Analyzing the performance of short-read classification tools on metagenomic samples toward proper diagnosis of diseases.

Accurate knowledge of the genome, virus and bacteria that have invaded our bodies is crucial for diagnosing many human diseases. The field of bioinformatics encompasses the complex computational methods required for this purpose. Metagenomics employs next-generation sequencing (NGS) technology to study and identify microbial communities in environmental samples. This technique allows for the measurement of the relative abundance of different microbes. Various tools are available for detecting bacterial species in sequenced metagenomic samples. In this study, we focus on well-known taxonomic classification tools such as MetaPhlAn4, Centrifuge, Kraken2, and Bracken, and evaluate their performance at the species level using synthetic and real datasets. The results indicate that MetaPhlAn4 exhibited high precision in identifying species in the simulated dataset, while Kraken2 had the best area under the precision-recall curve (AUPR) performance. Centrifuge, Kraken2, and Bracken showed accurate estimation of species abundances, unlike MetaPhlAn4, which had a higher L2 distance. In the real dataset analysis with samples from an inflammatory bowel disease (IBD) research, MetaPhlAn4, and Kraken2 had faster execution times, with differences in performance at family and species levels among the tools. Enterobacteriaceae and Pasteurellaceae were highlighted as the most abundant families by Centrifuge, Kraken2, and MetaPhlAn4, with variations in abundance among ulcerative colitis (UC), Crohn's disease (CD), and control non-IBD (CN) groups. Escherichia coli (E. coli) has the highest abundance among Enterobacteriaceae species in the CD and UC groups in comparison with the CN group. Bracken overestimated E. coli abundance, emphasizing result interpretation caution. The findings of this research can assist in selecting the appropriate short-read classifier, thereby aiding in the diagnosis of target diseases.

Unassigning bacterial species for microbiome studies.

The method of 16S rRNA marker gene sequencing has fueled microbiome research and continues to be relevant. A perceived weakness of the method is that taxonomic assignments are not possible to make at the rank of species. We show that by working to rule out bacterial or archaeal species membership, we can provide an answer that is more accurate and useful. The Unassigner software operates on 16S rRNA marker gene data and computes a rule-out probability for species membership using a beta-binomial distribution. We demonstrate that our approach is accurate based on full-genome comparisons. Our method is consistent with existing approaches and dramatically improves on them based on the percentage of reads it can associate with a species in a sample. The software is available at https://github.com/PennChopMicrobiomeProgram/unassigner.IMPORTANCEWhile existing methods do not provide reliable species-level assignments for 16S rRNA marker gene data, the Unassigner software solves this problem by ruling out species membership, allowing researchers to reason at the species level.

Christensenella strain resources, genomic/metabolomic profiling, and association with host at species level.

The gut commensal bacteria Christensenellaceae species are negatively associated with many metabolic diseases, and have been seen as promising next-generation probiotics. However, the cultured Christensenellaceae strain resources were limited, and their beneficial mechanisms for improving metabolic diseases have yet to be explored. In this study, we developed a method that enabled the enrichment and cultivation of Christensenellaceae strains from fecal samples. Using this method, a collection of Christensenellaceae Gut Microbial Biobank (ChrisGMB) was established, composed of 87 strains and genomes that represent 14 species of 8 genera. Seven species were first described and the cultured Christensenellaceae resources have been significantly expanded at species and strain levels. Christensenella strains exerted different abilities in utilization of various complex polysaccharides and other carbon sources, exhibited host-adaptation capabilities such as acid tolerance and bile tolerance, produced a wide range of volatile probiotic metabolites and secondary bile acids. Cohort analyses demonstrated that Christensenellaceae and Christensenella were prevalent in various cohorts and the abundances were significantly reduced in T2D and OB cohorts. At species level, Christensenellaceae showed different changes among healthy and disease cohorts. C. faecalis, F. tenuis, L. tenuis, and Guo. tenuis significantly reduced in all the metabolic disease cohorts. The relative abundances of C. minuta, C. hongkongensis and C. massiliensis showed no significant change in NAFLD and ACVD. and C. tenuis and C. acetigenes showed no significant change in ACVD, and Q. tenuis and Geh. tenuis showed no significant change in NAFLD, when compared with the HC cohort. So far as we know, this is the largest collection of cultured resource and first exploration of Christensenellaceae prevalences and abundances at species level.

Using short-read 16S rRNA sequencing of multiple variable regions to generate high-quality results to a species level.

Introduction: Short-read amplicon sequencing studies have typically focused on 1-2 variable regions of the 16S rRNA gene. Species-level resolution is limited in these studies, as each variable region enables the characterisation of a different subsection of the microbiome. Although long-read sequencing techniques take advantage of all 9 variable regions by sequencing the entire 16S rRNA gene, they are substantially more expensive. This work assessed the feasibility of accurate species-level resolution and reproducibility using a relatively new sequencing kit and bioinformatics pipeline developed for short-read sequencing of multiple variable regions of the 16S rRNA gene. In addition, we evaluated the potential impact of different sample collection methods on our outcomes. Methods: Using xGen™ 16S Amplicon Panel v2 kits, sequencing of all 9 variable regions of the 16S rRNA gene was carried out on an Illumina MiSeq platform. Mock cells and mock DNA for 8 bacterial species were included as extraction and sequencing controls respectively. Within-run and between-run replicate samples, and pairs of stool and rectal swabs collected at 0-5 weeks from the same participants, were incorporated. Observed relative abundances of each species were compared to theoretical abundances provided by ZymoBIOMICS. Paired Wilcoxon rank sum tests and distance-based intraclass correlation coefficients were used to statistically compare alpha and beta diversity measures, respectively, for pairs of replicates and stool/rectal swab sample pairs. Results: Using multiple variable regions of the 16S ribosomal Ribonucleic Acid (rRNA) gene, we found that we could accurately identify taxa to a species level and obtain highly reproducible results at a species level. Yet, the microbial profiles of stool and rectal swab sample pairs differed substantially despite being collected concurrently from the same infants. Conclusion: This protocol provides an effective means for studying infant gut microbial samples at a species level. However, sample collection approaches need to be accounted for in any downstream analysis.

Flower morphology of Allium (Amaryllidaceae) and its systematic significance.

Allium is a complicated genus that includes approximately 1000 species. Although its morphology is well studied, the taxonomic importance of many morphological traits, including floral traits, are poorly understood. Here, we examined and measured the floral characteristics of 87 accessions of 74 Allium taxa (belonging to 30 sections and nine subgenera) from Central to Eastern Asian countries. We then examined the taxonomic relationships between select flower characteristics and a phylogenetic tree based on ITS sequences. Our results confirm that floral morphology provides key taxonomic information to assess species delimitation in Allium. We found that perianth color is an important characteristic within the subg. Melanocrommyum, Polyprason, and Reticulatobulbosa. In subg. Allium, Cepa, and Rhizirideum, significant characteristics include ovary shape, perianth shape, and inner tepal apex. For species in subg. Angunium, the key taxonomic character is ovule number (only one ovule in per locule). In the subg. Allium, Cepa, Polyprason, and Reticulatobulbosa, which belong to the third evolutionary line of Allium, hood-like appendages occur in the ovary, although these do not occur in subg. Rhizirideum. Our results also indicated that the flower morphology of several species in some sections are not clearly distinguished, e.g., sect. Sacculiferum (subg. Cepa) and sect. Tenuissima (subg. Rhizirideum). This study provides detailed photographs and descriptions of floral characteristics and information on general distributions, habitats, and phenology of the studied taxa.

Species-level resolution for the vaginal microbiota with short amplicons.

Specific bacterial species have been found to play important roles in human vagina. Achieving high species-level resolution is vital for analyzing vaginal microbiota data. However, contradictory conclusions were yielded from different methodological studies. More comprehensive evaluation is needed for determining an optimal pipeline for vaginal microbiota. Based on the sequences of vaginal bacterial species downloaded from NCBI, we conducted simulated amplification with various primer sets targeting different 16S regions as well as taxonomic classification on the amplicons applying different combinations of algorithms (BLAST+, VSEARCH, and Sklearn) and reference databases (Greengenes2, SILVA, and RDP). Vaginal swabs were collected from participants with different vaginal microecology to construct 16S full-length sequenced mock communities. Both computational and experimental amplifications were performed on the mock samples. Classification accuracy of each pipeline was determined. Microbial profiles were compared between the full-length and partial 16S sequencing samples. The optimal pipeline was further validated in a multicenter cohort against the PCR results of common STI pathogens. Pipeline V1-V3_Sklearn_Combined had the highest accuracy for classifying the amplicons generated from both the NCBI downloaded data (84.20% ± 2.39%) and the full-length sequencing data (95.65% ± 3.04%). Vaginal samples amplified and sequenced targeting the V1-V3 region but merely employing the forward reads (223 bp) and classified using the optimal pipeline, resembled the mock communities the most. The pipeline demonstrated high F1-scores for detecting STI pathogens within the validation cohort. We have determined an optimal pipeline to achieve high species-level resolution for vaginal microbiota with short amplicons, which will facilitate future studies.IMPORTANCEFor vaginal microbiota studies, diverse 16S rRNA gene regions were applied for amplification and sequencing, which affect the comparability between different studies as well as the species-level resolution of taxonomic classification. We conducted comprehensive evaluation on the methods which influence the accuracy for the taxonomic classification and established an optimal pipeline to achieve high species-level resolution for vaginal microbiota with short amplicons, which will facilitate future studies.

Express barcoding with NextGenPCR and MinION for species-level sorting of ecological samples.

The use of DNA barcoding is well established for specimen identification and large-scale biodiversity discovery, but remains underutilized for time-sensitive applications such as rapid species discovery in field stations, identifying pests, citizen science projects, and authenticating food. The main reason is that existing express barcoding workflows are either too expensive or can only be used in very well-equipped laboratories by highly-trained staff. We here show an alternative workflow combining rapid DNA extraction with HotSHOT, amplicon production with NextGenPCR thermocyclers, and sequencing with low-cost MinION sequencers. We demonstrate the power of the approach by generating 250 barcodes for 285 specimens within 6 h including specimen identification through BLAST. The workflow required only the following major equipment that easily fits onto a lab bench: Thermocycler, NextGenPCR, microplate sealer, Qubit, and MinION. Based on our results, we argue that simplified barcoding workflows for species-level sorting are now faster, more accurate, and sufficiently cost-effective to replace traditional morpho-species sorting in many projects.

Population-level call properties of endangered Dryophytes suweonensissensu lato (Anura: Amphibia) in South Korea.

Calling is one of the unique amphibian characteristics that facilitates social communication and shows individuality; however, it also makes them vulnerable to predators. Researchers use amphibian call properties to study their population status, ecology, and behavior. This research scope has recently broadened to species identification and taxonomy. Dryophytes flaviventris has been separated from the endangered anuran species, D. suweonensis, based on small variations in genetic, morphometric, and temporal call properties observed in South Korea. The Chilgap Mountain (CM) was considered as the potential geographic barrier for the speciation. However, it initiated taxonomic debates as CM has been hardly used and is considered a potential barrier for other species. The calls of populations from both sides are also apparently similar. Thus, to verify the differences in call properties among populations of D. suweonensis sensu lato (s.l.; both of the species), we sampled and analyzed call data from five localities covering its distribution range, including the southern (S) and northern (N) parts of CM. We found significant differences in many call properties among populations; however, no specific pattern was observed. Some geographically close populations, such as Iksan (S), Wanju (S), and Gunsan (S), had significant differences, whereas many distant populations, such as Pyeongtaek (N) and Wanju (S), had no significant differences. Considering the goal of this study was only to observe the call properties, we cautiously conclude that the differences are at the population level rather than the species level. Our study indicates the necessity of further investigation into the specific status of D. flaviventris using robust integrated taxonomic approaches, including genetic and morphological parameters from a broader array of localities.

Functional traits and habitat heterogeneity explain tree growth in a warm temperate forest.

To explore how traits determine demographic performance is an important goal of plant community ecology in explaining the assembly and dynamics of ecological communities. However, whether the prediction of individual-level trait data is more precise compared to species average trait data is questioned. Here, we analyzed the growth and trait data for 11 species collected from October 2018 to October 2020 in a temperate forest, Donglingshan, Beijing. To quantify the relationships between traits and growth rate, we conducted linear regression models at both the species and individual levels, as well as developed structural equation models at both levels. We found there was a clear difference in growth between the warm and cold seasons, with tree growth mainly concentrated in the warm season. Growth rate was positively correlated with the specific leaf area, while negatively correlated with leaf thickness and wood density without considering environmental information. Adding important contextual information in the analysis of species-level structural equation modeling, growth rates were positively correlated with specific leaf area and leaf thickness. However, in the individual-level, there was a negative correlation between growth rate and wood density. Our study showed that individual-level trait data have better predictions for individual growth than species-level data. When we use multiple traits and establish links between traits and tree size, we generated strong predictive relationships between traits and growth rates. Furthermore, our study highlighted that the importance of incorporating topographical factors and considering different seasons to assess the relationship between tree growth and functional traits.

First Argentine database for the accurate identification of Brucella to species level by MALDI-TOF MS.

MALDI-TOF mass spectrometry (MS) has proven to be a fast and reliable method for the identification of a large number of taxonomic groups. It offers the advantage of being able to incorporate protein spectra of microorganisms that are absent or poorly represented in commercial databases, such as the genus Brucella. The aim of the study was to build the first database of protein spectra of local biological variants of Brucella in Argentina and of standard strains. First, the identification performance of a panel of 135 strains was evaluated with the Swedish database ¨Folkhälsomyndigheten¨ (containing protein spectra of several international standards of the genus Brucella) imported from the open access site https://spectra.folkhalsomyndigheten.se/spectra/. With this library 100 % of the strains were correctly identified by mass spectrometry to genus level, but not to species level. Due to the limitation found, an in-house database was designed with local Brucella isolates from Argentina and standard strains used in routine bacteriological diagnosis. For its validation, a panel of strains, different from those used to develop the extended local database (n: 177), was used to, simultaneously, challenge both libraries. The samples were processed by triplicate and the results obtained were: 177 strains correctly identified to genus and species level compared to the gold standard method (phenotypic typing), meeting the criteria accepted by the literature and the manufacturer as reliable identification. Only 2 of these isolates had score values lower than 2 (1.862) and were therefore not included in the calculation of results. According to these results, MALDI-TOF MS is a fast and reliable method for the routine identification of the different Brucella species, and even has the advantage of reducing the time of exposure to pathogenic microorganisms for laboratorians. It could be considered a valuable technique to replace, in the near future, the current conventional techniques due to the ease of transferring protein spectra, avoiding the use of reference strains that are difficult to find commercially available and commonly used in phenotypic typing.

Impact of Lactobacillus in the uterine microbiota on in vitro fertilization outcomes.

Abundant intrauterine Lactobacillus is associated with good in vitro fertilization (IVF) outcomes; however, whether specific species of Lactobacillus have any benefit remains unclear. So we examine the effect of Lactobacillus on the clinical outcomes of IVF at the species level. Uterine microbiota were classified as either Lactobacillus-dominant (LD) or non-Lactobacillus-dominant. In the LD group, we further investigated the clinical results for each Lactobacillus species and evaluated them in relation to IVF outcomes. In Uterine microbiome analysis, Lactobacillus was the most abundant, with the four species of L. crispatus, L. iners, L. gasseri, and L. jensenii accounting for the great majority. We compared the clinical outcomes of single frozen-thawed embryo transfer conducted by Lactobacillus species and found that the implantation rate was lowest in those in whom L. iners was dominant. This study is the first to conduct a species-level analysis of the uterine microbiota and report on a detailed investigation of Lactobacillus, which was believed to be particularly helpful for pregnancy.

Species-Level Taxonomic Characterization of Uncultured Core Gut Microbiota of Plateau Pika.

Rarely has the vast diversity of bacteria on Earth been profiled, particularly on inaccessible plateaus. These uncultured microbes, which are also known as "microbial dark matter," may play crucial roles in maintaining the ecosystem and are linked to human health, regarding pathogenicity and prebioticity. The plateau pika (Ochotona curzoniae) is a small burrowing steppe lagomorph that is endemic to the Qinghai-Tibetan Plateau and is a keystone species in the maintenance of ecological balance. We used a combination of full-length 16S rRNA amplicon sequencing, shotgun metagenomics, and metabolomics to elucidate the species-level community structure and the metabolic potential of the gut microbiota of the plateau pika. Using a full-length 16S rRNA metataxonomic approach, we clustered 618 (166 ± 35 per sample) operational phylogenetic units (OPUs) from 105 plateau pika samples and assigned them to 215 known species, 226 potentially new species, and 177 higher hierarchical taxa. Notably, 39 abundant OPUs (over 60% total relative abundance) are found in over 90% of the samples, thereby representing a "core microbiota." They are all classified as novel microbial lineages, from the class to the species level. Using metagenomic reads, we independently assembled and binned 109 high-quality, species-level genome bins (SGBs). Then, a precise taxonomic assignment was performed to clarify the phylogenetic consistency of the SGBs and the 16S rRNA amplicons. Thus, the majority of the core microbes possess their genomes. SGBs belonging to the genus Treponema, the families Muribaculaceae, Lachnospiraceae, and Oscillospiraceae, and the order Eubacteriales are abundant in the metagenomic samples. In addition, multiple CAZymes are detected in these SGBs, indicating their efficient utilization of plant biomass. As the most widely connected metabolite with the core microbiota, tryptophan may relate to host environmental adaptation. Our investigation allows for a greater comprehension of the composition and functional capacity of the gut microbiota of the plateau pika. IMPORTANCE The great majority of microbial species remain uncultured, severely limiting their taxonomic characterization and biological understanding. The plateau pika (Ochotona curzoniae) is a small burrowing steppe lagomorph that is endemic to the Qinghai-Tibetan Plateau and is considered to be the keystone species in the maintenance of ecological stability. We comprehensively investigated the gut microbiota of the plateau pika via a multiomics endeavor. Combining full-length 16S rRNA metataxonomics, shotgun metagenomics, and metabolomics, we elucidated the species-level taxonomic assignment of the core uncultured intestinal microbiota of the plateau pika and revealed their correlation to host nutritional metabolism and adaptation. Our findings provide insights into the microbial diversity and biological significance of alpine animals.

Nanopore Is Preferable over Illumina for 16S Amplicon Sequencing of the Gut Microbiota When Species-Level Taxonomic Classification, Accurate Estimation of Richness, or Focus on Rare Taxa Is Required.

Nanopore sequencing is a promising technology used for 16S rRNA gene amplicon sequencing as it can provide full-length 16S reads and has a low up-front cost that allows research groups to set up their own sequencing workflows. To assess whether Nanopore with the improved error rate of the Kit 12 chemistry should be adopted as the preferred sequencing technology instead of Illumina for 16S amplicon sequencing of the gut microbiota, we used a mock community and human faecal samples to compare diversity, richness, and species-level community structure, as well as the replicability of the results. Nanopore had less noise, better accuracy with the mock community, a higher proportion of reads from the faecal samples classified to species, and better replicability. The difference between the Nanopore and Illumina results of the faecal bacterial community structure was significant but small compared to the variation between samples. The results show that Nanopore is a better choice for 16S rRNA gene amplicon sequencing when the focus is on species-level taxonomic resolution, the investigation of rare taxa, or an accurate estimation of richness. Illumina 16S sequencing should be reserved for communities with many unknown species, and for studies that require the resolution of amplicon sequence variants.

Screening of potential chemical marker with interspecific differences in Pterocarpus wood and a spatially-resolved approach to visualize the distribution of the characteristic markers.

Profiling the spatial distributions and tissue changes of characteristic compounds with interspecific differences is critical to elucidate the complex species identification during tree species traceability, wood anti-counterfeiting verification and timber trade control. In this research, in order to visualize the spatial position of characteristic compounds in two species with similar morphology (Pterocarpus santalinus and Pterocarpus tinctorius), a high coverage MALDI-TOF-MS imaging method was used to found the mass spectra fingerprints of different wood species. 2-Mercaptobenzothiazole matrix was used to spray wood tissue section to enhance the detection effect of metabolic molecules, and the mass spectrometry imaging data were obtained. Based on this technology, the spatial location of fifteen potential chemical markers with remarkable interspecific differences in 2 Pterocarpus timber species were successfully obtained. Distinct chemical signatures obtained from this method can promote rapid identification at the wood species level. Thus, matrix-assisted laser desorption/time-of-flight/ionization mass spectrometry imaging (MALDI-TOF-MSI) provides a spatial-resolved way for traditional wood morphological classification and breaking through the limitations of traditional wood identification technology.

The spatial distribution and expansion of Eucalyptus in its hotspots: Implications on agricultural landscapes.

Fast coppicing plantations like Eucalyptus are becoming an ever increasingly important land use system globally, including the Eucalyptus hotspot highlands of Northwestern Ethiopia. However, comprehensive information regarding species composition is essential for proper planning and policy decisions. The current study mapped the spatial distribution of Eucalyptus globulus (hereafter referred to as Eucalyptus) and identified the key push factors for its expansion. The study used a mapping procedure that uses Landsat imagery together with ground truth data based on supervised training of a pixel-by-pixel classification algorithm within image regions to distinguish areas of Eucalyptus plantations from other classes. High-resolution multispectral and multi-temporal remote-sensing images were combined with ground truth data to produce robust features of Eucalyptus plantation distribution maps. Heckman's Two-Stage econometric model was also employed for determining the major driving factors of Eucalyptus expansion. The results of the mapping algorithm were Eucalyptus plantation distribution maps of 30 × 30 m resolution that showed temporal changes from 1999 to 2021. The findings revealed that Eucalyptus coverage increased by 55% during the period from 1999 to 2010 and the change expressively increased to 69% in 2021 with respect to the reference period. The study also found that a number of push factors influenced the size of land planted with Eucalyptus. The developed maps showing the spatial distribution and expansion of Eucalyptus will help policymakers properly manage the ecosystems and agricultural landscapes of Eucalyptus growing areas.

A needle in a haystack: A new metabarcoding approach to survey diversity at the species level of Arcellinida (Amoebozoa: Tubulinea).

Environmental DNA-based diversity studies have increased in popularity with the development of high throughput sequencing technologies. This permits the potential simultaneous retrieval of vast amounts of molecular data from many different organisms and species, thus contributing to a wide range of biological disciplines. Environmental DNA protocols designed for protists often focused on the highly conserved small subunit of the ribosome gene, that does not permit species-level assignments. On the other hand, eDNA protocols aiming at species-level assignments allow a fine level ecological resolution and reproducible results. These protocols are currently applied to organisms living in marine and shallow lotic freshwater ecosystems, often in a bioindication purpose. Therefore, in this study, we present a species-level eDNA protocol designed to explore diversity of Arcellinida (Amoebozoa: Tubulinea) testate amoebae taxa that is based on mitochondrial cytochrome oxidase subunit I (COI). These organisms are widespread in lentic water bodies and soil ecosystems. We applied this protocol to 42 samples from peatlands, estuaries and soil environments, recovering all the infraorders in Glutinoconcha (with COI data), except for Hyalospheniformes. Our results revealed an unsuspected diversity in morphologically homogeneous groups such as Cylindrothecina, Excentrostoma or Sphaerothecina. With this protocol we expect to revolutionize the design of modern distributional Arcellinida surveys. Our approach involves a rapid and cost-effective analysis of testate amoeba diversity living in contrasted ecosystems. Therefore, the order Arcellinida has the potential to be established as a model group for a wide range of theoretical and applied studies.

Laser transparent multiplexed SERS microneedles for in situ and real-time detection of inflammation.

It is a significant challenge to perform painless invasive detection of inflammation progression in relation to the evolution of pH, redox potential, and reactive oxygen species (ROS) levels in an in situ and real-time manner. In this work, polydopamine-modified, silver nanoparticle-decorated poly (methyl methacrylate) microneedles (AgNPs@PDA@MNs) have been developed as a multiplexed surface enhanced Raman scattering (SERS) diagnostic platform. Using rhodamine 6G as the Raman signal molecule, the AgNPs@PDA@MNs demonstrated a significant enhancement with reasonable linearity in the range of 10-3-10-9 mol/L and the limit of detection is 1.0 × 10-10 mol/L 4-mercaptobenzoic acid, anthraquinone-2-carboxylic acid and para-aminothiophenol were covalently anchored on AgNPs@PDA@MNs SERS substrate. I1143/I1183, I1606/I1667 and I1143/I1077 were used as assay standards for pH, redox potential and ROS level detection, respectively. The SERS multiplexed transparent microneedles (SERS mtMNs) linearly responded to pH in the range of 4.0-8.0, redox potential in the range of 417.0-599.8 mV, and ROS levels in the range of 0-480 ng/mL, demonstrating a significant ability to detect complex inflammation in vivo, in situ and in real-time.

The composition and function profile of the gut microbiota of patients with primary Sjögren's syndrome.

OBJECTIVES: This healthy volunteer control-based study was conducted to explore alterations of compositions and function of gut microbiota in Chinese pSS patients. METHOD: The high-throughput Illumina Miseq sequencing method, targeting the V3-V4 region of the 16S ribosomal RNA (rRNA) gene, was used to compare the microbiota communities between 30 pSS patients and 30 age-matched healthy volunteers. The intestinal dysbiosis of pSS patients was evaluated and its correlation with some disease phenotypes was analyzed. Furthermore, we performed the amino acid sequence alignment analysis to illustrate the molecular mimicry patterns of new microbial peptides. RESULTS: Compared with that in healthy controls, the composition and function of the gut microbiota significantly differed in pSS patients. Certain genera and species, including genera: Escherichia-Shigella, Sardovia, Veillonella, Insteinimonas, and Lactobacillales; species: Escherichia coli, Lactobacillus phage Sal3, Lactobacillus reuteri, Lactobacillus gasseri, Streptococcus lutetiensis, Streptococcus mutans, Scardovia wiggsiae, and Fusobacterrium ulcerans were found to be enriched in the feces of pSS patients, while butyrate-producing bacteria were less abundant in pSS patients. Certain genera (including Lactobacillales) and species (including Lactobacillus gasseri) were associated with disease severity and therapy resistance parameters. Autoantigen epitopes of "WPSALPT, NPARSFG, MNPARSFG, and AFGLAIGT" from aquaporin-5 were aligned perfectly with one enriched microbiota of patients with pSS, namely Escherichia coli. CONCLUSIONS: The composition and function of the gut microbiota significantly differed in pSS patients compared with that in healthy controls. Our study would facilitate the possible research on the role of gut microbiota in the pathogenesis of pSS.

Bacterial community development and diversity during the first year of production in a new salmon processing plant.

The bacterial diversity and load on equipment in food processing facilities is constantly influenced by raw material, water, air, and staff. Despite regular cleaning and disinfection, some bacteria may persist and thereby potentially compromise food quality and safety. Little is known about how bacterial communities in a new food processing facility gradually establish themselves. Here, the development of bacterial communities in a newly opened salmon processing plant was studied from the first day and during the first year of operation. To focus on the persisting bacterial communities, surface sampling was done on strategical sampling points after cleaning and disinfection. To study the diversity dynamics, isolates from selected sampling and time points were classified by Oxford Nanopore Technology-based rep-PCR amplicon sequencing (ON-rep-seq) supplemented by 16S rRNA gene or rpoD gene sequencing (for Pseudomonas). An overall increase in bacterial numbers was only observed for food-contact surfaces in the slaughter department, but not in filleting department, on non-food contact surfaces or on the fish. Changes in temporal and spatial diversity and community composition were observed and our approach revealed highly point-specific bacterial communities.

Species-level termite methane production rates.

Termites consume substantial amounts of plant material across tropical and subtropical ecosystems. During the process of lignocellulose digestion, the symbiotic methanogenesis within termites' guts produces the potent greenhouse gas methane (CH4 ). Termites contribute an estimated 1%-5% of global CH4 emissions, with these estimates derived from the product of termite biomass and termite CH4 production rate per unit of termite biomass. However, termite CH4 production rates vary significantly across species, genus, family, and feeding group, yet our understanding of this variation remains poor. Here, we reviewed papers published from 1975 to 2021 to create a single consistently derived list of species-level termite CH4 production rates. We searched the Google Scholar using two key words: termite and methane. We only included studies that had measured termite CH4 production rates using the incubation method. For each eligible study, we extracted and tabulated termite CH4 production rates and other relevant variables (e.g., feeding groups). We used µg CH4 g-1 (termite) h-1 as the standardized unit, and if other units were presented, we converted them into this standardized unit. Overall, these data include 134 termite species from 65 genera and 5 families. Termite CH4 production rates ranged from 0 to 25.26 µg CH4 g-1 (termite) h-1 , with an average rate of 3.74 (standard deviation = 4.08, n = 251). Reported CH4 production rates were largely concentrated in the family Termitidae. Across feeding groups, soil feeders tended to have higher CH4 production rates than wood feeders. However, published data represent fewer than 5% of described termite species, and therefore we hope that our study will initiate a community-wide effort to fill data gaps and advance our understanding of the role of termites in critical biogeochemical cycles and other ecosystem processes. The data set is in the public domain under a Creative Commons Zero (CC0) license waiver.