in the dry season. The results of canonical correspondence analysis showed that soil easily oxidized carbon was the main factor controlling AOB community diversity and Actinobacteria abundance. Soil bulk density and temperature were the main factors affecting Proteobacteria abundance. Soil pH, microbial biomass carbon, water content, ammonium nitrogen, bulk density, and temperature were the main factors controlling the abundances of Nitrosospira, Nitrosomonas, and Nitrosovibrio. Therefore, tropical forest restoration can regulate the change of relative abundance of dominant AOB taxa via mediating the changes of soil temperature, bulk density, and readily oxidized carbon, leading to an increase in soil AOB community diversity.

L. plantarum and L. casei synergistically mitigate Gastro-Intestinal Acute Radiation Syndrome (GI-ARS)

Introduction: Incidental or accidental acute exposure to ionizing radiation causes radiation toxicity, for which there are no known medical countermeasures (MCMs). Ionizing radiation alters host gut epithelium as well as the gut microbiome. We sought to investigate if radiation induced gut dysbiosis occurred as a result of depletion of gut-protective bacteria, and if probiotic supplementation of such bacteria could help mitigate GI-ARS post ionizing radiation exposure. Methods: Adult C57BL/6 mice were subjected to total body irradiation, and a defined concentration of probiotics (either individually or combined) were given 24 h after radiation exposure. Mice were sacrificed 24 hours post treatment (i.e., 48 h post irradiation). Vascular-to-luminal flux of FITC-inulin was measured to evaluate intestinal mucosal permeability and endotoxemia by measuring plasma lipopolysaccharide. Gut microbiota was analyzed by 16S rRNA sequencing. Intestinal epithelial junctions were analyzed by immunofluorescence confocal microscopy and mucosal inflammatory response by RT-PCR for cytokine expression. Systemic inflammation was evaluated by ELISA for plasma cytokines. Results and conclusion: Our data show that radiation altered the taxonomic composition of the microbiota compared to age-matched sham treated mice. Shannon index analysis showed a significant decrease in α-diversity in irradiated mice. Bray-Curtis analysis indicated significant differences in microbiota composition between Sham and IR groups. E. coli abundance was increased whereas Lactobacillus abundance was decreased, particularly L. plantarum and L. casei. Probiotic supplementation with individual Lactobacillus species each mitigated radiation induced intestinal barrier dysfunction, gut specific as well as systemic inflammatory cytokine expression and endotoxemia. Our preliminary data further indicates that L. plantarum affects Epidermal Growth Factor Receptor (EGFR)-mediated signaling whereas L. casei was EGFR-independent. Interestingly, combined supplementation in a 1:1 ratio further enhanced recovery compared to adding the individual effects. Individual supplementation of L. plantarum and L. casei to irradiated mice reduced intestinal (ileal) permeability by 2-fold and 3-fold respectively, whereas combined supplementation reduced ileal permeability almost 8-fold compared to irradiated but untreated mice. This data indicates that L. plantarum and L. casei mitigate GI-ARS by distinct cellular mechanisms. Furthermore, data show that a mixture of these probiotic species is more effective in radio-mitigation than individually. Further mechanistic analysis will be required to identify cross-talking targets between mechanisms of these probiotics and synergistic radio-mitigation. In conclusion, Lactobacillus species are potential MCMs for the treatment of GI-ARS. Funding acknowledgements: NIH/NIAID, UO1-AI170019, UO1-AI172991. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Paneth cell-specific TCF4 down-regulation potentiates alcohol-induced dysbiosis of gut microbiota and tissue injury at the gut-liver axis

Introduction: Alcohol misuse results in hepatitis, pancreatitis, and neurodegenerative disorders. Alcohol consumption alters gut microbiota and increases gut permeability, leading to endotoxemia and multiple organ damage. However, the cellular and molecular mechanisms of alcohol-induced microbiota dysbiosis and barrier dysfunction remain poorly defined. Antimicrobial peptides such as α-defensins, secreted by the Paneth cells, regulate gut microbiota homeostasis. We previously reported that ethanol (EtOH) feeding reduces α-defensin expression in mice. α-Defensin expression is regulated by Wnt signaling and T-cell factor 4 (TCF4). We investigated the role of Paneth cell TCF4 in alcohol-induced microbiota dysbiosis and tissue injury at the gut-liver axis. Materials and methods: TCF4fl/wt (WT) and TCF4fl/wt-Defa6Cre (KD; heterozygous Paneth cell-specific knockout of TCF4) mice were fed a Lieber-DiCarli liquid diet with or without EtOH (0% 2d, 1% 2d, 2% 2d, 4% 1wk, 5% 1wk, & 6% 1wk) (EF). Control groups were pair-fed (PF) isocaloric EtOH-free diet. Intestinal permeability was measured by the vascular-to-luminal flux of FITC-inulin (6 kDa) in vivo, and tight junction (TJ) and adherens junction (AJ) integrity were assessed by confocal microscopy for occludin, ZO-1, E-cadherin, and β-catenin. Paneth cell function and mucosal inflammation were assessed by RT-PCR for defensins and cytokines. Gut microbiota was analyzed by 16S rRNA sequencing of colonic flushing. Plasma lipopolysaccharide (LPS) and cytokines were measured to evaluate endotoxemia and systemic inflammation. Liver damage was assessed by measuring plasma AST, liver triglyceride, and cytokine mRNA. Results and conclusion: EtOH reduced TCF4 expression in the ileum in both WT and KD mice; lowest TCF4 expression was observed in KD-EF mice. Similarly, the expression of DEFA5 and DEFA6 was reduced by EtOH in WT and KD mice, with the lowest expression in KD-EF mice. EtOH-induced mucosal permeability was associated with reduced staining for TJ and AJ proteins, indicating the mucosal barrier dysfunction. EtOH increased intestinal mRNA for IL-1β, IL-6, TNFα, and MCP-1, indicating the mucosal inflammatory response. EtOH-induced gut permeability, TJ/AJ disruption, and mucosal inflammation were significantly higher in KD-EF mice than in WT-EF mice. Shannon index analysis indicated that EtOH reduced α-diversity of microbiota in KD but not in WT mice. Firmicutes: Bacteriodetes ratio and the abundance of Verrucomicrobia were reduced by EtOH in WT but not in KD mice. The abundance of Bacillus was increased by EtOH both in WT and KD mice; however, this effect was more severe in KD mice. EtOH-induced plasma LPS and cytokine elevations were higher in KD mice than in WT mice. Elevation of plasma AST, liver triglyceride, and liver cytokine mRNA indicated EtOH-induced liver damage; the damage was more severe in KD mice. These data indicate that Paneth cell TCF4 downregulation exacerbates alcohol-induced microbiota dysbiosis, gut barrier dysfunction, endotoxemia, systemic inflammation, and liver damage; suggesting that Paneth cell Wnt signal downregulation plays a crucial role in alcohol-associated organ damage. NIH/NIAA - R01AA012307, AA029270; Veterans Administration - IO1BX003014. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Prediction and causal inference of hyperuricemia using gut microbiota.

Hyperuricemia (HUA) is a symptom of high blood uric acid (UA) levels, which causes disorders such as gout and renal urinary calculus. Prolonged HUA is often associated with hypertension, atherosclerosis, diabetes mellitus, and chronic kidney disease. Studies have shown that gut microbiota (GM) affect these chronic diseases. This study aimed to determine the relationship between HUA and GM. The microbiome of 224 men and 254 women aged 40years was analyzed through next-generation sequencing and machine learning. We obtained GM data through 16S rRNA-based sequencing of the fecal samples, finding that alpha-diversity by Shannon index was significantly low in the HUA group. Linear discriminant effect size analysis detected a high abundance of the genera Collinsella and Faecalibacterium in the HUA and non-HUA groups. Based on light gradient boosting machine learning, we propose that HUA can be predicted with high AUC using four clinical characteristics and the relative abundance of nine bacterial genera, including Collinsella and Dorea. In addition, analysis of causal relationships using a direct linear non-Gaussian acyclic model indicated a positive effect of the relative abundance of the genus Collinsella on blood UA levels. Our results suggest abundant Collinsella in the gut can increase blood UA levels.

Microbial community structure and carbon transformation characteristics of different aggregates in black soil.

Previous research on whole-soil measurements has failed to explain the spatial distribution of soil carbon transformations, which is essential for a precise understanding of the microorganisms responsible for carbon transformations. The microorganisms involved in the transformation of soil carbon were investigated at the microscopic scale by combining 16S rDNA sequencing technology with particle-level soil classification. In this experiment,16S rDNA sequencing analysis was used to evaluate the variations in the microbial community structure of different aggregates in no-tillage black soil. The prokaryotic microorganisms involved in carbon transformation were measured before and after the freezing and thawing of various aggregates in no-tillage black soil. Each sample was divided into six categories based on aggregate grain size: >5, 2-5, 1-2, 0.5-1, 0.25-0.5, <0.25 mm, and bulk soil. The relative abundance of Actinobacteria phylum in <0.25 mm aggregates was significantly higher compared to that in other aggregates. The Chao1 index, Shannon index, and phylogenetic diversity (PD) whole tree index of <0.25 mm aggregates were significantly smaller than those of in bulk soil and >5 mm aggregates. Orthogonal partial least-squares discrimination analysis showed that the microbial community composition of black soil aggregates was significantly different between <1 and >1 mm. The redundancy analysis (RDA) showed that the organic carbon conversion rate of 0.25-0.5 mm agglomerates had a significantly greater effect on their bacterial community structure. Moreover, humic acid conversion rates on aggregates <0.5 mm had a greater impact on community structure. The linear discriminant analysis effect size (LEfSe) analysis and RDA analysis were combined. Bradyrhizobium, Actinoplane, Streptomyces, Dactylosporangium, Yonghaparkia, Fleivirga, and Xiangella in <0.25 mm aggregates were positively correlated with soil organic carbon conversion rates. Blastococcus and Pseudarthrobacter were positively correlated with soil organic carbon conversion rates in 0.25-0.5 mm aggregates. In aggregates smaller than 1 mm, the higher the abundance of functional bacteria that contributed to the soil's ability to fix carbon and nitrogen. There were large differences in prokaryotic microbial community composition between <1 and >1 mm aggregates. The <1 mm aggregates play an important role in soil carbon transformation and carbon fixation. The 0.25-0.5 mm aggregates had the fastest organic carbon conversion rate and increased significantly more than the other aggregates. Some genus or species of Actinobacteria and Proteobacteria play a positive role in the carbon transformation of <1 mm aggregates. Such analyses may help to identify microbial partners that play an important role in carbon transformation at the micro scale of no-till black soils.

Characterization of dry-cured ham microbiota at 12 months of seasoning obtained from different rearing strategies using 16S rRNA profiling

In this study, we investigated the microbiota of 72 Italian ham samples collected after 12 months of seasoning. The hams were elaborated from pigs fed different rearing methods, including the traditional restricted medium protein diet chosen as control (C group); restrictive low protein diet (LP group); two ad libitum high-protein diet groups (HP9M group: slaughter at 9 months of age; HP170 group: slaughter at 170 kg). A multi-amplicon 16S metabarcoding approach was used, and a total of 2845 Amplicon Sequence Variants were obtained from the 72 ham samples. Main phyla included: Firmicutes (90.8%), Actinobacteria (6.2%), Proteobacteria (2.7%), and Bacteroidota (0.12%). The most common genera were Staphylococcus, Tetragenococcus, and Brevibacterium. Shannon index for α-diversity was found statistically significant, notably for the HP9M group, indicating higher diversity compared to C. PERMANOVA test on β-diversity showed significant differences in rearing methods between HP170 and C, HP170 and LP, and HP9M vs. C. All three rearing methods revealed associations with characteristic communities: the HP9M group had the highest number of associations, many of which were due to spoilage bacteria, whereas the LP group had the highest number of seasoning-favourable genera.

Association between childhood obesity and gut microbiota: 16S rRNA gene sequencing-based cohort study.

This study aimed to identify characteristic gut genera in obese and normal-weight children (8-12 years old) using 16S rDNA sequencing. The research aimed to provide insights for mechanistic studies and prevention strategies for childhood obesity. Thirty normal-weight and thirty age- and sex-matched obese children were included. Questionnaires and body measurements were collected, and fecal samples underwent 16S rDNA sequencing. Significant differences in body mass index (BMI) and body-fat percentage were observed between the groups. Analysis of gut microbiota diversity revealed lower α-diversity in obese children. Di-fferences in gut microbiota composition were found between the two groups. Prevotella and Firmicutes were more abundant in the obese group, while Bacteroides and Sanguibacteroides were more prevalent in the control group. To identify the characteristic gut genera in obese and normal-weight children (8-12-year-old) using 16S rDNA sequencing, and provide a basis for subsequent mechanistic studies and prevention strategies for childhood obesity. Thirty each normal-weight, 1:1 matched for age and sex, and obese children, with an obese status from 2020 to 2022, were included in the control and obese groups, respectively. Basic information was collected through questionnaires and body measurements were obtained from both obese and normal-weight children. Fecal samples were collected from both groups and subjected to 16S rDNA sequencing using an Illumina MiSeq sequencing platform for gut microbiota diversity analysis. Significant differences in BMI and body-fat percentage were observed between the two groups. The Ace and Chao1 indices were significantly lower in the obese group than those in the control group, whereas differences were not significant in the Shannon and Simpson indices. Kruskal-Wallis tests indicated significant differences in unweighted and weighted UniFrac distances between the gut microbiota of normal-weight and obese children (P < 0.01), suggesting substantial disparities in both the species and quantity of gut microbiota between the two groups. Prevotella, Firmicutes, Bacteroides, and Sanguibacteroides were more abundant in the obese and control groups, respectively. Heatmap results demonstrated significant differences in the gut microbiota composition between obese and normal-weight children. Obese children exhibited lower α-diversity in their gut microbiota than did the normal-weight children. Significant differences were observed in the composition of gut microbiota between obese and normal-weight children.

Influence of physicochemical parameters on the biodiversity indices of fresh water snails in selected rivers of Osun State, Nigeria

Studies have investigated the influence of environmental factors on distribution of vectors of parasites of public health importance but little is known on the role of these factors on the biodiversity indices of the vectors. This study is therefore set to assess the role of physicochemical parameters on biodiversity indices of fresh water snails. The study was carried out in three randomly selected communities across the three senatorial regions of Osun state namely Ere Ijesha, Ede and Erin-Osun. Through reports from community members, a mostly visited river from each community was selected. Three contact points with evident human water contact were identified for snail and water sampling. Morphological identification of snails was done. Physicochemical parameters of water were measured while snail biodiversity indices were determined using Shannon index, snail richness and abundance. Relationship between continuous variables was determined using Spearman’s correlation. There is a significant difference between pH values of Ere Ijesa and Erin Osun while Ede and Erin Osun also show a significant difference in their chloride concentration. A significant positive correlation was observed between pH and diversity (correlation coefficient (rho)= 0.64, P&lt;0.05), pH and Bulinus abundance (rho= 0.68, P&lt; 0.05), chloride and snail richness (rho= -0.65, P&lt; 0.05), chloride and diversity (rho= -0.88, P&lt; 0.01), BOD and snail richness (rho= -0.78, P &lt; 0.05), BOD and diversity (rho= -0.64, P&lt;0.05) COD and snail richness (rho= -0.61, P&lt; 0.05). Ede had highest diversity index while Ere Ijesa had highest Bulinus abundance. Erin Osun was the least in terms of snail richness, diversity and Bulinus abundance. Snail diversity, snail richness and Bulinus abundance significantly differ across the sampling locations (P&lt; 0.01). Physicochemical parameters such as pH, chloride content, BOD and COD have significant role to play in fresh water snail richness, snail diversity and Bulinus abundance.

Effects of combined microplastic and cadmium pollution on sorghum growth, Cd accumulation, and rhizosphere microbial functions

The interaction between microplastics (MPs) and cadmium (Cd) poses a threat to agricultural soil environments, and their effects on plant growth and rhizosphere microbial community functions are not yet clear. In this study, energy sorghum was used as a test plant to investigate the effects of two types of MPs, polystyrene (PS) and polyethylene (PE), at different particle sizes (13 μm, 550 μm) and concentrations (0.1%, 1% w/w), and Cd, as well as their interactions, on the growth of sorghum in a soil-cultivation pot experiment. The results showed that the combined effects of MP and Cd pollution on the dry weight and Cd accumulation rate in sorghum varied depending on the type, concentration, and particle size of the MPs, with an overall trend of increasing stress from combined pollution with increasing Cd content and accumulation. High-throughput sequencing analysis revealed that combined MP and Cd pollution increased bacterial diversity, and the most significant increase was observed in the abundance-based coverage estimator (ACE), Shannon, and Sobs indices in the 13 μm 1% PS+Cd treatment group. Metagenomic analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways revealed that 19 groups of metabolic pathways, including microbial metabolism and methane metabolism, differed significantly under combined MP and Cd pollution. Hierarchical clustering results indicated that Cd treatment and combined MP and Cd treatment affected the abundances of sorghum rhizosphere soil nitrogen (N) and phosphorus (P) cycling genes and that the type of MP present was an important factor affecting N and P cycling genes. The results of this study provide a basis for exploring the toxic effects of combined MP and Cd pollution and for conducting soil environmental risk assessments.

Elevated Altitude and Limestone Soil Promoted Fungal Diversity in Rhizosphere Soil of Sophora japonica

Soil microorganisms play a crucial role in mediating material transformation and nutrient cycling. However, little attention has been paid to the relationships between microbial communities and altitude and lithology in karst regions. Sophora japonica cv. Jinhuai is an officinal plant cultivated in karst areas, and there is a correlation between the dynamics of microbial community and ecological factors. This study examined the diversity of microbial communities in the rhizosphere of S. japonica under different lithologies and altitudes in karst regions of northern Guangxi, China using high-throughput sequencing technology. It was found that the bacterial community consisted of 37 phyla, including Proteobacteria. The fungal community mainly comprised 15 phyla, including Ascomycota. The fungal Shannon and Chao1 indices increased with altitude, while the bacterial Shannon index decreased. The fungal Shannon indices in limestone soil were higher than those in dolomite. The soil’s microbial Shannon and Chao1 indices were positively affected by pH, while the available phosphorus and potassium had the opposite effect. Research shows that altitude, lithology, pH, and available phosphorus were the crucial factors influencing the rhizosphere soil microbial community. This study provides references for understanding the relationship between plants and microorganisms and the microbial distribution strategy of rocky desertification habitats in the future.

Fertilising Maize with Bio-Based Mineral Fertilisers Gives Similar Growth to Conventional Fertilisers and Does Not Alter Soil Microbiome

The production of mineral fertilisers relies heavily on mineral deposits that are becoming depleted or is based on processes that are highly energy demanding. In this context, and in line with the circular economy and the European Green Deal, the recovery of nitrogen (N), phosphorus (P), and potassium (K) from organic wastes using chemical technologies is an important strategy to produce secondary raw materials for incorporation into mineral fertilisers, partially replacing the traditional sources of N, P, and K. However, there are very few studies on the agronomic and environmental effects of such substitution. The aim of this work was to evaluate plant growth under microcosm conditions and the effect on the soil microbiome of mineral fertilisers in which part of the N, P, or K content comes from bio-based materials (BBMFs), namely ash, struvite, and a patented chemical process. The crop was maize, and a metataxonomic approach was used to assess the effect on the soil microbiome. The BBMF treatments were compared with a control treated with a conventional mineral fertiliser. The conventional fertiliser performed significantly better than the bio-based fertilisers in terms of maize biomass production at the first sampling point 60 days after sowing (DAS), but at the last sampling point, 90 DAS, the BBMFs showed comparable or even better biomass production than the conventional one. This suggests that BBMFs may have a slightly slower nutrient release rate. The use of fertiliser, whether conventional or BBMF, resulted in a significant increase in microbiome biodiversity (Shannon index), while it did not affect species richness. Interestingly, the use of fertilisers modulated the composition of the bacterial community, increasing the abundance of beneficial bacterial taxa considered to be plant-growth-promoting bacteria, without significant differences between the conventional mineral fertilisers and the BBMFs. The predominance of PGPRs in the rhizosphere of crops when BBMFs are used could be part of the reason why BBMFs perform similarly or even better than conventional fertilisers, even if the rate of nutrient release is slower. This hypothesis will be tested in future field trials. Thus, BBMFs are an interesting option to make the food chain more sustainable.

Dietary honokiol supplementation improves antioxidant capacity, enhances intestinal health, and modulates cecal microbial composition and function of broiler chickens

Honokiol is a multifunctional polyphenol present in Magnolia officinalis. The effects of honokiol as a supplement in broiler chicken diets, and the underlying mechanisms, remain unclear. Therefore, the aim of the present study was to investigate the effects of honokiol on the growth performance, antioxidant capacity, and intestinal histomorphology of broiler chickens and to explore the underlying mechanisms. In total, 240 one-day-old broilers were randomly allocated to 5 dietary treatments, with 6 replicate pens and 8 birds per pen. Birds were fed a basal diet supplemented with 0 (blank control, BC), 100, 200, or 400 mg/kg honokiol (H100, H200, and H400), or 200 mg/kg bacitracin zinc (PC) for 42 d. The results showed that H200 and H400 increased body weight gain (BWG) and decreased feed conversion ratio (FCR) during the starter period (P < 0.05). H100 and H200 increased total superoxide dismutase (T-SOD) activity in the serum and decreased malondialdehyde (MDA) amount in the jejunum on d 42 (P < 0.05). Moreover, H100 increased villus height-to-crypt depth ratio in both the jejunum and ileum on d 21 (P < 0.05). PCR analysis showed that honokiol upregulated intestinal expression of glutathione peroxidase (GSH-Px) and downregulated intestinal expression of inducible nitric oxide synthase (iNOS) on d 42 (P < 0.05). The Shannon index, which represents the microbial alpha diversity, was reduced for the PC, H200, and H400 groups. Notably, honokiol treatment altered the cecal microbial community structure and promoted the enrichment of several bacteria, including Firmicutes and Lactobacillus. Higher production of short-chain fatty acids was observed in the cecal digesta of H100 birds, accompanied by an enriched glycolysis/gluconeogenesis pathway, according to the functional prediction of the cecal microbiota. This study provides evidence that honokiol improves growth performance, antioxidant capacity, and intestinal health of broiler chickens, possibly by manipulating the composition and function of the microbial community.

Ecological values of Ourkiss wetland (Oum El Bouaghi province - Algeria), an overview of waterbirds diversity and richness

The monitoring of waterbirds’ abundance and richness serves as the primary method for scientists to characterize the ecological values and diversity profile of wetlands. This survey was specifically conducted in Ourkiss wetland, situated in the Oum El Bouaghi province of East Algeria, spanning from January to May 2013. The study aimed to elucidate the ecological significance of Ourkiss wetland by analyzing various parameters, including the abundance, richness, diversity profile, and conservation status of its waterbird population. A total of 23 species, representing 11 families, were documented during the survey period, with Anatidae and Rallidae emerging as the most prevalent taxa. Notably, Ourkiss wetland exhibited two distinct populations: the “wintering population” and the “breeding population,” with significant waterbird activity observed during migration between the northern and southern regions. The presence of the endangered species Oxyura leucocephala further underscores the ecological importance of this wetland. Noteworthy peaks in waterbird diversity were particularly observed in April, as indicated by richness and Shannon indices. To safeguard the ecological integrity of Ourkiss wetland, it is strongly recommended to intensify conservation efforts and implement effective management plans.

The Potential Mechanism of the Anti-Liver Fibrotic Effect of Curcumin in the Gut-Liver Axis.

This study aimed to explore the curative effect of curcumin on liver fibrosis and its correlation with the gut-liver axis in animal models. Histological staining was utilized to conduct histological analysis of the liver and intestine. An automatic biochemical analyzer or enzyme-linked immunosorbent assay system was utilized for analyzing the biochemical indexes in mice. Western blotting was employed to examine the level of relevant proteins. Furthermore, 16S rRNA high-throughput sequencing was performed to explore the impact of curcumin on intestinal microorganisms in rats with liver fibrosis. Ultrahigh-performance liquid chromatography with quadrupole-orbitrap mass spectrometry was utilized to analyze the effect of curcumin on rat feces metabolites. Our results showed that curcumin reduced the formation of collagen fibers caused by carbon tetrachloride in a dose-dependent manner. In addition, curcumin was able to restore intestinal permeability in rats with liver fibrosis. By adopting α diversity analysis (Chao 1 index, Shannon index, and Simpson index), we observed that both the diversity and the abundance of intestinal flora in rats with liver fibrosis were increased. The principal component analysis diagram demonstrated that curcumin could enhance the abundance and diversity of intestinal flora, and also restore the composition of model rat flora, which was similar to that in normal rats, thereby correcting the imbalance of flora in rats with liver fibrosis. In addition, curcumin regulated feces metabolites and their signaling pathways, including glycerophospholipid metabolism, pantothenate and CoA biosynthesis. Our findings suggest that curcumin exhibits antiliver fibrosis effects, and its antiliver fibrosis effects might correlate with gut-liver axis.

Short-term supplementation with uncoated and encapsulated Enterococcus faecium affected growth performance, gut microbiome and intestinal barrier integrity in broiler chickens

Enterococcus faecium (E. faecium) is an alternative to antibiotics, while the probiotic effect of short-term application in mature broiler chickens remains unclear. In the current study, 48 Arbor Acres male broilers were chosen to investigate the effects of E. faecium on growth performance, the gut microbiome and intestinal health during the finishing period. Forty-eight birds were randomly allocated to 4 treatment groups that were fed a corn-soybean meal basal diet (Con), a basal diet supplemented with 1 g/kg amoxicillin (ABX), 5×106 CFU/g encapsulated E. faecium (cEF), or 5×106 CFU/g uncoated E. faecium (EF) from d 33 to 42. The results showed that 10 d of antibiotic treatment decreased the growth performance of the broilers (P < 0.05). The feed conversion ratio of the cEF and EF groups were lower than that of the Con group by 0.13 and 0.07, respectively (P > 0.05). The abundance of viable ileal and cecal E. faecium in the cEF group was greater than that in the EF group (P < 0.05), and both groups were markedly greater than those in the Con and ABX groups (P < 0.05). The ABX treatment decreased the Shannon and Chao1 indices of the cecal microbiota, while the dietary E. faecium treatment resulted in significant differences in the β diversity of the ileal and cecal microbiota (P < 0.05). Mantel correlation revealed that the ileal microbiota at the genus level was significantly correlated with the growth performance of broilers, with Lactobacillus, Bacillus and Escherichia-Shigella showing positive and strong correlations (P < 0.05). In the ileum, the crypt depth was lower in the cEF group than in the Con group, but the villi height-to-crypt depth ratio was greater in the cEF group than in the other groups (P = 0.037). However, the expression of the ZO-2 and Occludin genes was downregulated in the E. faecium-fed birds (P < 0.05). In the cecum, the acetate, butyrate and total SCFA levels were greater in the EF group (P < 0.05), while the propionate, isobutyrate and isovalerate levels were lower in the ABX group (P < 0.05). In summary, 10 d of dietary supplementation with E. faecium markedly increased colonization in mature broilers and potentially improved growth performance by modulating the ileal microbiota. Encapsulation techniques could enable a slow release of E. faecium in the intestine, thereby reducing the negative impacts of rapid expansion of E. faecium on the intestinal epithelium.

Increase in HIV reservoir and T cell immune response after CoronaVac vaccination in people living with HIV

IntroductionCoronaVac, an inactivated vaccine developed by Sinovac Life Sciences, has been widely used for protection against Coronavirus Disease 2019 (COVID-19). This study investigates its effect on the HIV reservoir and T cell repertoires in people living with HIV (PLWHs). MethodsBlood samples were collected from fifteen PLWHs who were administered at least two doses of CoronaVac between April 2021 and February 2022. The levels of cell-associated HIV RNA (CA HIV RNA) and HIV DNA, as well as the T cell receptor (TCR) repertoire profiles, TCR clustering and TCRβ annotation, were studied. ResultsA significant increase was observed in CA HIV RNA at 2 weeks (431.5 ± 164.2 copies/106 cells, P = 0.039) and 12 weeks (330.2 ± 105.9 copies/106 cells, P = 0.019) after the second dose, when compared to the baseline (0 weeks) (73.6 ± 23.7 copies/106 cells). Various diversity indices of the TCRβ repertoire, including Shannon index, Pielou's evenness index, and Hvj Index, revealed a slight increase (P < 0.05) following CoronaVac vaccination. The proportion of overlapping TCRβ clonotypes increased from baseline (31.9 %) to 2 weeks (32.5 %) and 12 weeks (40.4 %) after the second dose. We also found that the breadth and depth of COVID-19-specific T cells increased from baseline (0.003 and 0.0035) to 12 weeks (0.0066 and 0.0058) post the second dose. ConclusionsOur study demonstrated an initial increase in HIV reservoir and TCR repertoire diversity, as well as an expansion in the depth and breadth of COVID-19-specific T-cell clones among CoronaVac-vaccinated PLWHs. These findings provide important insights into the effects of COVID-19 vaccination in PLWHs.

Flooding soil with biogas slurry suppresses root-knot nematodes and alters soil nematode communities

Root-knot nematodes (RKNs) pose a serious threat to crop production. Flooding soil with biogas slurry, combined with soil heating before crop planting, has the potential for RKN disease suppression. However, the actual effect of this method has not been verified under field conditions. Here, we present the results of a two-year field experiment in a greenhouse demonstrating the control effect on RKN disease and plant growth using this method, as well as its influence on the soil nematode community. Four treatments were set: untreated control (CK), local control method for RKN (CC), soil flooded with 70 % biogas slurry (BS70), and soil flooded with undiluted biogas slurry (BS100). In the first year, all three RKN control treatments significantly reduced the root-knot index (p < 0.05). In the next year, only BS70 and BS100 still presented significantly suppressed effects (p < 0.05), and it was more obvious under BS70 with a relative control effect of 74.6 %. In the first year, BS70 and BS100 significantly inhibited the plant height of watermelon (p < 0.05). In the next year, however, all three RKN control treatments promoted the growth of watermelon, and their stem diameter was significantly greater than that of CK. The application of biogas slurry (BS70 and BS100) significantly increased nematode richness and the Shannon index in the second year (p < 0.05). However, the structure index showed no significant difference among treatments (p > 0.05), indicating that biogas slurry application did not increase the soil food web complex. Principal component analysis showed that the application of biogas slurry changed the nematode community, especially under BS70, which presented a more lasting influence. The high-level input of biogas slurry also caused soil NH4+-N and heavy-metal and arsenic accumulation in the first year, but these soil-pollution risks disappeared in the second year.

Whole-plant silage maize to improve fiber digestive characteristics and intestinal microbiota of Hezuo pigs.

Utilizing roughage resources is an effective approach to alleviate the shortage of corn-soybean feed and reducing the costs in the swine industry. Hezuo pig is one group of plateau type local Tibetan pig with strong tolerance to crude feeding. Nevertheless, current research on the roughage tolerance in Hezuo pigs and the microbiological mechanisms behind it is still minimally.This study explored the impact of various ratios of whole-plant silage (WPS) maize on the pH, cellulase activity, short-chain fatty acids (SCFAs), and intestinal microbiota in Hezuo pigs. Thirty-two Hezuo pigs were randomly divided into four groups (n = 8). The control group received a basal diet, while experimental groups I, II, and III were given diets with incremental additions of 5%, 10%, and 15% air-dried WPS maize, respectively, for 120 days. The findings revealed that compared with the control group, in Group II, the pH of cecum and colon were notably decreased (p < 0.05), while acid detergent fiberdigestibility, the concentration of propionic and isobutyric acid in the cecum, and the concentration of isobutyric acid in the colon were significantly increased (p < 0.05). Also, carboxymethyl cellulase activity in the cecum in group II of Hezuo pigs was significantly higher than that in the other three groups (p < 0.05). Furthermore, the cecum microbiota showed a higher diversity in the group II of Hezuo pigs than that in the control group, as shown by the Simpson and Shannon indices. Specifically, 15 and 24 bacterial species showed a significant difference in relative abundance at the family and genus levels, respectively. Correlation analyses revealed significant associations between bacterial genera and SCFAs concentrations in the cecum. The abundance of Bacteroides and NK4A214_group was positively correlated with amounts of valeric and isovaleric acid but negatively with propionic acid (p < 0.05). The abundance of UCG-010 was positively linked with acetic acid and negatively correlated with butyric acid (p < 0.05). Actinobacillus abundance was positively associated with butyric acid levels (p < 0.05). In conclusion, a 10% WPS maize diet improved crude fiber digestibility by lowering cecal and colonic chyme pH, enhancing intestinal cellulase activity, improving SCFA production, and increasing intestinal microbiota diversity.

Comparative assessment of woody species diversity, structure and carbon stock of PFM and Non-PFM forests and its implication for REDD+ in Ethiopia

Maintaining forest biodiversity and carbon sequestration potential of forest resources enhances the provision capacity of forest ecosystem services. Experience from around the world and in Ethiopia has shown that shifting forest management from state-centred to community-centred arrangement can result in a better forest stock. Therefore, this study examined the status of woody species diversity, regeneration and total living biomass carbon stock of forests under participatory forest management (PFM) and the adjacent state managed non-participatory forest management (Non-PFM) in South eastern Ethiopia and implications to REDD+. Data were collected from 89 (44 PFM and 45 Non-PFM) nested circular plots from four PFM and three Non-PFM selected forest sites with transects laid systematically. Tree DBH and height were measured, the number of saplings, seedlings, mature trees were counted and species names were recorded. Woody species diversity was estimated using shannon, simpson, and evenness diversity indices. A total of 29 and 23 woody species were recorded in PFM and Non-PFM forests, respectively. Woody species diversity did not show significant difference between PFM and Non-PFM forests but it was relatively higher in PFM forest. The density per hectare of seedlings, sapling and mature trees were significantly greater in PFM forest than in Non-PFM forest. The mean aboveground biomass carbon stock of PFM forest (225.50±26.54) was significantly greater than that of the Non-PFM (156.24±15.72) forest. Hence, managing forests through participatory approaches contributes to the enhancement of sustainable management and climate change mitigation potentials through reducing emission from deforestation and forest degradation.

Gut microbiota and its relationship with early vascular ageing in a Spanish population (MIVAS study).

Gut microbiota and its by-products are increasingly recognized as having a decisive role in cardiovascular diseases. The aim is to study the relationship between gut microbiota and early vascular ageing (EVA). A cross-sectional study was developed in Salamanca (Spain) in which 180 subjects aged 45-74 years were recruited. EVA was defined by the presence of at least one of the following: carotid-femoral pulse wave velocity (cf-PWV), cardio-ankle vascular index (CAVI) or brachial-ankle pulse wave velocity (ba-PWV) above the 90th percentile of the reference population. All other cases were considered normal vascular ageing (NVA). cf-PWV was measured by SphygmoCor® System; CAVI and ba-PWV were determined by Vasera 2000® device. Gut microbiome composition in faecal samples was determined by 16S rRNA Illumina sequencing. Mean age was 64.4 ± 6.9 in EVA group and 60.4 ± 7.6 years in NVA (p < .01). Women in EVA group were 41% and 53% in NVA. There were no differences in the overall composition of gut microbiota between the two groups when evaluating Firmicutes/Bacteriodetes ratio, alfa diversity (Shannon Index) and beta diversity (Bray-Curtis). Bilophila, Faecalibacterium sp.UBA1819 and Phocea, are increased in EVA group. While Cedecea, Lactococcus, Pseudomonas, Succiniclasticum and Dielma exist in lower abundance. In logistic regression analysis, Bilophila (OR: 1.71, 95% CI: 1.12-2.6, p = .013) remained significant. In the studied Spanish population, early vascular ageing is positively associated with gut microbiota abundance of the genus Bilophila. No relationship was found between phyla abundance and measures of diversity.