Members of the genus Streptococcus inhabit a variety of sites in humans and other animals and some species are prolific producers of proteinaceous antibiotics (bacteriocins). As little is known about ...(i) streptococci inhabiting domestic pets, and (ii) whether novel bacteriocin-producing streptococci can be isolated from domestic pets, the aim of this study is to address these gaps in the research literature. In this study, Streptococcus equinus MDC1, isolated from a healthy dog, was found to exhibit potent antibacterial activity against Micrococcus luteus in a simultaneous antagonism assay, suggesting that strain MDC1 produces a lantibiotic bacteriocin. The inhibitory activity spectrum of S. equinus MDC1, determined using agar-based deferred antagonism assays against >70 indicator strains, was found to be similar to that of nisin U (a lantibiotic produced by Streptococcus uberis). However, the spectra of the two bacteriocins differed by 23 strains, mainly with the MDC1 bacteriocin having no inhibitory activity towards certain streptococci of human origin (e.g., Streptococcus gordonii, Streptococcus anginosus, Streptococcus salivarius). The genome of S. equinus MDC1, which was sequenced completely using single-molecule real-time (SMRT) next-generation DNA sequencing technology, comprises a single 1,936,555-basepair chromosome containing seven copies of the ribosomal RNA operon, 69 tRNA genes and nearly 1900 putative coding sequences. Analysis of the MDC1 genome sequence using the bacteriocin detection algorithms BAGEL4 and antiSMASH revealed the location of a 13,164-basepair 11-gene locus, designated nmd, which encoded a mature nisin E peptide that differed from nisin U by only two amino acids (Ile15→Ala and Leu21→Ile) and an extra C-terminal asparagine residue, and the proteins required for post-translational modification of the bacteriocin, processing, export, and producer immunity. Despite the high homology (90.6% identity, 93.8% similarity) between nisin E and nisin U, there was considerably less homology (47.4–76.3% identity, 68.4–88.8% similarity) between the other proteins encoded by their respective biosynthetic loci. This new natural variant of nisin, called nisin E, represents the first nisin variant to be reported for S. equinus; additionally, its differences with nisin U may provide some insight into the amino acids that influence bacteriocin potency and killing spectrum.
In the last two decades, the field of metagenomics has greatly expanded due to improvement in sequencing technologies allowing for a more comprehensive characterization of microbial communities. The ...use of these technologies has led to an unprecedented understanding of human, animal, and environmental microbiomes and have shown that the gut microbiota are comparable to an organ that is intrinsically linked with a variety of diseases. Characterization of microbial communities using next-generation sequencing-by-synthesis approaches have revealed important shifts in microbiota associated with debilitating diseases such as Clostridium difficile infection. But due to limitations in sequence read length, primer biases, and the quality of databases, genus- and species-level classification have been difficult. Third-generation technologies, such as Pacific Biosciences' single molecule, real-time (SMRT) approach, allow for unbiased, more specific identification of species that are likely clinically relevant. Comparison of Illumina next-generation characterization and SMRT sequencing of samples from patients treated for C. difficile infection revealed similarities in community composition at the phylum and family levels, but SMRT sequencing further allowed for species-level characterization - permitting a better understanding of the microbial ecology of this disease. Thus, as sequencing technologies continue to advance, new species-level insights can be gained in the study of complex and clinically-relevant microbial communities.
Abstract
Background
Papilio bianor Cramer, 1777 (commonly known as the Chinese peacock butterfly) (Insecta, Lepidoptera, Papilionidae) is a widely distributed swallowtail butterfly with a wide number ...of geographic populations ranging from the southeast of Russia to China, Japan, India, Vietnam, Myanmar, and Thailand. Its wing color consists of both pigmentary colored scales (black, reddish) and structural colored scales (iridescent blue or green dust). A high-quality reference genome of P. bianor is an important foundation for investigating iridescent color evolution, phylogeography, and the evolution of swallowtail butterflies.
Findings
We obtained a chromosome-level de novo genome assembly of the highly heterozygous P. bianor using long Pacific Biosciences sequencing reads and high-throughput chromosome conformation capture technology. The final assembly is 421.52 Mb on 30 chromosomes (29 autosomes and 1 Z sex chromosome) with 13.12 Mb scaffold N50. In total, 15,375 protein-coding genes and 233.09 Mb of repetitive sequences were identified. Phylogenetic analyses indicated that P. bianor separated from a common ancestor of swallowtails ∼23.69–36.04 million years ago. Demographic history suggested that the population expansion of this species from the last interglacial period to the last glacial maximum possibly resulted from its decreased natural enemies and its adaptation to climate change during the glacial period.
Conclusions
We present a high-quality chromosome-level reference genome of P. bianor using long-read single-molecule sequencing and Hi-C–based chromatin interaction maps. Our results lay the foundation for exploring the genetic basis of special biological features of P. bianor and also provide a useful data source for comparative genomics and phylogenomics among butterflies and moths.
Background
The skin microbiome is essential in guarding against harmful pathogens and responding to environmental changes by generating substances useful in the cosmetic and pharmaceutical ...industries. Among these microorganisms,
Streptococcus
is a bacterial species identified in various isolation sources. In 2021, a strain of
Streptococcus infantis
, CX-4, was identified from facial skin and found to be linked to skin structure and elasticity. As the skin-derived strain differs from other
S. infantis
strains, which are usually of oral origin, it emphasizes the significance of bacterial variation by the environment.
Objective
This study aims to explore the unique characteristics of the CX-4 compared to seven oral-derived
Streptococcus
strains based on the Whole-Genome Sequencing data, focusing on its potential role in skin health and its possible application in cosmetic strategies.
Methods
The genome of the CX-4 strain was constructed using PacBio Sequencing, with the assembly performed using the SMRT protocol. Comparative whole-genome analysis was then performed with seven closely related strains, utilizing web-based tools like PATRIC, OrthoVenn3, and EggNOG-mapper, for various analyses, including protein association analysis using STRING.
Results
Our analysis unveiled a substantial number of Clusters of Orthologous Groups in diverse functional categories in CX-4, among which sphingosine kinase (SphK) emerged as a unique product, exclusively present in the CX-4 strain. SphK is a critical enzyme in the sphingolipid metabolic pathway, generating sphingosine-1-phosphate. The study also brought potential associations with isoprene formation and retinoic acid synthesis, the latter being a metabolite of vitamin A, renowned for its crucial function in promoting skin cell growth, differentiation, and maintaining of skin barrier integrity. These findings collectively suggest the potential of the CX-4 strain in enhancing of skin barrier functionality.
Conclusion
Our research underscores the potential of the skin-derived
S. infantis
CX-4 strain by revealing unique bacterial compounds and their potential roles on human skin.
Single molecule real‐time (SMRT) sequencing has recently been used to obtain full‐length cDNA sequences that improve genome annotation and reveal RNA isoforms. Here, we used one such method called ...isoform sequencing from Pacific Biosciences (PacBio) to sequence a cDNA library from the Asian malaria mosquito Anopheles stephensi. More than 600 000 full‐length cDNAs, referred to as reads of insert, were identified. Owing to the inherently high error rate of PacBio sequencing, we tested different approaches for error correction. We found that error correction using Illumina RNA sequencing (RNA‐seq) generated more data than using the default SMRT pipeline. The full‐length error‐corrected PacBio reads greatly improved the gene annotation of Anopheles stephensi: 4867 gene models were updated and 1785 alternatively spliced isoforms were added to the annotation. In addition, six trans‐splicing events, where exons from different primary transcripts were joined together, were identified in An. stephensi. All six trans‐splicing events appear to be conserved in Culicidae, as they are also found in Anopheles gambiae and Aedes aegypti. The proteins encoded by trans‐splicing events are also highly conserved and the orthologues of these proteins are cis‐spliced in outgroup species, indicating that trans‐splicing may arise as a mechanism to rescue genes that broke up during evolution.
The salt‐reducing pickling method has been applied to the industrial production of zhacai. In order to reveal the succession of the microbial community structure and flavor components during the ...pickling process, this study used PacBio Sequel to sequence the full length of 16S rRNA (bacteria, 1400 bp) and ITS (fungi, 1200 bp) genes, and detected flavor components simultaneously, including organic acids, volatile flavor components (VFC), monosaccharides, and amino acids. Eleven phyla and 148 genera were identified in the bacterial community, and 2 phyla and 60 genera in the fungal community. During the four stages of pickling, the dominant bacterial genera were Leuconostoc, Lactobacillus, Leuconostoc, and Lactobacillus, while the dominant fungal genera were Aspergillus, Kazachstania, Debaryomyces, and Debaryomyces, respectively. There were 32 main flavor components (5 organic acids, 19 VFCs, 3 monosaccharides, and 5 amino acids). Correlation heat mapping and bidirectional orthogonal partial least squares (O2PLS) analysis showed that the flora having close relation to flavor components included 14 genera of bacteria (Leuconostoc, Clostridium, Devosia, Lactococcus, Pectobacterium, Sphingobacterium, Serratia, Stenotrophomonas, Halanaerobium, Tetragenococcus, Chromohalobacter, Klebsiella, Acidovorax, and Acinetobacter) and 3 genera of fungi (Filobasidium, Malassezia, and Aspergillus). This study provides detailed data regarding the microbial community and flavor components during the salt‐reducing pickling process of zhacai, which can be used as a reference for the development and improvement of salt‐reducing pickling methods.
This study investigated a whole process of the salt‐reducing pickling of zhacai. The microbial community structure during the four stages was analyzed by using the PacBio Sequel platform to sequence full‐length 16S rRNA and ITS genes, the flavor components were measured (organic acids, VFCs, monosaccharides and amino acids), the correlations between microbial communities and flavor components were analyzed using correlation heat mapping and O2PLS modeling, the core functional flora were inferred through integrated correlation analysis, and the predicted functions of the microbial communities after using PICRUSt2 analysis were highlighted.
In Kazakhstan, traditional artisanal cheeses have a long history and are widely consumed. The unique characteristics of local artisanal cheeses are almost completely preserved. However, their ...microbial communities have rarely been reported. The current study firstly generated the Single Molecule, Real-Time (SMRT) sequencing bacterial diversity profiles of 6 traditional artisanal cheese samples of Kazakhstan origin, followed by comparatively analyzed the microbiota composition between the current dataset and those from cheeses originated from Belgium, Russian Republic of Kalmykia (Kalmykia) and Italy.
Across the Kazakhstan cheese samples, a total of 238 bacterial species belonging to 14 phyla and 140 genera were identified. Lactococcus lactis (28.93%), Lactobacillus helveticus (26.43%), Streptococcus thermophilus (12.18%) and Lactobacillus delbrueckii (12.15%) were the dominant bacterial species for these samples. To further evaluate the cheese bacterial diversity of Kazakhstan cheeses in comparison with those from other geographic origins, 16S rRNA datasets of 36 artisanal cheeses from Belgium, Russian Republic of Kalmykia (Kalmykia) and Italy were retrieved from public databases. The cheese bacterial microbiota communities were largely different across sample origins. By principal coordinate analysis (PCoA) and multivariate analysis of variance (MANOVA), the structure of the Kazakhstan artisanal cheese samples was found to be different from those of the other geographic origins. Furthermore, the redundancy analysis (RDA) identified 16 bacterial OTUs as the key variables responsible for such microbiota structural difference.
Our results together suggest that the diversity of bacterial communities in different groups is stratified by geographic region. This study does not only provide novel information on the bacterial microbiota of traditional artisanal cheese of Kazakhstan at species level, but also interesting insights into the bacterial diversity of artisanal cheeses of various geographical origins.
Kiwifruit an important horticultural crop that is widely cultivated and is known as the king of fruits. Recently, a new seedless kiwifruit cultivar, ‘Chengxiang’ (Actinidia arguta), was discovered by ...field transplantation. It exhibited distinguishable characteristics such as parthenocarpy, and a unique flavor and appearance when compared to other cultivated type. Flavonoids are known to play an important role in fertility and parthenocarpy in plants. However, the genes responsible for flavonoid biosynthesis in seedless kiwifruit remain largely unknown. Especially, chalcone synthase (CHS), as a key enzyme catalyzing the first committed step in the flavonoid pathway, remains a mystery. In this study, we combined a full-length transcriptome survey by PacBio single-molecule real-time (SMRT) sequencing, CHS gene family analysis, and analysis of the gene expression involved in flavonoid pathways to further enhance the understanding of parthenocarpy. Based on SMRT, we obtained 80,615 high-quality full-length consensus transcripts. In total, 52,406 (90.79%) transcripts were functionally annotated, and more than 80% of the transcripts were longer than 1Kb. Among them, 39,117 (74.64%) transcripts were assigned to GO terms, the majority of which were associated with the cell (19,089, 48.80%) and metabolic process (19,859, 50.77%). Furthermore, 25,289 (48.26%) transcripts were mapped into 129 KEGG pathways. We identified the majority of putative genes as being involved in the flavonoid biosynthesis pathway, including 14 key enzyme gene families, such as CHS, chalcone isomerase (CHI), flavonol synthase (FLS), and so on. Moreover, we also identified 13 CHS genes and characterized the CHS gene family in seedless kiwifruit. We further evaluated the expression pattern of 10 flavonoid-related key enzyme genes in flowers using quantitative real-time PCR. This is the first time that the full-length transcriptome have been studied in seedless kiwifruit, and the findings enhance our understanding the molecular mechanisms of parthenocarpy.
So-called 936-type phages are among the most frequently isolated phages in dairy facilities utilising Lactococcus lactis starter cultures. Despite extensive efforts to control phage proliferation and ...decades of research, these phages continue to negatively impact cheese production in terms of the final product quality and consequently, monetary return.
Whole genome sequencing and in silico analysis of three 936-type phage genomes identified several putative (orphan) methyltransferase (MTase)-encoding genes located within the packaging and replication regions of the genome. Utilising SMRT sequencing, methylome analysis was performed on all three phages, allowing the identification of adenine modifications consistent with N-6 methyladenine sequence methylation, which in some cases could be attributed to these phage-encoded MTases. Heterologous gene expression revealed that M.Phi145I/M.Phi93I and M.Phi93DAM, encoded by genes located within the packaging module, provide protection against the restriction enzymes HphI and DpnII, respectively, representing the first functional MTases identified in members of 936-type phages.
SMRT sequencing technology enabled the identification of the target motifs of MTases encoded by the genomes of three lytic 936-type phages and these MTases represent the first functional MTases identified in this species of phage. The presence of these MTase-encoding genes on 936-type phage genomes is assumed to represent an adaptive response to circumvent host encoded restriction-modification systems thereby increasing the fitness of the phages in a dynamic dairy environment.
Europa se posljednjih desetljeća hrva sa samom sobom. Kulturološke promjene koje su se dogodile bitno su uzdrmale njezin identitet, a poštovanje temeljnih načela i vrednota našlo se pred novim ...izazovom. Nove antropološke paradigme proizašle iz postmodernizma utjecale su na zaborav kršćanskih korijena i istina, koje su dobrim dijelom odredile smjer razvoja europske kulture. Posljedično, Europa kakvu poznajemo umire. Osnovna nakana ovog rada jest vidjeti u kakvom su odnosu umiranje
Europe i migracijska kriza. Ne govori se o smrti (i životu) kao biološkom procesu, nego o filozofsko-teološkom promatranju „umiranja“ i „oživljavanja“ svega europskoga, kršćanskoga, ljudskoga... Na temelju promatranja najvažnijih današnjih kulturoloških obilježja Europe te vjerskih istina kršćanstva i islama, posebno u poimanju života i smrti, odgovorit ćemo na pitanje jesu li migranti i izbjeglice nositelji života
ili smrti na europskom kontinentu. Čuvajući se idealiziranja imigranata
kao spasitelje Europe, ali i njihova demoniziranja kao jedinih krivaca propadanja Europe, pokušat ćemo vidjeti može li pozitivan stav prema njima pružiti bitan preduvjet za plodnu integraciju. Život ili smrt Europe ovisi o njoj samoj, a migranti i izbjeglice mogu doprinijeti jednoj i drugoj stvarnosti. Ipak, za kršćane jest obveza ljubavi, za koju ne smijemo zaboraviti da ima snagu oživljavati i mijenjati.
Europe has been wrestling with itself in recent decades. The cultural changes that have taken place have shaken its identity significantly, and adherence to fundamental principles and values has faced a new challenge. New anthropological paradigms arising from postmodernism have
influenced the oblivion of Christian roots and truths, which have largely determined the direction of the development of European culture.
Consequently, Europe as we know it is dying. The main purpose of this paper is to see the relationship between the dying of Europe and the migration crisis. It is not about death (and life) as a biological process, but more about a philosophical-theological observation of “dying “and “reviving “of all that is European, Christian, human ... On the basis of the observation of today's most important cultural features
of Europe and religious truths of Christianity and Islam, especially on
the understanding of life and death, we will answer the question of whether migrants and refugees are the bearers of life or death on the European continent. Being careful not to idealize immigrants as saviours
of Europe, but also not to demonize them as the only culprits of Europe's decline, we will try to see if a positive attitude towards them
can provide an essential precondition for fruitful integration. Europe's life or death depends on itself, and migrants and refugees can contribute to both realities. Yet for Christians there is an obligation of love, and we must not forget that it has the power to revive and change.
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