Number Of Operational Taxonomic Units Research Articles

Multiple-trait genomic prediction for swine meat quality traits using gut microbiome features as a correlated trait.

Traits such as meat quality and composition are becoming valuable in modern pork production; however, they are difficult to include in genetic evaluations because of the high phenotyping costs. Combining genomic information with multiple-trait indirect selection with cheaper indicator traits is an alternative for continued cost-effective genetic improvement. Additionally, gut microbiome information is becoming more affordable to measure using targeted rRNA sequencing, and its applications in animal breeding are becoming relevant. In this paper, we investigated the usefulness of microbial information as a correlated trait in selecting meat quality in swine. This study incorporated phenotypic data encompassing marbling, colour, tenderness, loin muscle and backfat depth, along with the characterization of gut (rectal) microbiota through 16S rRNA sequencing at three distinct time points of the animal's growth curve. Genetic progress estimation and cross-validation were employed to evaluate the utility of utilizing host genomic and gut microbiota information for selecting expensive-to-record traits in crossbred individuals. Initial steps involved variance components estimation using multiple-trait models on a training dataset, where the top 25 associated operational taxonomic units (OTU) for each meat quality trait and time point were included. The second step compared the predictive ability of multiple-trait models incorporating different numbers of OTU with single-trait models in a validation set. Results demonstrated the advantage of including genomic information for some traits, while in some instances, gut microbial information proved advantageous, namely, for marbling and pH. The study suggests further investigation into the shared genetic architecture between microbial features and traits, considering microbial data's compositional and high-dimensional nature. This research proposes a straightforward method to enhance swine breeding programs for improving costly-to-record traits like meat quality by incorporating gut microbiome information.

Sequence analysis of microbiota in clinical human cases with diabetic foot ulcers from China

BackgroundDiabetic foot ulcers (DFU) seriously threaten the health and quality of life of patients. The microbiota is the primary reason for the refractory and high recurrence of DFU. This study aimed to determine the wound microbiota at different DFU stages. MethodsWound samples were collected from 48 patients with DFU and divided into three phases: inflammatory (I, n = 49), proliferation (P, n = 22), and remodeling (R, n = 19). The wound samples obtained at different stages were then subjected to 16S rRNA gene sequencing. The number of operational taxonomic units (OTUs) in the different groups was calculated according to the criterion of 97% sequence similarity. The diversity of the microbiota differentially presented bacterial taxa at the phylum and genus levels, and important phyla and genera in the different groups were further explored. ResultsAfter sequencing, 3351, 925, and 777 OTUs were observed in groups I, P, and R, respectively, and 175 OTUs overlapped. Compared with the inflammatory stage, the α-diversity of wound microbiota at proliferation and remodeling stages was significantly decreased (P < 0.05). At the phylum level, Firmicutes, Proteobacteria, Actinobacteriota, and Bacteroidota were the dominant phyla, accounting for more than 90% of all the phyla. At the genus level, Random Forest and linear discriminant analysis effect size analyses showed that Peptoniphilus, Lactobacillus, Prevotella, Veillonella, Dialister, Streptococcus, and Ruminococcus were the signature wound microbiota for the inflammatory stage; Anaerococcus, Ralstonia, Actinomyces, and Akkermansia were important species for the proliferation stage; and the crucial genera for the remodeling stage were Enterobacter, Pseudomonas, Sondgrassella, Bifidobacterium, and Faecalibacterium. ConclusionsThere were significant differences in the composition and structure of the wound microbiota in patients with DFU at different stages, which may lay a foundation for effectively promoting wound healing in DFU.

An optimal combined slow-release nitrogen fertilizer and urea can enhance the decomposition rate of straw and the yield of maize by improving soil bacterial community and structure under full straw returning system.

Under a full straw returning system, the relationship between soil bacterial community diversity and straw decomposition, yield, and the combined application of slow-release nitrogen and urea remains unclear. To evaluate these effects and provide an effective strategy for sustainable agricultural production, a 2-year field positioning trial was conducted using maize as the research object. Six experimental treatments were set up: straw returning + no nitrogen fertilizer (S1N0), straw returning + slow-release nitrogen fertilizer:urea = 0:100% (S1N1), straw returning + slow-release nitrogen fertilizer:urea = 30%:70% (S1N2), straw returning + slow-release nitrogen fertilizer:urea = 60%:40% (S1N3), straw returning + slow-release nitrogen fertilizer:urea = 90%:10% (S1N4), and straw removal + slow-release nitrogen fertilizer:urea = 30%:70% (S0N2). Significant differences (p < 0.05) were observed between treatments for Proteobacteria, Acidobacteriota, Myxococcota, and Actinobacteriota at the jointing stage; Proteobacteria, Acidobacteriota, Myxococcota, Bacteroidota, and Gemmatimonadota at the tasseling stage; and Bacteroidota, Firmicutes, Myxococcota, Methylomirabilota, and Proteobacteria at the maturity stage. The alpha diversity analysis of the soil bacterial community showed that the number of operational taxonomic units (OTUs) and the Chao1 index were higher in S1N2, S1N3, and S1N4 compared with S0N2 at each growth stage. Additionally, the alpha diversity measures were higher in S1N3 and S1N4 compared with S1N2. The beta diversity analysis of the soil bacterial community showed that the bacterial communities in S1N3 and S1N4 were more similar or closely clustered together, while S0N2 was further from all treatments across the three growth stages. The cumulative straw decomposition rate was tested for each treatment, and data showed that S1N3 (90.58%) had the highest decomposition rate. At the phylum level, straw decomposition was positively correlated with Proteobacteria, Actinobacteriota, Myxococcota, and Bacteroidota but significantly negatively correlated with Acidobacteriota. PICRUSt2 function prediction results show that the relative abundance of bacteria in soil samples from each treatment differed significantly. The maize yield of S1N3 was 15597.85 ± 1477.17 kg/hm2, which was 12.80 and 4.18% higher than that of S1N1 and S0N2, respectively. In conclusion, a combination of slow-release nitrogen fertilizer and urea can enhance the straw decomposition rate and maize yield by improving the soil bacterial community and structure within a full straw returning system.

Assessing the impacts of aquaculture on local fish communities using environmental DNA metabarcoding analysis

AbstractFish aquaculture potentially affects the local ecosystem through feed (leftovers) and feces. However, evaluation of its impacts on biodiversity, especially those of mobile organisms such as fish, is not straightforward. Here, we report a case study in which environmental DNA (eDNA) metabarcoding with MiFish universal primers for the 12S rRNA region of fish is used to detect and assess the impact of aquaculture on local fish communities. In Shizugawa Bay, Minamisanriku Town, Miyagi Prefecture, Japan, Oncorhynchus kisutch (coho salmon) is aquacultured in sea cages from November to July, but is absent from August to October. We conducted eDNA surveys in June, August, October, and December 2021 of water at depths of 5 m and 1 m above the bottom obtained from two sites, one approximately 100 m and the other approximately 2500 m from the nearest aquaculture site. The total number of operational taxonomic units (OTUs) detected was 122, with a maximum of 50 and a minimum of 10. With distance‐based redundancy analysis (dbRDA) and PERMANOVA applied to the eDNA‐based community compositional data, we detected a significant effect of the presence of O. kisutch aquaculture on fish biodiversity. The generalized linear model (GLM) applied to each detected OTUs indicated that the aquaculture was associated positively with Leucopsarion petersii (ice goby), and Oncorhynchus spp. and negatively with Chaenogobius annularis (forktongue goby). Environmental DNA metabarcoding surveys, combined with multivariate statics, are a promising tool to identify the dimension of biodiversity that human activity affects and would serve as a basic survey for sustainable use of the sea.

Cyanobacterial and moss biocrusts shape soil nematode community in dryland mountain ecosystems with increasing aridity

Soil nematodes are the most abundant animals on Earth and play critical roles in regulating numerous ecosystem processes, from enhancing primary productivity to mineralizing multiple nutrients. In dryland soils, a rich community of microphyte organisms (biocrusts) provide critical habitats for soil nematodes, but their presence is being threatened by increasing aridity induced by global climate change. Despite its importance, how types of biocrusts and aridity index influence soil nematode community in dryland mountain ecosystems remains largely unknown. To fill these knowledge gaps, we conducted a field survey with contrasting aridity indexes (0.2, 0.4, and 0.6) and three types of biocrusts (cyanobacterial, cyanobacterial-moss mixed, and moss crusts) in the topsoil (0–5 cm) from the northern Chinese Loess Plateau. We found that the abundance (number of individuals per gram of soil), richness (number of Operational Taxonomic Units; OTUs), and diversity (number of different species) of soil nematodes were remarkably higher under biocrusts than in bare soils, regardless of aridity index and types of biocrusts. Our results also showed that the same variables had the highest values in moss crusts compared to cyanobacterial and cyanobacterial-moss mixed crusts. Structural equation modelling further revealed that biocrust types and traits (i.e., biocrust thickness, chlorophyll content, shear force, and penetration resistance) are the most important factors associated with both nematode abundance and richness. Together, our findings indicate that biocrusts, especially moss cover, and less stressful aridity conditions favor soil nematodes community in dryland mountain regions. Such knowledge is critical for anticipating the distribution of these animals under climate change scenarios and, ultimately, the numerous ecosystem services supported by soil nematodes.

Do Concurrent Peri-Implantitis and Periodontitis Share Their Microbiotas? A Pilot Study.

The microbial compositions from concurrent peri-implant and periodontal lesions were compared, since the results reported in the literature on the etiological relationship between these oral pathologies are contradictory. Microbial compositions from nine patients were evaluated using Illumina MiSeq sequencing of 16S rRNA gene amplicons and Principal Components Analysis. Comparisons between the use of curettes or paper points as collection methods and between bacterial composition in both pathologies were performed. Paper points allowed the recovery of a higher number of bacterial genera. A higher bacterial diversity was found in peri-implantitis compared to periodontal samples from the same patient, while a greater number of operational taxonomic units (OTUs) were present in the corresponding periodontal samples. A higher abundance of oral pathogens, such as Porphyromonas or Treponema, was found in peri-implantitis sites. The opposite trend was observed for Aggregatibacter abundance, which was higher in periodontal than in peri-implantitis lesions, suggesting that both oral pathologies could be considered different but related diseases. Although the analysis of a higher number of samples would be needed, the differences regarding the microbial composition provide a basis for further understating the pathogenesis of peri-implant infections.

Comparison of DNA metabarcoding and microscopy in analysing planktonic protists from the European Arctic

In the era of climate change-related restructuring of planktonic protist communities, it is especially important to identify possible shifts in their taxonomic composition. While traditional microscopy-based morphological classification is time-consuming and requires experienced taxonomists, metabarcoding seems to substantially accelerate the determination of taxonomic composition. In this study, based on samples collected in summer 2019 from the West Spitsbergen Current, we analysed planktonic protists using both methods. Metabarcoding, based on high-throughput sequencing of the V4 region of the 18S rRNA gene, resulted in a much higher number of operational taxonomic units (OTUs) and sample diversity than microscopy, although the resolution of taxonomic identification ranged from species to phyla. Most morphology-based identification was performed at the species or genus level, additionally allowing us to include information about dominants and size fractions. The highest proportion of 45% shared taxa by both methods was recorded at the class level. The composition of dominant protists differed between the approaches, with most similarities being observed in Bacillariophyceae, for which two genera, Thalassiosira and Eucampia, were found to be the most abundant with both methods. For Dinophyceae, the most abundant representatives identified by microscopy were Gymnodinium spp., Prorocentrum minimum and Gonyaulax gracilis, while in the metabarcoding approach, most dinoflagellates were identified to the class level only. Given the different levels of accuracy of taxonomic determinations and possible biases in results connected to the chosen methodology, we advocate using an integrative taxonomic approach for the classification of planktonic protists based on the combination of microscopy and molecular methods.

Asymptomatic Enteric Virus Infections and Association with the Gut Microbiome in Rural Residents of Northern Laos.

Viral gastrointestinal infections are an important public health concern, and the occurrence of asymptomatic enteric virus infections makes it difficult to prevent and control their spread. This study aimed to determine the prevalence of and factors associated with asymptomatic enteric virus infection in adults in northern Laos. Fecal samples were collected from apparently healthy participants who did not report diarrhea or high fever at the time of the survey in northern Laos, and enteric viruses were detected using polymerase chain reaction (PCR) and reverse transcription (RT)-PCR. Individual characteristics, including the gut microbiome, were compared between asymptomatic carriers and noncarriers of each enteric virus. Of the participants (N = 255), 12 (4.7%) were positive for norovirus genogroup I (GI), 8 (3.1%) for human adenovirus, and 1 (0.4%) for norovirus GII; prevalence tended to be higher in less-modernized villages. Gut microbial diversity (evaluated by the number of operational taxonomic units) was higher in asymptomatic carriers of norovirus GI or human adenovirus than in their noncarriers. Gut microbiome compositions differed significantly between asymptomatic carriers and noncarriers of norovirus GI or human adenovirus (permutational analysis of variance, P <0.05). These findings imply an association between asymptomatic enteric virus infection and modernization and/or the gut microbiome in northern Laos.

Microbiome Analysis Revealed Acholeplasma as a Possible Factor Influencing the Susceptibility to Bacterial Leaf Blight Disease of Two Domestic Rice Cultivars in Vietnam.

The microbiomes of two important rice cultivars in Vietnam which differ by their susceptibility to the bacterial leaf blight (BLB) disease were analyzed through 16S rRNA amplicon technology. A higher number of operational taxonomic units and alpha-diversity indices were shown in the BLB-resistant LA cultivar than in the BLB-susceptible TB cultivar. The BLB pathogen Xanthomonas was scantly found (0.003%) in the LA cultivar, whereas was in a significantly higher ratio in the TB cultivar (1.82%), reflecting the susceptibility to BLB of these cultivars. Of special interest was the genus Acholeplasma presented in the BLB-resistant LA cultivar at a high relative abundance (22.32%), however, was minor in the BLB-sensitive TB cultivar (0.09%), raising a question about its roles in controlling the Xanthomonas low in the LA cultivar. It is proposed that Acholeplasma once entered the host plant would hamper other phytopathogens, i.e. Xanthomonas, by yet unknown mechanisms, of which the triggering of the host plants to produce secondary metabolites against pathogens could be a testable hypothesis.

Effects of γ-polyglutamic acid supplementation on alfalfa growth and rhizosphere soil microorganisms in sandy soil

This study aimed at exploring the effects of γ-polyglutamic acid on the growth of desert alfalfa and the soil microorganisms in the rhizosphere. The study examined the effects of varying concentrations of γ-polyglutamic acid (0%-CK, 2%-G1, 4%-G2, 6%-G3) on sandy soil, the research investigated its impact on the growth characteristics of alfalfa, nutrient content in the rhizosphere soil, and the composition of bacterial communities. The results indicated that there were no significant differences in soil organic matter, total nitrogen, total phosphorus, total potassium, and available phosphorus content among the G1, G2, and G3 treatments. Compared to CK, the soil nutrient content in the G2 treatment increased by 14.81–186.67%, showing the highest enhancement. In terms of alfalfa growth, the G2 treatment demonstrated the best performance, significantly increasing plant height, chlorophyll content, above-ground biomass, and underground biomass by 54.91–154.84%. Compared to the CK treatment, the number of OTUs (operational taxonomic units) in the G1, G2, and G3 treatments increased by 14.54%, 8.27%, and 6.84%, respectively. The application of γ-polyglutamic acid altered the composition and structure of the bacterial community, with Actinobacteriota, Proteobacteria, Chloroflexi, Acidobacteriota, and Gemmatimonadota accounting for 84.14–87.89% of the total bacterial community. The G2 treatment significantly enhanced the diversity and evenness of soil bacteria in the rhizosphere. Redundancy analysis revealed that organic matter, total nitrogen, total potassium, moisture content, and pH were the primary factors influencing the structure of bacterial phyla. At the genus level, moisture content emerged as the most influential factor on the bacterial community. Notably, moisture content exhibited a strong positive correlation with Acidobacteriota, which in turn was positively associated with indicators of alfalfa growth. In summary, the application of γ-polyglutamic acid at a 4% ratio has the potential for improving sandy soil quality, promoting plant growth, and regulating the rhizosphere microbial community.

Severe fever with thrombocytopenia syndrome virus infection shapes gut microbiome of the tick vector Haemaphysalis longicornis

BackgroundTicks serve as vectors for a diverse array of pathogens, including viruses responsible for both human and livestock diseases. Symbiotic bacteria hold significant potential for controlling tick-borne disease. However, the alteration of tick gut bacterial community in response to pathogen infection has not been analyzed for any tick-borne viruses. Here, the impact of severe fever with thrombocytopenia syndrome virus (SFTSV) infection on bacterial diversity in the gut of Haemaphysalis longicornis is investigated.MethodsUnfed tick females were artificially infected with SFTSV. The gut samples were collected and the genomic DNA was extracted. We then investigated alterations in gut bacterial composition in response to SFTSV infection through 16S rRNA gene sequencing.ResultsThe study found that a reduction in the number of operational taxonomic units (OTUs) in the tick gut following SFTSV infection. However, there were no significant changes in alpha diversity indices upon infection. Four genera, including Corynebacterium, Arthrobacter, Sphingomonas, and Escherichia, were identified as biomarkers for the tick gut without SFTSV infection. Notably, the predicted correlation network indicated that the biomarkers Sphingomonas and Escherichia exhibited positive correlations within the same subcommunity, which was altered upon viral infection.ConclusionsThese findings revealed that the change in tick gut bacterial composition upon SFTSV infection and could facilitate the discovery new target for tick-borne viral disease control.Graphical

Effects of running time on biological activated carbon filters: water purification performance and microbial community evolution.

Ozone-biologically activated carbon (BAC) filtration is an advanced treatment process that can be applied to remove recalcitrant organic micro-pollutants in drinking water treatment plants (DWTPs). In this study, we continuously monitored a new and an old BAC filter in a DWTP for 1year to compare their water purification performance and microbial community evolution. The results revealed that, compared with the new filter, the use of the old BAC filter facilitated a slightly lower rate of dissolved organic carbon (DOC) removal. In the case of the new BAC filter, we recorded general increases in the biomass and microbial diversity of the biofilm with a prolongation of operating time, with the biomass stabilizing after 7months. For both new and old BAC filters, Proteobacteria and Acidobacteria were the dominant bacterial phyla. At the genus level, the microbial community gradually shifted over the course of operation from a predominance of Herminiimonas and Hydrogenophaga to one predominated by Bradyrhizbium, Bryobacter, Hyphomicrobium, and Pedomicrobium, with Bradyrhizobium being established as the most abundant genus in the old BAC filter. Regarding spatial distribution, we detected reductions in the biomass and number of operational taxonomic units with increasing biofilm depth, whereas there was a corresponding increase in microbial diversity. However, compared with the effects of time, the influence of depth on the composition of the biofilm microbial community was considerably smaller. Furthermore, co-occurrence network analysis revealed that the microbial community network of the new filter after 11months of operation was the most tightly connected, although its modular coefficient was the lowest of those assessed. We speculate that the positive and negative interactions within the network may be attributable to symbiotic or competitive relationships among species. Moreover, there may have been a significant negative interaction between SWB02 and Acidovorax, plausibly associated with a competition for substrates.

Distribution of rhizosphere fungi of Kobresia humilis on the Qinghai-Tibet Plateau.

Kobresia humilis is a major species in the alpine meadow communities of the Qinghai-Tibet Plateau (QTP); it plays a crucial role in maintaining the ecological balance of these meadows. Nevertheless, little is known about the rhizosphere fungi associated with K. humilis on the Qinghai Tibet Plateau. In this study, we used Illumina Miseq to investigate the fungal diversity, community structure, and ecological types in the root and rhizosphere soil of K. humilis across eight areas on the QTP and analyzed the correlation between rhizosphere fungi of K. humilis and environmental factors. A total of 19,423 and 25,101 operational taxonomic units (OTUs) were obtained from the roots and rhizosphere soil of K. humilis. These were classified into seven phyla, 25 classes, 68 orders, 138 families, and 316 genera in the roots, and nine phyla, 31 classes, 76 orders, 152 families, and 407 genera in the rhizosphere soil. There were 435 and 415 core OTUs identified in root and rhizosphere soil, respectively, which were categorized into 68 and 59 genera, respectively, with 25 shared genera. Among them, the genera with a relative abundance >1% included Mortierella, Microscypha, Floccularia, Cistella, Gibberella, and Pilidium. Compared with the rhizosphere soil, the roots showed five differing fungal community characteristics, as well as differences in ecological type, and in the main influencing environmental factors. First, the diversity, abundance, and total number of OTUs in the rhizosphere soil of K. humilis were higher than for the endophytic fungi in the roots by 11.85%, 9.85%, and 22.62%, respectively. The composition and diversity of fungal communities also differed between the eight areas. Second, although saprotroph-symbiotrophs were the main ecological types in both roots and rhizosphere soil; there were 62.62% fewer pathotrophs in roots compared to the rhizosphere soil. Thirdly, at the higher altitude sites (3,900-4,410 m), the proportion of pathotroph fungi in K. humilis was found to be lower than at the lower altitude sites (3,200-3,690 m). Fourthly, metacommunity-scale network analysis showed that during the long-term evolutionary process, ZK (EICZK = 1) and HY (EICHY = 1) were critical sites for development of the fungal community structure in the roots and rhizosphere soil of K. humilis, respectively. Fifthly, canonical correspondence analysis (CCA) showed that key driving factors in relation to the fungal community were longitude (R2 = 0.5410) for the root community and pH (R2 = 0.5226) for the rhizosphere soil community. In summary, these results show that K. humilis fungal communities are significantly different in the root and rhizosphere soil and at the eight areas investigated, indicating that roots select for specific microorganisms in the soil. This is the first time that the fungal distribution of K. humilis on the QTP in relation to long-term evolutionary processes has been investigated. These findings are critical for determining the effects of environmental variables on K. humilis fungal communities and could be valuable when developing guidance for ecological restoration and sustainable utilization of the biological resources of the QTP.

The effect of type and combination of fertilizers on eukaryotic microbiome of date palm rhizosphere

The date palm (Phoenix dactylifera) is an important cultivated crop in arid areas. Here, we studied the effect of plant genotype and type of fertilizers on the eukaryotic community structures of the date palm rhizosphere. Samples were collected from one wild population, five cultivars from two farms, and a factorial fertilizer experiment (organic, chemical, and biofertilizer) in Qatar. The eukaryotic communities were sequenced using a next-generation sequencing method. A total of 2422 Operational Taxonomic Units (OTUs) were identified as belonging to 15 phyla, Chlorophyta, Streptophyta, Imbricatea, Chytridiomycota, Ascomycota, Olpidiomycota, being dominant. The wild-type date palms showed a low number of OTUs compared to cultivated date palms, potentially due to the strong influence of soil salinity and low moisture level. However, the wild-type date palm hosted the highest number of unique OTUs. PCA revealed that the eukaryotic microbiome of the wild date palms was separated from the cultivated date palms and that the eukaryotic microbial diversity varied between date palm cultivars in similar environments. Using the highest amounts of biofertilizer and chemical fertilizer decreased the species diversity within the samples. However, a high concentration of biofertilizer combined with a low concentration of chemical fertilizers enhanced the eukaryotic diversity within the samples. We conclude that cultivar type (biotic factor), type of fertilizer, and dosage (abiotic factor) play significant roles in determining the microbiome diversity of the rhizosphere. The wild date palm population could potentially host salt and drought-tolerating eukaryotes that should be further investigated for future development of biofertilizers suitable for drylands.

P1213 The effects of Escherichia coli Nissle 1917 on the gut microbiota composition in ulcerative colitis patients

Abstract Background Escherichia coli Nissle (EcN) 1917 is a Gram-negative bacterium currently used as probiotic in the management of infectious gastroenteritis and ulcerative colitis (UC). We evaluated the effect of administration of EcN on the composition of the gut microbiota and on intestinal permeability in patients affected by UC. Methods Five patients with stable UC were treated with EcN one pill daily for ten days followed by two pills per day for further twenty days. Fecal samples were collected before the treatment (T0), after ten days (T1) and after one month of treatment (T2). Alpha diversity, microbiota composition and taxonomy were analyzed. Results Alpha diversity increased through treatment: Good’s coverage index revealed an increase in the number of operational taxonomic units (OTUs) at T2. At phylum taxonomic level, Firmicutes relative abundance decreased at T1 compared to T0. At family level, Clostridiacae relative abundance at T1 was higher than T0 and T2. The T test on gut microbiota variations at species level reveals the variability at the two timepoints (T0 and T2), with significant increase for Actinomyces, Anaerostipes, Bacteroides, Bulleidia, Corynebacterium, Dialister, Enterobacteriaceae, Erysipelotrichaceae, Finegoldia, Granulicatella, Lactobacillaceae, Peptoniphilus, Phascolarctobacterium, Roseburia, Serratia, Veillonellaceae, Veillonella dispar. Furthermore, the administration of EcN improved intestinal permeability, assessed on a CaCO2 monolayer. Conclusion Treatment with EcN leads to an improvement in the qualitative composition of the gut microbiota in patients affected by UC, in terms of both diversity and taxonomy. These effects are stronger at the end of treatment.

Comparison of mucosal microbiomes from biliary tract among patients with extrahepatic cholangiocarcinoma, patients with chronic cholecystitis, and healthy controls.

550 Background: Cholangiocarcinoma (CCA) is a malignancy associated with a poor prognosis. Gut microbiome dysbiosis is considered to be related with multiple disease, including and cancer. However, relationship between mucosal microbiome dysbiosis and CCA remains unclear. In this study, we evaluated mucosal microbiome of patients with extrahepatic-CCA (EH-CCA) and compared it with patients with chronic cholecystitis (CC) and living liver donors who served as healthy control (HC), to understand the role of microbiome in development EH-CCA. Methods: A total of 18 patients with EH-CCA, 21 patients with CC, and 17 HC were included. During operation, swab sample were obtained from cancer tissue of patient with EH-CCA and from gallbladder in other participants, respectively. The bacterial 16S rRNA gene (V3/V4 region) was amplified using PCR and sequenced on the Illumina MiSeq platform. The QIIME 2 pipelines were used to analyze the raw data. Results: The median age were 71, 53, and 29 years for patients with EH-CCA, patients with CC, and HC, respectively. The mean number of operational taxonomic unit were significantly higher in the CCA (13,037 [SD 9,676]) compared to HC (5,045 [12,679]; p&lt;0.001). Among the sample from HC, the most abundant taxa at phylum level was Firmicutes (74.47%), followed by Bacteroidota (14.8%), and Proteobacteria accounted for only 2%. In the CC group, Firmicutes is most abundant (63.15%) phylum, followed by Proteobacteria (22.09%). In contrast, among the samples from CCA, Proteobacteria were the most common phylum (50.43%). Pairwise comparison of α-diversity measured by Chao1 index showed that richness was higher in samples from CC compared to other groups (vs HC, p=0.02; vs CCA, p&lt;0.001). In terms of α-diversity measured by Shannon index, samples from cancer have lower diversity compared to healthy controls ( p&lt;0.001), however, no significant differences were found between samples from cancer and CC ( p=0.1). The Principal Coordinate Analysis plot based on Bray-Curtis distance showed that all three groups formed significantly separate clusters (p=0.001). The linear discriminant analysis effect size showed that the most abundant taxa from samples from CCA were Enterobacter, Klebsiella, and Fusobacterium. In the samples from HC, Limosilactobacillus, Lachnospiraceae_NK4A136_group, and Faecalibacterium were most significant, while Lactobacillus and Pseudomonas were most abundant among the CC group. Conclusions: This study compared the mucosal microbiome from biliary tract among patients with CCA, patients with CC, and HC. All three groups showed significantly different microbiome profiles. In CCA sample, the proportion of Proteobacteria is high, and diversity were low, suggesting mucosal microbial dysbiosis. Further studies are needed to investigate the clinical implications of microbial dysbiosis in CCA.

Diversity of Arbuscular Mycorrhizal Fungi in Distinct Ecosystems of the North Caucasus, a Temperate Biodiversity Hotspot.

Investigations that are focused on arbuscular mycorrhizal fungus (AMF) biodiversity is still limited. The analysis of the AMF taxa in the North Caucasus, a temperate biodiversity hotspot, used to be limited to the genus level. This study aimed to define the AMF biodiversity at the species level in the North Caucasus biotopes. The molecular genetic identification of fungi was carried out with ITS1 and ITS2 regions as barcodes via sequencing using Illumina MiSeq, the analysis of phylogenetic trees for individual genera, and searches for operational taxonomic units (OTUs) with identification at the species level. Sequences from MaarjAM and NCBI GenBank were used as references. We analyzed >10 million reads in soil samples for three biotopes to estimate fungal biodiversity. Briefly, 50 AMF species belonging to 20 genera were registered. The total number of the AM fungus OTUs for the "Subalpine Meadow" biotope was 171/131, that for "Forest" was 117/60, and that for "River Valley" was 296/221 based on ITS1/ITS2 data. The total number of the AM fungus species (except for virtual taxa) for the "Subalpine Meadow" biotope was 24/19, that for "Forest" was 22/13, and that for "River Valley" was 28/24 based on ITS1/ITS2 data. Greater AMF diversity, as well as number of OTUs and species, in comparison with that of forest biotopes, characterized valley biotopes (disturbed ecosystems; grasslands). The correlation coefficient between "Percentage of annual plants" and "Glomeromycota total reads" r = 0.76 and 0.81 for ITS1 and ITS2, respectively, and the correlation coefficient between "Percentage of annual plants" and "OTUs number (for total species)" was r = 0.67 and 0.77 for ITS1 and ITS2, respectively. High AMF biodiversity for the river valley can be associated with a higher percentage of annual plants in these biotopes and the active development of restorative successional processes.

Diversity and composition of active and total bacteria in rhizospheric soil in response to continuous cropping years of Panax notoginseng.

The synchronous research and analysis of total and active soil microbial communities can provide insight into how these communities are impacted by continuous cropping years and pathogen infection. The diversity of total and active bacteria in rhizospheric soil of 2-year-old and 3-year-old healthy and diseased Panax notoginseng can comprehensively reveal the bacterial response characteristics in continuous cropping practice. The results showed that 4916 operational taxonomic units (OTUs) were found in the rhizospheric soil bacterial community of P. notoginseng at the DNA level, but only 2773 OTUs were found at the RNA level. The rhizospheric environment had significant effects on the active and bacterial communities, as indicated by the number of OTUs, Shannon, Chao1, Faith's phylogenetic diversity (Faith's PD), and Simpson's diversity indexes. The DNA level can better show the difference in diversity level before and after infection with root rot. The bacterial Chao1 and Faith's PD diversity indexes of 2-year-old root rot-diseased P. notoginseng rhizospheric soil (D2) were higher than that of healthy plants, while the bacterial Shannon diversity index of 3-year-old root rot-diseased P. notoginseng rhizospheric soil (D3) was the lowest in the total bacteria. Principal coordinate analysis (PCoA) illustrated that the total bacterial species composition changed markedly after root rot disease. There were significant differences in the composition of active bacterial species between the 2-year and 3-year rhizospheres. In conclusion, the total and active edaphic rhizospheric bacterial communities could provide important opportunities to understand the responses of bacteria to continuous cropping of P. notoginseng. Differential responses of total and active edaphic rhizosphere bacterial communities to continuous cropping of Panax notoginseng.

Insights into the composition and assembly mechanism of microbial communities on intertidal microsand grains

IntroductionMarine microorganisms are essential in marine ecosystems and have always been of interest. Currently, most marine microbial communities are studied at the bulk scale (millimeters to centimeters), and the composition, function and underlying assembly mechanism of microbial communities at the microscale (sub-100 micrometers) are unclear.MethodsThe microbial communities on microsand grains (40–100 µm, n = 150) from marine sediment were investigated and compared with those on macrosand grains (400–1000 µm, n = 60) and bulk sediments (n = 5) using amplicon sequencing technology.ResultsThe results revealed a significant difference between microsand grains and macrosand grains. Microsand grains had lower numbers of operational taxonomic units (OTUs(97%)) and predicted functional genes than macrosand grains and bulk-scale samples. Microsand grains also showed greater intersample differences in the community composition and predicted functional genes than macrosand grains, suggesting a high level of heterogeneity of microbial communities at the microscale. Analyses based on ecological models indicated that stochastic processes dominated the assembly of microbial communities on sand grains. Consistently, cooccurrence network analyses showed that most microbial cooccurrence associations on sand grains were highly unstable. Metagenomic sequencing and further genome-scale metabolic modeling revealed that only a small number (1.3%) of microbe pairs showed high cooperative potential.DiscussionThis study explored the microbial community of marine sediments at the sub-100 µm scale, broadening the knowledge of the structure and assembly mechanism of marine microbial communities.

Effects of hydroxy methionine zinc on growth performance, immune response, antioxidant capacity, and intestinal microbiota of red claw crayfish (Procambarus clarkii)

This study aimed to evaluate the effects of varying zinc (Zn) levels on the growth performance, non-specific immune response, antioxidant capacity, and intestinal microbiota of red claw crayfish (Procambarus clarkii (P. clarkii)). Adopting hydroxy methionine zinc (Zn-MHA) as the Zn source, 180 healthy crayfish with an initial body mass of 6.50 ± 0.05 g were randomly divided into the following five groups: X1 (control group) and groups X2, X3, X4, and X5, which were fed the basal feed supplemented with Zn-MHA with 0, 15, 30, 60, and 90 mg kg−1, respectively. The results indicated that following the addition of various concentrations of Zn-MHA to the diet, the following was observed: Specific growth rate (SGR), weight gain rate (WGR), total protein (TP), total cholesterol (TC), the activities of alkaline phosphatase (AKP), phenoloxidase (PO), total antioxidant capacity (T-AOC), total superoxide dismutase (T-SOD) and catalase (CAT), the expression of CTL, GPX, and CuZn-SOD genes demonstrated a trend of rising and then declining—with a maximum value in group X4—which was significantly higher than that in group X1 (P < 0.05). Zn deposition in the intestine and hepatopancreas, the activity of GSH-PX, and the expression of GSH-PX were increased, exhibiting the highest value in group X5. The malonaldehyde (MDA) content was significantly reduced, with the lowest value in group X4, and the MDA content of the Zn-MHA addition groups were significantly lower than the control group (P < 0.05). In the analysis of the intestinal microbiota of P. clarkii, the number of operational taxonomic units in group X4 was the highest, and the richness and diversity indexes of groups X3 and X4 were significantly higher than those in group X1 (P < 0.05). Meanwhile, the dietary addition of Zn-MHA decreased and increased the relative abundance of Proteobacteria and Tenericutes, respectively. These findings indicate that supplementation of dietary Zn-MHA at an optimum dose of 60 mg kg−1 may effectively improve growth performance, immune response, antioxidant capacity, and intestinal microbiota richness and species diversity in crayfish.