Composition, antibiotic resistance, and virulence analysis of microbiota in dormitory drain pipes.

Introduction: Dormitory washbasins can breed microorganisms that produce odorous gases, polluting the indoor environment. Methods: We utilized metagenome sequencing to analyze the microbiota of 40 samples from the drain pipes of dormitory washbasins. Our study aimed to investigate the microbial community structure, antibiotic resistance genes, and virulence factors, and to identify potential influencing factors such as gender, hometown, frequency of hand sanitizer usage, and number of dormitory residents. Results: The analysis revealed 12 phyla and 147 genera, with Proteobacteria and Actinobacteria being the dominant phyla, and Mycobacterium and Nakamurella being the dominant genera. We found that the factors influencing the microbial community structure of the dormitory washbasin drain pipe are complex. The investigated factors have a slight influence on the drain pipe microbial community, with gender exerting a discernible influence. The annotation results revealed the presence of various virulence factors, pathogenic toxins and antibiotic resistance genes, including 246 different toxin types and 30 different types of antibiotic resistance genes. In contrast to the observed differences in microbial composition among samples, the distribution of resistance genes shows relatively small changes among samples. Antibiotics should be a contributing factor in the overall increase of antibiotic resistance genes in drain pipes. Discussion: Overall, our study provides important insights into the community structure and function of microorganisms in dormitory drainage systems, and can guide efforts to prevent and control microbial pollution.

The Draft Genome of the "Golden Tide" Seaweed, Sargassum horneri: Characterization and Comparative Analysis.

Sargassum horneri, a prevalent species of brown algae found along the coast of the northwest Pacific Ocean, holds significant importance as a valuable source of bioactive compounds. However, its rapid growth can lead to the formation of a destructive "golden tide", causing severe damage to the local economy and coastal ecosystems. In this study, we carried out de novo whole-genome sequencing of S. horneri using next-generation sequencing to unravel the genetic information of this alga. By utilizing a reference-guided de novo assembly pipeline with a closely related species, we successfully established a final assembled genome with a total length of 385 Mb. Repetitive sequences made up approximately 30.6% of this genome. Among the identified putative genes, around 87.03% showed homology with entries in the NCBI non-redundant protein database, with Ectocarpus siliculosus being the most closely related species for approximately one-third of these genes. One gene encoding an alkaline phosphatase family protein was found to exhibit positive selection, which could give a clue for the formation of S. horneri golden tides. Additionally, we characterized putative genes involved in fucoidan biosynthesis metabolism, a significant pathway in S. horneri. This study represents the first genome-wide characterization of a S. horneri species, providing crucial insights for future investigations, such as ecological genomic analyses.

sBGC-hm: an atlas of secondary metabolite biosynthetic gene clusters from the human gut microbiome.

SUMMARY: Microbial secondary metabolites exhibit potential medicinal value. A large number of secondary metabolite biosynthetic gene clusters (BGCs) in the human gut microbiome, which exhibit essential biological activity in microbe-microbe and microbe-host interactions, have not been adequately characterized, making it difficult to prioritize these BGCs for experimental characterization. Here, we present the sBGC-hm, an atlas of secondary metabolite BGCs allows researchers to explore the potential therapeutic benefits of these natural products. One of its key features is the ability to assist in optimizing the BGC structure by utilizing the gene co-occurrence matrix obtained from Human Microbiome Project data. Results are viewable online and can be downloaded as spreadsheets. AVAILABILITY AND IMPLEMENTATION: The database is openly available at https://www.wzubio.com/sbgc. The website is powered by Apache 2 server with PHP and MariaDB.

Preliminary study on the effect of catabolite repression gene knockout on p-nitrophenol degradation in Pseudomonas putida DLL-E4.

P-nitrophenol (PNP) is a carcinogenic, teratogenic, and mutagenic compound that can cause serious harm to the environment. A strain of Pseudomonas putida DLL-E4, can efficiently degrade PNP in a complex process that is influenced by many factors. Previous studies showed that the expression level of pnpA, a key gene involved in PNP degradation, was upregulated significantly and the degradation of PNP was obviously accelerated in the presence of glucose. In addition, the expression of crc, crcY, and crcZ, key genes involved in catabolite repression, was downregulated, upregulated, and upregulated, respectively. To investigate the effect of the carbon catabolite repression (CCR) system on PNP degradation, the crc, crcY, and crcZ genes were successfully knocked out by conjugation experiments. Our results showed that the knockout of crc accelerated PNP degradation but slowed down the cell growth. However, the knockout of crcY or crcZ alone accelerated PNP degradation when PNP as the sole carbon source, but that knockout slowed down PNP degradation when glucose was added. The results indicate that the CCR system is involved in the regulation of PNP degradation, and further work is required to determine the details of the specific regulatory mechanism.

A Type III Polyketide Synthase (SfuPKS1) Isolated from the Edible Seaweed Sargassum fusiforme Exhibits Broad Substrate and Catalysis Specificity.

A type III polyketide synthase (SfuPKS1) from the edible seaweed Sargassum fusiforme was molecularly cloned and biochemically characterized. The recombinant SfuPKS1 catalyzed the condensation of fatty acyl-CoA with two or three malonyl-CoA using lactone-type intramolecular cyclization to produce tri- and/or tetraketides. Moreover, it can also utilize phenylpropanoyl-CoA to synthesize phloroglucinol derivatives through Claisen-type cyclization, exhibiting broad substrate and catalysis specificity. Furthermore, the catalytic efficiency (kcat/KM) for acetyl-CoA was 11.8-fold higher than that for 4-coumaroyl-CoA. A pathway for the synthesis of naringenin involving SfuPKS1 was also constructed in Escherichia coli by recombinant means, resulting in 4.9 mg of naringenin per liter.

The complete chloroplast genome of Sargassum fusiforme.

The complete chloroplast genome sequence of Sargassum fusiforme is presented here. Circular mapping revealed that the complete chloroplast DNA sequence of S. fusiforme was 124,298 bp in length and had an overall AT content of 69.57%, including 137 protein-coding genes, 2 open reading frames, 28 transfer RNA genes, and 6 ribosomal RNA genes. The phylogenetic tree based on Bayesian shows that all kinds of Phaeophyceae were clustered into two monophyletic groups.

The complete mitochondrial genome of brown algae: Sargassum fusiforme (Harvey) Setchell.

We describe the complete mitochondrial genome sequence of Sargassum fusiforme. This mitogenome is a circular molecule of 34,695 bp in length and had an overall GC content of 37.54%%. Gene annotation showed that 35 protein-coding genes, 2 open reading frames, 25 transfer RNA genes, and 3 ribosomal RNA genes. The phylogenetic tree based on Bayesian shows that S. fusiforme belongs to genus Sargassum, support current taxonomic systems.

The complete mitochondrial genome of Pseudoxenodon stejnegeri (Squamata: Colubridae: Pseudoxenodontinae) and its phylogeny.

The mitochondrial genome sequence of Pseudoxenodon stejnegeri (Squamata: Colubridae: Pseudoxenodontinae) from Taishun County, Zhejiang Province, China, which is 18,475 bp in length and contains 25 tRNAs (including extra two tRNA-Tyr genes and extra one tRNA-Met gene), two rRNAs, 13 protein-coding genes and two identical control regions. The overall AT content of the mitogenome is 59.6% (A = 32.6%, T = 27%, C = 27%, G = 13.4%). In BI and ML phylogenetic analyses, the monophyly of the family Colubridae was well supported and P. stejnegeri was a basal clade of Colubridae.

A Comparative Analysis of Biosynthetic Gene Clusters in Lean and Obese Humans.

Obesity is intrinsically linked with the gut microbiome, and studies have identified several obesity-associated microbes. The microbe-microbe interactions can alter the composition of the microbial community and influence host health by producing secondary metabolites (SMs). However, the contribution of these SMs in the prevention and treatment of obesity has been largely ignored. We identified several SM-encoding biosynthetic gene clusters (BGCs) from the metagenomic data of lean and obese individuals and found significant association between some BGCs, including those that produce hitherto unknown SM, and obesity. In addition, the mean abundance of BGCs was positively correlated with obesity, consistent with the lower taxonomic diversity in the gut microbiota of obese individuals. By comparing the BGCs of known SM between obese and nonobese samples, we found that menaquinone produced by Enterobacter cloacae showed the highest correlation with BMI, in agreement with a recent study on human adipose tissue composition. Furthermore, an obesity-related nonribosomal peptide synthetase (NRPS) was negatively associated with Bacteroidetes, indicating that the SMs produced by intestinal microbes in obese individuals can change the microbiome structure. This is the first systemic study of the association between gut microbiome BGCs and obesity and provides new insights into the causes of obesity.

Tumor classification and biomarker discovery based on the 5'isomiR expression level.

BACKGROUND: The miRNA isoforms (isomiRs) have been suggested to regulate the same pathways as the canonical miRNA and play an important biological role in miRNA-mediated gene regulation. Recently, a study has demonstrated that the presence or absence of all isomiRs could efficiently discriminate amongst 32 TCGA cancer types. Besides, an effective reduction of distinguishing isomiR features for multiclass tumor discrimination must have a major impact on our understanding of the disease and treatment of cancer. METHODS: In this study, we have constructed a combination of the genetic algorithms (GA) with Random Forest (RF) algorithms to detect reliable sets of cancer-associated 5'isomiRs from TCGA isomiR expression data for multiclass tumor classification. RESULTS: We obtained 100 sets of the optimal predictive features, each of which comprised of 50-5'isomiRs that could effectively classify with an average sensitivity of 92% samples from 32 different tumor types. We calculated the frequency with which a 5'isomiR found in these sets as measuring its importance for tumor classification. Many highly frequent 5'isomiRs with different 5' loci from canonical miRNAs were detected in these sets, supporting that the isomiRs play a significant role in the multiclass tumor classification. The further functional enrichment analysis showed that the target genes of the 10 most frequently appearing 5'isomiRs were involved in the activity of transcription activator and protein kinase and cell-cell adhesion. CONCLUSIONS: The findings of the present study indicated that the 5'isomiRs might be employed for multiclass tumor classification and the suggested that GA/RF model could perform effective tumor classification by a series of largely independent optimal predictor 5' isomiR sets.

Characterization of the complete chloroplast genome of Sargassum fusiforme and its phylogenomic position within phaeophyceae.

Sargassum fusiforme is an important economic seaweed in East Asia. In this study, we characterized the complete chloroplast genome sequence of S. fusiforme using PacBio long-read sequencing technology. It had a circular mapping molecular with the length of 124,286 bp, with a large single-copy region (LSC, 73,437 bp) and a small single copy region (SSC, 40,131 bp) separated by a pair of inverted repeats (IRs, 5,359 bp). The cp genome contained 173 genes including 139 protein-coding, 6 rRNA, and 28 tRNA genes. The phylogenomic analysis indicated that S. fusiforme is closely related to S. thunbergii.

Characterization of the secondary metabolite biosynthetic gene clusters in archaea.

Secondary metabolites are a range of bioactive compounds yielded by bacteria, fungi and plants, etc. The published archaea genomic data provide the opportunity for efficient identification of secondary metabolite biosynthetic gene clusters (BGCs) by genome mining. However, the study of secondary metabolites in archaea is still rare. By using the antiSMASH, we found two main putative secondary metabolite BGCs, bacteriocin and terpene in 203 Archaea genomes. Compared with the genomes of Euryarchaeota that usually lives in less complexity of environment, the genomes of Crenarchaeota usually contained more abundant bacteriocin. In these archaea genomes, we also found the positive correlation between the abundance of bacteriocin and the abundance of CRISPR spacer, suggesting the bacteriocin might be a crucial component of the innate immune system that defense the microbe living in the common environment. The structure analysis of the bacteriocin gene clusters gave a clue that the assisted genes located at the edge of clusters evolved faster than the core biosynthetic genes. To the best of our knowledge, we are the first to systematically explore the distribution of secondary metabolites in archaea, and the investigation of the relationship between BGC and CRISPR spacer expands our understanding of the evolutionary dynamic of these functional molecules.

Gut microbiome-based secondary metabolite biosynthetic gene clusters detection in Parkinson's disease.

The microbiota of individuals with Parkinson's disease (PD) has been the focus of research in recent years. However, the mechanisms underlying the interactions between the gut microbiome and the brain, as well as its role in PD pathogenesis, remain to be elucidated. In this study, we used a systematic approach to predict putative biosynthetic gene clusters (BGCs) from the raw metagenomic data of the gut microbiome, and identified 43 BGCs that were significantly enriched in the PD patients. Fourteen of these clusters originated from microbes that were not increased in the patients, and the most significantly enriched one encoded a putative efflux protein and a radical SAM protein, indicating a potential role in PD. Based on a random forest classifier, these BGCs can be used to correctly discriminate between PD patients and healthy controls, with a cross-validated AUC of 0.91 from the 31 early stage PD patients and 28 healthy controls. Our study provides an alternative method to analyze the microbiota of PD patients, and further increase our understanding of this disease.

Distinct Effects of Multivalent Macroion and Simple Ion on the Structure and Local Electric Environment of a Weak Polyelectrolyte in Aqueous Solution.

Adding ionic species can critically affect the structure of weak polyelectrolyte (PE) chains, whose charge density in aqueous solution can be greatly regulated by bathing solution conditions such as pH and added ions. Distinct from simple ions that can be treated as point charges, multivalent macroions of finite size, including many charged nanoparticles and biopolymers, could show strong electrostatic coupling with PEs and effectively modify the conformation and assembly of PEs in aqueous solution. In this work, we have compared the effects of hydrophilic multivalent macroion of finite size and simple divalent ion on the conformational transition of a model weak polybase, poly(2-vinylpyridine) (P2VP), in dilute aqueous solution. By using fluorescence correlation spectroscopy combined with photon counting histogram analysis, we have examined the swollen-to-collapsed conformational transition and local electric potential of a P2VP chain in ionic aqueous solution at a single-molecule level. Adding inorganic polytungstate ([W12]) macroion bearing eight negative charges per [W12] of ∼0.8 nm in diameter at increased concentration from 10-9 to 10-5 mM can lead to a shift of the critical conformational transition pH, pHcr, of P2VP to lower pH values, in an opposite trend to the previously reported effect of adding simple monovalent anion. Conversely, adding simple divalent sulfate anion can lead to a nonmonotonic change of pHcr when increasing its concentration from 0.03 to 15 mM. Additionally, at pH < pHcr where P2VP is highly protonated and adopts a swollen conformation, a monotonic decrease of P2VP size is observed with increased sulfate ionic concentration, exhibiting the typical ionic screening effect. In contrast, the size of the P2VP chain shows little change with increasing [W12] concentration before the precipitation of P2VP from water. To investigate the distinct effects of multivalent ion and macroion on the conformational transition of P2VP in aqueous solution, we have also measured the local proton concentration in the vicinity to a P2VP chain by an attached pH-sensitive fluorescence probe. In both cases, we have observed the monotonic reduction of the local electric potential of a swollen P2VP chain with increased ionic concentration, despite the increased protonation degree of P2VP. The results suggest that counterion condensation of multivalent ion and macroion can modify the effective net charge density of P2VP chains in dilute aqueous solution. However, possibly due to its high multivalency and finite size, multivalent [W12] macroion is much more effective in modifying the local electric environment and structure of P2VP chains at 3-7 orders of magnitude lower concentrations than simple sulfate counterion.

Sargassum fusiforme polysaccharides activate antioxidant defense by promoting Nrf2-dependent cytoprotection and ameliorate stress insult during aging.

Aging is a complex issue, which results in a progressive decline process in cellular protection and physiological functions. Illustrating the causes of aging and pharmaceutical interference with the aging process has been a pivotal issue for thousands of years. Sargassum fusiforme (S. fusiforme), a kind of brown alga, is also named the "longevity vegetable" as it is not only a kind of food, but also used as an herb in traditional Chinese Medicine for maintaining health and treatment of thyroid disease, cardiovascular disease and so on. But how S. fusiforme promotes longevity is vastly equivocal. We got clues from S. fusiforme polysaccharides, which exhibited antioxidant activity, but the underlying mechanisms remained unclear. In this study, we evaluated the antioxidant effect and the possible mechanisms that S. fusiforme polysaccharides have against d-galactose-induced aging and chronic aging. We selected the SFPS as the candidate for antioxidant defense evaluation, which is a type of S. fusiforme polysaccharide with strong free radical scavenging activity and non-toxicity. It revealed that the antioxidant defense of the d-galactose-induced mice was markedly recovered when they were intragastrically administrated with the SFPS. However, oxidative damage may not be the only cause of aging. We further evaluated the function of the SFPS in the chronic aging mice. Intriguingly, we even found an obvious aging phenotype in the middle aged male ICR mice, which showed a significant decline in Nrf2-dependent cytoprotection. When 9-month old male ICR mice were treated with the SFPS for 2 months or even 11 months to their mean survival age, experimental measurements showed that the SFPS significantly promoted the antioxidant defense and mitochondrial integrity during aging. Furthermore, we suggest that the SFPS promotes Nrf2-dependent cytoprotection by upregulating the nuclear Nrf2 translocation, which may be mediated by p21 and JNK dependent pathways. These results suggest that the SFPS may decelerate the aging process by enhancing Nrf2-dependent cytoprotection, especially antioxidant defense.

Improving the microbial community reconstruction at the genus level by multiple 16S rRNA regions.

BACKGROUND: 16S rRNA genes have been widely used for phylogenetic reconstruction and the quantification of microbial diversity through the application of next-generation sequencing technology. However, long-read sequencing is still costly, while short-read sequencing carries less information for complex microbial community profiling; therefore, the applications of high throughput sequencing platforms still remain challenging in microbial community reconstruction analysis. RESULTS: Here, we developed a method to investigate the profile of aligned 16S rRNA gene sequences and to measure the proper region for microbial community reconstruction, as a step in creating a more efficient way to detect microorganism at the genus level. Finally, we found that each genus has its own preferential genus-specific amplicons for a genus assignment, which are not always located in hyper variable regions (HVRs). It was also noted that the rare genera should contribute less than dominant ones to the common profile of the aligned 16S rRNA sequences and have lower affinity to the common universal primer. CONCLUSIONS: Therefore, using multiple 16S rRNA regions rather than one "universal" region can significantly improve the ability of microbial community reconstruction. In addition, we found that a short fragment is suitable for most genera identifications, and the proper conserved regions used for primer design are larger than before.

Dysregulation of miRNA isoform level at 5' end in Alzheimer's disease.

Alzheimer's disease (AD) is the most common form of dementia, whose mechanism is still not yet fully understood. A miRNA-based signature method, commonly according to the changes of expression levels, is widely used for AD analysis in previous studies. Recently, miRNA isoforms called as isomiR variants, which is considered to play important biological roles, have been demonstrated as the applications of high throughput sequencing platforms. Here, we presented an entropy-based model to detect the miRNA isoform level at the 5' end, and found many miRNAs with significant changes of isoform levels between the early stage and the late stage of AD by the application of this model to the public data. The statistical significance of the overlap between isoform-level changed miRNAs and AD related miRNAs extracted from HMDD2 supports that these miRNA isoforms are not degradation products. Based on the most common isomiR seed analysis of isoform-level changed AD related miRNAs, the predicted targets are also found to be enriched for genes involved in transcriptional regulation and the nervous system. After comparing with the expression level based method, we detected that changes of 5' isoform levels are more stable than those of expression levels for AD related miRNA detecting.

Entropy-based model for miRNA isoform analysis.

MiRNAs have been widely studied due to their important post-transcriptional regulatory roles in gene expression. Many reports have demonstrated the evidence of miRNA isoform products (isomiRs) in high-throughput small RNA sequencing data. However, the biological function involved in these molecules is still not well investigated. Here, we developed a Shannon entropy-based model to estimate isomiR expression profiles of high-throughput small RNA sequencing data extracted from miRBase webserver. By using the Kolmogorov-Smirnov statistical test (KS test), we demonstrated that the 5p and 3p miRNAs present more variants than the single arm miRNAs. We also found that the isomiR variant, except the 3' isomiR variant, is strongly correlated with Minimum Free Energy (MFE) of pre-miRNA, suggesting the intrinsic feature of pre-miRNA should be one of the important factors for the miRNA regulation. The functional enrichment analysis showed that the miRNAs with high variation, particularly the 5' end variation, are enriched in a set of critical functions, supporting these molecules should not be randomly produced. Our results provide a probabilistic framework for miRNA isoforms analysis, and give functional insights into pre-miRNA processing.

Quality control of RNA-seq experiments.

Direct sequencing of the complementary DNA (cDNA) using high-throughput sequencing technologies (RNA-seq) is widely used and allows for more comprehensive understanding of the transcriptome than microarray. In theory, RNA-seq should be able to precisely identify and quantify all RNA species, small or large, at low or high abundance. However, RNA-seq is a complicated, multistep process involving reverse transcription, amplification, fragmentation, purification, adaptor ligation, and sequencing. Improper operations at any of these steps could make biased or even unusable data. Additionally, RNA-seq intrinsic biases (such as GC bias and nucleotide composition bias) and transcriptome complexity can also make data imperfect. Therefore, comprehensive quality assessment is the first and most critical step for all downstream analyses and results interpretation. This chapter discusses the most widely used quality control metrics including sequence quality, sequencing depth, reads duplication rates (clonal reads), alignment quality, nucleotide composition bias, PCR bias, GC bias, rRNA and mitochondria contamination, coverage uniformity, etc.