Abundance-based Coverage Estimator Research Articles

Variation in Pesticide Toxicity in the Western Honey Bee (Apis mellifera) Associated with Consuming Phytochemically Different Monofloral Honeys.

Insecticide toxicity to insect herbivores has long been known to vary across different host plants; this phenomenon has been widely documented in both foliage-feeders and sap-feeders. Species-specific phytochemical content of hostplant tissues is assumed to determine the pattern of induction of insect enzymes that detoxify insecticides, but specific phytochemicals have rarely been linked to host plant-associated variation in pesticide toxicity. Moreover, no studies to date have examined the effects of nectar source identity and phytochemical composition on the toxicity of insecticides to pollinators. In this study, we compared LD50 values for the insecticide bifenthrin, a frequent contaminant of nectar and pollen in agroecosystems, in the western honey bee, Apis mellifera, consuming three phytochemically different monofloral honeys: Nyssa ogeche (tupelo), Robinia pseudoacacia (black locust), and Fagopyrum esculentum (buckwheat). We found that bifenthrin toxicity (LD50) values for honey bees across different honey diets is linked to their species-specific phytochemical content. The profiles of phenolic acids and flavonoids of buckwheat and locust honeys are richer than is the profile of tupelo honey, with buckwheat honey containing the highest total content of phytochemicals and associated with the highest bifenthrin LD50 in honey bees. The vector fitting in the ordination analysis revealed positive correlations between LD50 values and two honey phytochemical richness estimates, Chao1 and Abundance-based Coverage Estimator (ACE). These findings suggest unequal effects among different phytochemicals, consistent with the interpretation that certain compounds, including ones that are rare, may have a more pronounced effect in mitigating pesticide toxicity.

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.

NRT1.1B mediates rice plant growth and soil microbial diversity under different nitrogen conditions

Interactions between microorganisms and plants can stimulate plant growth and promote nitrogen cycling. Nitrogen fertilizers are routinely used in agriculture to improve crop growth and yield; however, poor use efficiency impairs the optimal utilization of such fertilizers. Differences in the microbial diversity and plant growth of rice soil under different nitrogen application conditions and the expression of nitrogen-use efficiency-related genes have not been previously investigated. Therefore, this study investigates how nitrogen application and nitrogen-use efficiency-related gene NRT1.1B expression affect the soil microbial diversity and growth indices of two rice varieties, Huaidao 5 and Xinhuai 5. In total, 103,463 and 98,427 operational taxonomic units were detected in the soils of the Huaidao 5 and Xinhuai 5 rice varieties, respectively. The Shannon and Simpson indices initially increased and then decreased, whereas the Chao and abundance-based coverage estimator indices decreased after the application of nitrogen fertilizer. Nitrogen fertilization also reduced soil bacterial diversity and richness, as indicated by the reduced abundances of Azotobacter recorded in the soils of both rice varieties. Nitrogen application initially increased and then decreased the grain number per panicle, yield per plant, root, stem, and leaf nitrogen, total nitrogen content, glutamine synthetase, nitrate reductase, urease, and root activities of both varieties. Plant height showed positive linear trends in response to nitrogen application, whereas thousand-grain weights showed a negative trend. Our findings may be used to optimize nitrogen fertilizer use for rice cultivation and develop crop-variety-specific strategies for nitrogen fertilizer application.

Soil bacterial community in a photovoltaic system adopted different survival strategies to cope with small-scale light stress under different vegetation restoration modes.

Solar photovoltaic (PV) power generation is a major carbon reduction technology that is rapidly developing worldwide. However, the impact of PV plant construction on subsurface microecosystems is currently understudied. We conducted a systematic investigation into the effects of small-scale light stress caused by shading of PV panels and sampling depth on the composition, diversity, survival strategy, and key driving factors of soil bacterial communities (SBCs) under two vegetation restoration modes, i.e., Euryops pectinatus (EP) and Loropetalum chinense var. rubrum (LC). The study revealed that light stress had a greater impact on rare species with relative abundances below 0.01% than on high-abundance species, regardless of the vegetation restoration pattern. Additionally, PV shadowing increased SBCs' biomass by 20-30% but had varying negative effects on the numbers of Operational Taxonomic Unit (OTU), Shannon diversity, abundance-based coverage estimator (ACE), and Chao1 richness index. Co-occurrence and correlation network analysis revealed that symbiotic relationships dominated the key SBCs in the LC sample plots, with Chloroflexi and Actinobacteriota being the most ecologically important. In contrast, competitive relationships were significantly increased in the EP sample plots, with Actinobacteriota having the most ecological importance. In the EP sample plot, SBCs were found to be more tightly linked and had more stable ecological networks. This suggests that EP is more conducive to the stability and health of underground ecosystems in vulnerable areas when compared with LC. These findings offer new insights into the effects of small-scale light stress on subsurface microorganisms under different vegetation restoration patterns. Moreover, they may provide a reference for optimizing ecological restoration patterns in fragile areas.

The Changes, Aggregation Processes, and Driving Factors for Soil Fungal Communities during Tropical Forest Restoration.

Soil fungal communities play crucial roles in mediating the functional associations between above- and belowground components during forest restoration. Forest restoration shapes the alterations in plant and soil environments, which exerts a crucial effect on soil fungal assemblages. However, the changes, assembly processes, and driving factors of soil fungi communities during tropical forest restoration are still uncertain. We used Illumina high-throughput sequencing to identify the changes of soil fungal communities across a tropical secondary forest succession chronosequence (i.e., 12-, 42-, and 53-yr stages) in Xishuangbanna. During forest restoration, the dominant taxa of soil fungi communities shifted from r- to K-strategists. The relative abundance of Ascomycota (r-strategists) decreased by 10.0% and that of Basidiomycota (K-strategists) increased by 4.9% at the 53-yr restoration stage compared with the 12-yr stage. From the 12-yr to 53-yr stage, the operational taxonomic unit (OTU), abundance-based coverage estimator (ACE), Chao1, and Shannon index of fungal communities declined by 14.5-57.4%. Although the stochastic processes were relatively important in determining fungal assemblages at the late stage, the fungal community assembly was dominated by deterministic processes rather than stochastic processes. The shifts in soil properties resulting from tropical forest restoration exerted significant effects on fungal composition and diversity. The positive effects of microbial biomass carbon, readily oxidizable carbon, and soil water content explained 11.5%, 9.6%, and 9.1% of the variations in fungal community composition, respectively. In contrast, microbial biomass carbon (40.0%), readily oxidizable carbon (14.0%), and total nitrogen (13.6%) negatively contributed to the variations in fungal community diversity. Our data suggested that the changes in fungal composition and diversity during tropical forest restoration were primarily mediated by the positive or negative impacts of soil carbon and nitrogen pools.

Analysis of subgingival bacterial and fungal diversity in patients with peri-implantitis based on 16sRNA and internal transcribed spacer sequencing.

Aim: To analyze subgingival fungal diversity in peri-implant inflammation patients and their relationship with bacteria. Methods: We collected saliva samples from four groups. 16sRNA and internal transcribed spacer sequencing was performed preceded by quantitative PCR and enzyme-linked immunosorbent assay tests. Analyses were done usingR and Cytoscape software. Results: Significant differences were observed in the Abundance-based Coverage Estimator(ACE) index between control and peri-implantitis samples. Basidiomycota was the dominant fungal species, while Firmicutes dominated thebacteria. The most abundant fungal and bacterial species were 's_unclassified g Apiotrichum' and 's_unclassified g Streptococcus', respectively. Dothiorella was strongly associated with immunoglobulin G levels, with positive correlations between specific microorganisms and peri-implantitis in Q-PCR. Conclusion: Our findings have significant clinical implications, suggesting specific fungal and bacterial taxaroles in peri-implant inflammation.

Composition of gut microbiota and non-alcoholic fatty liver disease: A systematic review and meta-analysis.

The present systematic review and meta-analysis aimed to summarize the associations between gut microbiota composition and non-alcoholic fatty liver disease. To compare the differences between individuals with or without NAFLD, the standardized mean difference and 95% confidence interval were computed for each α-diversity index and relative abundance of gut microbes. The β-diversity indices were summarized in a qualitative manner. A total of 54 studies with 8894 participants were included. Overall, patients with NAFLD had moderate reduction in α-diversity indices including Shannon (SMD = -0.36, 95% CI = [-0.53, -0.19], p < 0.001) and Chao 1 (SMD = -0.42, 95% CI = [-0.68, -0.17], p = 0.001), but no significant differences were found for Simpson, observed species, phylogenetic diversity, richness, abundance-based coverage estimator, and evenness (p ranged from 0.081 to 0.953). Over 75% of the included studies reported significant differences in β-diversity. Although there was substantial interstudy heterogeneity, especially for analyses at the phylum, class, and family levels, the majority of the included studies showed alterations in the depletion of anti-inflammatory microbes (i.e., Ruminococcaceae and Coprococcus) and the enrichment of proinflammatory microbes (i.e., Fusobacterium and Escherichia) in patients with NAFLD. Perturbations in gut microbiota were associated with NAFLD, commonly reflected by a reduction in beneficial species and an increase in the pathogenic species.

Microbiome Analysis of Organic and Conventional Chickens Processed Using Whole Carcass Enrichment and Rinse Methods

Investigating the chicken microbiome is important to establish control measures for pathogens to protect consumers. This study aimed at evaluating the comparative efficiency of human pathogen detection through 16S rRNA sequencing of organic and conventional chickens processed using whole carcass enrichment (WCE) and rinse (WCR) methods. Organic and conventional whole broiler carcasses (n = 31) were vigorously shaken with 500 mL buffered peptone water (BPW). For the rinse method, a 30 mL aliquot was mixed with 30 mL of BPW. The rest of the sample, including the carcass, was used for the enrichment method. All samples were incubated at 37°C for 24 h. The samples were divided into five groups [Negative Control: only BPW without chicken (n = 5), Organic-Rinsed (n = 7), -Enriched (n = 8), Conventional-Rinsed (n = 7), and -Enriched (n = 9)]. Fifty milliliters of each sample were subjected to DNA extraction followed by 16S rRNA sequencing. Proteobacteria and Firmicutes predominated the microbiota of both conventional and organic chickens, followed by low abundances of Bacteroidetes and Fusobacterium. While the abundance of Proteobacteria and Firmicutes remained unchanged in organic chicken irrespective of the methods used, a noticeable shift in the Proteobacteria and Firmicutes ratio (59%:39% in rinsed to 38%:60% in enriched) was observed in conventional chicken. Furthermore, the choice of method did not yield any differences in Abundance-Based Coverage Estimator, and Jackknife, among conventional and organic chickens but resulted in a statistically significant difference in the Shannon, Simpson, Chao1, and phylogenetic diversity indices (p < 0.05). The relative abundance of Salmonella and Campylobacter was less than 0.1%. The results suggested the WCE method provides a broad range of information on the chicken microbiome.

Effects of polyethylene microplastics on properties, enzyme activities, and the succession of microbial community in Mollisol: At the aggregate level

Soil, as a heterogeneous body, is composed of different-sized aggregates. There is limited data available on the potential role of microplastics (MPs) in microbial properties at the soil aggregate level. In this study, changes in microbial construction and diversity in farmland bulk soil and aggregates induced by polyethylene MPs (PE-MPs) were investigated at a dose of 0.5% (w/w) through 16s rDNA sequencing and enzyme activity measurements of different particle size aggregates in incubated soil. The presence of low-dose PE-MPs increased the proportion of >1 mm soil aggregates fraction, and decreased soil available nitrogen and available phosphorus in bulk soils. Furthermore, low-dose PE-MPs increased bacterial richness and diversity in 1–0.5 and < 0.25 mm fractions and decreased operational taxonomic unit, abundance-based coverage estimator, and Chao1 indices in bulk soil and >1 mm fractions. The levels of predicted functional genes taking part in the biodegradation and metabolism of exogenous substances also increased. At the phylum level, PE-MPs changed the proportion of Proteobacteria and Actinobacteria. The variations in soil aggregate properties were significantly correlated with the bacterial communities’ composition and diversity. This study deepens our perception of the soil microenvironment, microbial community composition, and diversity in response to PE-MPs.

Effect of the oil from the fatty tissues of Crocodylus siamensis on gut microbiome diversity and metabolism in mice.

Dietary fat can alter host metabolism and gut microbial composition. Crocodile oil (CO) was extracted from the fatty tissues of Crocodylus siamensis. CO, rich in monounsaturated- and polyunsaturated fatty acids, has been reported to reduce inflammation, counter toxification, and improve energy metabolism. The aim of this study was to investigate the effect of CO on gut microbiota (GM) in laboratory mice as well as the accompanying metabolic changes in the animals. Forty-five C57BL/6 male mice were randomly divided into five groups and orally administrated either sterile water (control [C]); 1 or 3% (v/w) CO (CO-low [CO-L] and CO-high [CO-H], respectively); or 1 or 3% (v/w) palm oil (PO-low and PO-high, respectively) for 11 weeks. Body weight gain, food intake, energy intake, blood glucose levels, and blood lipid profiles were determined. Samples from colon tissue were collected and the 16S rRNA genes were pyrosequenced to clarify GM analyses. The results showed that there were no differences in body weight and blood glucose levels. Food intake by the mice in the CO-L and CO-H groups was statistically significantly less when compared to that by the animals in the C group. However, neither CO treatment had a statistically significant effect on calorie intake when compared to the controls. The CO-H exhibited a significant increase in serum total cholesterol and low-density lipoprotein but showed a downward trend in triglyceride levels compared to the control. The GM analyses revealed that both CO treatments have no significant influence on bacterial diversity and relative abundance at the phylum level, whereas increases of Choa1 and abundance-based coverage estimator indexes, distinct β-diversity, and Proteobacteria abundance were observed in the PO-high group compared with the C group. Furthermore, the abundance of Azospirillum thiophilum and Romboutsia ilealis was significantly higher in the CO-L and CO-H groups which could be associated with energy metabolic activity. Thus, CO may be an alternative fat source for preserving host metabolism and gut flora.

Effects of grazing prohibition on nirK- and nirS-type denitrifier communities in salt marshes.

Grazing prohibition is an effective management practice to restore salt marsh functioning. However, the effects of grazing exclusion on denitrifying microbial communities and their controlling factors in salt marshes remain unclear. In this study, we surveyed soil physicochemical properties and above- and below-ground biomass and using quantitative polymerase chain reaction and Illumina MiSeq high-throughput sequencing technology to determine the relative abundance, composition, and diversity of nitrite reductase nirS- and nirK-type denitrifying bacterial communities associated with grazing prohibition treatments and elevations. The abundance of nirS-type denitrifiers increased with grazing prohibition time, whereas the abundance of nirK-type denitrifiers remained unaltered. Moreover, nirS-type denitrifiers were more abundant and diverse than nirK-type denitrifiers in all treatments. Grazing prohibition significantly altered the operational taxonomic unit richness, abundance-based coverage estimator, and Chao1 indices of the nirS-type denitrifying bacterial communities, whereas it only minimally affected the structure of the nirK-type denitrifying bacterial community. The results imply that the nirS community, rather than nirK, should be the first candidate for use as an indicator in the process of salt marsh restoration after grazing prohibition. Substances of concern, total nitrogen, and salinity were the key environmental factors affecting the abundance and community composition of nirS and nirK denitrifiers. The findings of this study provide novel insights into the influence of the length of grazing prohibition and elevation on nirS- and nirK-type denitrifying bacterial community composition in salt marshes.

Ischaemic stroke patients present sex differences in gut microbiota.

Gut microbiota plays a role in the pathophysiology of ischaemic stroke (IS) through the bidirectional gut-brain axis. Nevertheless, little is known about sex-specific microbiota signatures in IS occurrence. A total of 89 IS patients and 12 healthy controls were enrolled. We studied the taxonomic differences of the gut microbiota between men and women with IS by shotgun metagenomic sequencing. To evaluate the causal effect of several bacteria on IS risk, we performed a two-sample Mendelian randomisation (MR) with inverse-variance weighting (IVW) using genome-wide association analysis (GWAS) summary statistics from two cohorts of 5959 subjects with genetic and microbiota data and 1,296,908 subjects with genetic and IS data, respectively. α-Diversity analysis measured using Observed Species (p = 0.017), Chao1 (p = 0.009) and Abundance-based Coverage Estimator (p = 0.012) indexes revealed that IS men have a higher species richness compared with IS women. Moreover, we found sex-differences in IS patients in relation to the phylum Fusobacteria, class Fusobacteriia, order Fusobacteriales and family Fusobacteriaceae (all Bonferroni-corrected p < 0.001). MR confirmed that increased Fusobacteriaceae levels in the gut are causally associated with an increased risk of IS (IVW p = 0.02, β = 0.32). Our study is the first to indicate that there are gut microbiome differences between men and women with IS, identifying high levels of Fusobacteriaceae in women as a specific risk factor for IS. Incorporating sex stratification analysis is important in the design, analysis and interpretation of studies on stroke and the gut microbiota.

Perturbations in gastrointestinal tract microbiota composition and function in individuals with yellow-greasy tongue coating

ObjectiveTo study the composition and function of tongue coating (TC) and gastrointestinal tract (GIT) microbiota in participants with yellow-greasy tongue coating (YGTC), and to explore the representative metabolite markers and pathways in this group. MethodsSubjects with YGTC or thin-white tongue coating (TWTC) were recruited from December 1, 2021 to October 30, 2022, and the TC and fecal samples were collected. Samples were subjected to both whole-genome shotgun (WGS), and 16S rRNA gene sequencing. The α-diversity analysis, principal component analysis (PCA), and Spearman correlation analysis were performed for two groups. Ultra-performance liquid chromatography combined with tandem mass spectrometry (UPLC–MS/MS) analysis was used to analyze metabolomics and enrichment of metabolic pathways. ResultsThe results revealed 20 YGTC participates and 19 TWTC participates. At the genus level, the dominant bacterial species of TC flora and intestinal flora in the two groups were roughly the same, but the relative kurtosis difference was marked, and the abundance of potentially pathogenic bacteria in TC and fecal samples of YGTC subjects was higher. There were 9 down-regulated microorganisms in the TC samples, 26 down-regulated microorganisms, and 6 up-regulated microorganisms in YGTC subjects. The α-diversity analysis indicated that the Chao and abundance-based coverage estimator (ACE) indices of TC bacteria in the YGTC subjects showed a decreasing trend, but the difference was not statistically significant (P > 0.05). The α-diversity of fecal samples and the Chao and ACE indices decreased significantly (P < 0.05). PCA showed that the microflora structure of TC and fecal samples were significantly different between the two groups. Spearman correlation analysis showed that there was no correlation between TC and fecal microorganisms at phyla and genus levels in the same subjects (P > 0.05). The metabolomics results demonstrated that fumarate reductase, V/A ATPase, and phosphatidylethanolamine were increased, and glycerate-3p, UDP-glucose, and quinone oxidoreductase metabolites were decreased in YGTC TC samples. Inosine monophosphate (IMP), uridine monophosphate (UMP), and gamma-aminobutyric acid (GABA) were increased in YGTC fecal samples, while the contents of ribo-5P, histidine, biotin, and cobalamin were decreased. Metabolic pathway analysis indicated that the abundance of the TC and fecal samples of the YGTC subjects was relatively low in various metabolic pathways, including amino acid metabolism, carbohydrate metabolism, nitrogen metabolism, and energy metabolism. ConclusionStructural and functional changes in TC and GIT microbiota or metabolite markers could be potential biological bases of YGTC formation.

Soil centipedes (Chilopoda, Geophilomorpha) in the Val Camonica forests (Southern Alps): species composition and richness.

Soil centipedes (Chilopoda, Geophilomorpha) are a widespread group of predators in the forest soils of the European Alps. While in the eastern and western parts of the Southern Prealps, larger efforts were devoted to sample and study the geophilomorph fauna, little is known about species richness and composition of geophilomorph communities in the central part of Southern Prealps. In this work, five sites located in the Val Camonica were surveyed by hand searching, between November 2021 and July 2022 and their species richness was estimated applying non-parametrical statistical methods (Chao-1 and Abundance-based Coverage Estimator) to account for incomplete detection. A total of 18 species were found amongst the five sites. A maximum of 12 species were recorded in each single site, while estimates suggest that another 1-3 species were likely undetected. Species composition were found highly variable also between sites with similar species richness.

Supplementation of exogenous bile acids improve antitrichomonal activity and enhance intestinal health in pigeon (Columba livia)

The study investigated the effects of supplementation of bile acids in drinking water on antitrichomonal activity, growth performance, immunity and microbial composition of pigeon. A total of 180 pairs of White King parent pigeons were randomly assigned to 5 treatments of 6 replications with 6 pairs of parent pigeons and 12 squabs in each replicate. The control (CON) group drank water without any additions. The metronidazole (MTZ) group drank water with 500 μg/mL metronidazole for 7 d and without any additions in other days. The else groups drank water with 500, 750, and 1,250 μg/mL bile acid (BAL, BAM, BAH) for 28 d. The results showed that Trichomonas gallinae (T. gallinae) in MTZ, BAL, BAM, and BAH groups were lower than that in CON group at 14, 21, and 28 d of parent pigeons (P < 0.05) and at 21 and 28 d of squabs (P < 0.05). Albumin and alanine transaminase in CON group were higher than those in MTZ, BAL, and BAH groups (P < 0.05). The levels of soluble CD8 were higher in MTZ and BAH groups compared with CON group (P < 0.05). The lesions in oral mucosa, thymus, liver, and spleen tissues of CON group could be observed. Abundance-based coverage estimator (ACE) index in BAH group was higher than that in CON and MTZ groups. Simpson index in CON and BAH groups was higher than MTZ group (P < 0.05). Lactobacillus was the highest colonized colonic bacteria in genera that were 77.21, 91.20, and 73.19% in CON, MTZ, and BAH, respectively. In conclusion, drinking water supplemented with 500, 750, and 1,250 μg/mL bile acid could inhibit growth of T. gallinae in both parent pigeons and squabs. Squabs infected with T. gallinae in control group had higher mortality rate and more serious tissue lesions. Squabs in bile acids treated group had more sCD8 in serum and abundant intestinal morphology. Bile acids could be an efficient drinking supplements to inhibit T. gallinae and improve pigeon adaptive immunity and intestinal health.

Altered gut microbiota and microbial metabolism in children with hepatic glycogen storage disease: a case-control study.

Accumulating evidence has demonstrated that gut microbiota dysbiosis correlated with altered metabolism are implicated in liver metabolic diseases. However, data on pediatric hepatic glycogen storage disease (GSD) are limited. Here, we aimed to investigate the features of the gut microbiota and metabolites in hepatic GSD children from China. Totals of 22 hepatic GSD patients and 16 age- and gender-matched healthy children were enrolled from the Shanghai Children's Hospital, China. Pediatric GSD patients were confirmed as having hepatic GSD via genetic diagnosis and/or liver biopsy pathology. The control group comprised children without any history of chronic diseases or clinically relevant GSD or symptoms of any other metabolic diseases. The baseline characteristics of the two groups were gender- and age-matched matched using chi-squared test and the Mann-Whitney U test, respectively. The gut microbiota, bile acids (BAs), and short chain fatty acids (SCFAs) were determined from the feces using 16S ribosomal RNA (rRNA) gene sequencing, ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS), and gas chromatography-mass spectrometry (GC-MS), respectively. The alpha diversity of fecal microbiome was significantly lower in hepatic GSD patients [observed species richness (Sobs): P=0.011; abundance-based coverage estimator (ACE): P=0.011; Chao: P=0.011; Shannon: P<0.001], and their microbial community was more distanced from that of the control [principal coordinate analysis (PCoA) on genus level, unweighted UniFrac: P=0.011]. Relative abundances of phyla Firmicutes (P=0.030) and Bacteroidetes (P=0.029), families Lachnospiraceae (P=0.012), Ruminococcaceae (P=0.008), and Peptostreptococcaceare (P=0.031), genera Blautia (P=0.017), Eubacterium_hallii_group (P=0.032), and Faecalibacterium (P=0.017) were decreased, whereas phyla Actinobacteria (P=0.033), Proteobacteria (P=0.049), families Bifidobacteriaceae (P=0.030), Lactobacillaceae (P=0.034), and Veillonellaceae (P=0.033), genera Lactobacillus (P=0.011), Enterobater (P=0.034), and Veillonella (P=0.014) were increased in hepatic GSD. Altered microbial metabolisms were characterized by increased abundances of primary BAs (P=0.009) and decreased concentrations of SCFAs in hepatic GSD children. Furthermore, the altered bacterial genera were correlated with the changes of both fecal BAs and SCFAs. The hepatic GSD patients in this study presented with gut microbiota dysbiosis which correlated with altered BAs metabolism and fecal SCFAs changes. Further studies are needed to investigate the driver of these changes mediated by either the genetic defect, disease status, or diet therapy.

Comparison of Soil Bacterial Communities under Canopies of Pinus tabulaeformis and Populus euramericana in a Reclaimed Waste Dump

To compare the effects of different remediation tree species on soil bacterial communities and provide a theoretical basis for the selection of ecosystem function promotion strategies after vegetation restoration, the characteristic changes in soil bacterial communities after Pinus tabulaeformis and Populus euramericana reclamation were explored using high-throughput sequencing and molecular ecological network methods. The results showed that: (1) With the increase in reclamation years, the reclaimed soil properties were close to the control group, and the soil properties of Pinus tabulaeformis were closer to the control group than those of P. euramericana. (2) The dominant bacteria under the canopies of P. tabulaeformis and P. euramericana was the same. Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Gemmatimonadetes, Planctomycetes, Bacteroidetes, and Cyanobacteria were the dominant bacteria in the restored soil, accounting for more than 95% of the total abundance. The average values of the Shannon diversity index, Simpson diversity index, Chao 1 richness estimator, and abundance-based coverage estimator of the bacterial community in the P. euramericana reclaimed soil were higher than those in the P. tabulaeformis reclaimed soil. The influence of reclamation years on the bacterial community of samples is greater than that of species types. (3) The results of ecological network construction showed that the total number of nodes, total number of connections, and average connectivity of the soil bacterial network under P. euramericana reclamation were greater than those under P. tabulaeformis reclamation. The bacterial molecular ecological network under P. euramericana was more abundant. (4) Among the dominant bacteria, the relative abundance of Actinobacteria was negatively correlated with soil pH, soil total nitrogen content, and the activities of urease, invertase, and alkaline phosphatase, while the relative abundance of Proteobacteria and Bacteroidetes was positively correlated with these environmental factors. The relationship between the soil bacterial community of P. tabulaeformis and P. euramericana and the environmental factors is not completely the same, and even the interaction between some environmental factors and bacteria is opposite.

Fecal Microbiome Does Not Represent Whole Gut Microbiome

The current gut microbiome research relies on the fecal microbiome under the assumption that the fecal microbiome represents the microbiome of the entire gastrointestinal (GI) tract. However, there have been growing concerns about using feces as a proxy to study the gut microbiome. Here, we comprehensively analyzed the composition of microbiome and metabolites in the feces and at 14 different locations of GI tracts of genetically homogenous sibling pigs to evaluate the validity of using feces as a proxy to the whole gut microbiome. The composition of intestinal microbes constituting the gut microbiome at each intestinal content and feces and their metabolic compositions were thoroughly investigated through metagenome sequencing and an ultraperformance LC-MS/MS, respectively. The fluctuation in the composition of the microbiome in the stomach and the small intestine became stabilized from the large intestine to feces and was able to be categorized into 3 groups. The taxonomic α-diversities measured by ACE (abundance-based coverage estimator) richness and Shannon diversity indicated that the microbiome in the large intestine was much more diverse than those of the small intestine and feces. The highly independent intestinal microbes in the stomach and the small intestine became flourished in the large intestine and converged into a community with tightly connected networks. β-Diversity analyses by NMDS plots, PCA, and unsupervised hierarchical clustering all showed that the diversities of microbiome compositions were lowest in feces while highest in the large intestine. In accordance with fluctuation of the composition of gut microbiome along with the GI tract, the metabolic composition also completely differed in a location-specific manner along with the GI tract. Comparative analysis of the fecal microbiome and metabolites with those of the whole GI tract indicated that fecal microbiome is insufficient to represent the whole gut microbiome.

Estimating total species richness: Fitting rarefaction by asymptotic approximation

AbstractEstimating the number of species in a community is important for assessments of biodiversity. Previous species richness estimators are mainly based on nonparametric approaches. Although parametric asymptotic models have been applied, they received limited attention due to specific limitations. Here, we introduce parametric models fitting the probability‐based rarefied species richness curve that allow us to estimate the “Total Expected Species” (TES) in a community based on species' abundance data. We develop two approaches to calculate TES (termed “TESa” and “TESb”), based on two slightly different mathematical assumptions regarding Expected Species (ES) models. We provide R functions to calculate both these estimation approaches and their standard deviation. The function also enables users to visualize the estimation. We test the performance of TESa, TESb, and their average (TESab) across simulated and empirical data, and compare their bias, precision, and accuracy with other commonly used, nonparametric species richness estimators: the bias‐corrected (bc‐)Chao1 and the abundance‐based coverage estimator (ACE). Simulation reveals that in small samples TESa shows a tendency to overestimate and TESb to underestimate overall species richness. TESab performs well in bias, precision, and accuracy when compared with (bc‐)Chao1 and ACE estimators. Results from empirical data show that the variance generated from TES estimates is comparable with that for (bc‐)Chao1 and ACE. Our study demonstrates that rarefaction theory in combination with parametric approximation models provides a valuable new approach to estimate the species richness of incompletely sampled communities. Robust estimates are likely to be obtained where the observed number of species is greater than half of the TES estimation. When the ratio of TESa to the observed richness is ≫2, we suggest the use of TESb or TESab. Although more comprehensive comparisons with other estimators are suggested, we encourage researchers to consider the TES approach in their biodiversity studies as a complement to current existing estimators.

The Potential Use of Endophyte-Free inebrians as Sheep Feed Evaluated with In Vitro Fermentation

Endophytic fungal infection is the major reason for intoxication of animals caused by drunken horse grass. Fortunately, it has been established that seed detoxification techniques and isolation of endophytic fungi infect non-endophytic fungi populations with the same genetic background as endophyte-infected Achnatherum inebrians. Moreover, sheep can use endophyte-free Achnatherum inebriants (EF) without obvious toxicity symptoms. The present study selected EF as a representative grass, consisting of five different replacement levels, EF0, EF25, EF50, EF75, and EF100, corresponding to 0%, 25%, 50%, 75%, and 100% of the fermentation substrate, respectively. Simultaneously, in vitro fermentation and the 16S rRNA amplicon sequencing method was used to explore the effect of EF on sheep ruminal fermentation and microbial diversity. The results revealed that EF100 had the highest values for pH, acetate: propionate, the Patescibacteria, Kiritimatiellaeota, and Synergistetes phylum levels, Ruminococcaceae, Prevotellaceae, and Saccharofermentans genus levels than the other treatments (p &lt; 0.05). In contrast, EF25 was associated with higher levels of abundance-based coverage estimator (ACE), Chaol index of the phyla Synergistetes and Bacteroidetes, and of the genus Erysipelotrichaceae, Rikenellaceae, and Prevotella as compared with other treatments (p &lt; 0.05). EF50 resulted in the greatest values for the genus Christensenellaceae and Lachnospiraceae as compared with other treatments (p &lt; 0.05). EF75 resulted in the greatest values for the Shannon index as compared with other treatments (p &lt; 0.05). EF0 resulted in the greatest values for gas production (GP), ammonia nitrogen (NH3-N), total volatile fatty acid (TVFA), acetate, propionate, butyrate, valerate, isobutyrate, isovalerate, and the phyla Firmicutes, Proteobacteria, and Spirochaetes, and the genus Succiniclasticum, Ruminobacter, Family_XIII and Treponema as compared with other treatments (p &lt; 0.05). PICRUSt2 analysis indicated that most of the functional prediction pathways were involved in Carbohydrate metabolism and, Amino acid metabolism. Therefore, the recommended ratio of EF in sheep diet should range from 25% to 50%, and the maximum proportion should not exceed 75%.