Characterizing the microbial communities inhabiting specimens is one of the primary objectives of microbiome studies. A short-read sequencing platform for reading partial regions of the 16S rRNA gene ...is most commonly used by reducing the cost burden of next-generation sequencing (NGS), but misclassification at the species level due to its length being too short to consider sequence similarity remains a challenge. Loop Genomics recently proposed a new 16S full-length-based synthetic long-read sequencing technology (sFL16S). We compared a 16S full-length-based synthetic long-read (sFL16S) and V3-V4 short-read (V3V4) methods using 24 human GUT microbiota samples. Our comparison analyses of sFL16S and V3V4 sequencing data showed that they were highly similar at all classification resolutions except the species level. At the species level, we confirmed that sFL16S showed better resolutions than V3V4 in analyses of alpha-diversity, relative abundance frequency and identification accuracy. Furthermore, we demonstrated that sFL16S could overcome the microbial misidentification caused by different sequence similarity in each 16S variable region through comparison the identification accuracy of Bifidobacterium, Bacteroides, and Alistipes strains classified from both methods. Therefore, this study suggests that the new sFL16S method is a suitable tool to overcome the weakness of the V3V4 method.
Background
Acinetobacter baumannii
is a major opportunistic pathogen causing nosocomial infections.
Acinetobacter baumannii
possesses a quorum sensing system consisting of
abaI
, encoding an ...autoinducer synthase, and
abaR
, encoding a putative LuxR type regulator. AbaI is required for motility and biofilm formation in
A. baumannii
. However, the functions of AbaR on the expression of
abaI
, motility, and the formation of biofilm and pellicle have not yet been explored.
Objective
The aim of this study was to investigate the effects of
abaR
mutation on the expression of
abaI
, motility, and the formation of biofilm and pellicle.
Methods
Functions of AbaR were assessed by the construction of an isogenic mutant and by evaluating the effects of
abaR
mutation on the expression of
abaI
, motility, and the formation of biofilm and pellicle.
Results
The
abaR
mutant revealed a significant decrease in the expression of
abaI
. The disruption of
abaR
resulted in substantial defects in motility and the formation of biofilm and pellicle. Introduction of
abaR in trans
complemented the defects.
Conclusions
AbaR of
A
.
baumannii
is required for the expression of
abaI
and plays important roles in motility and the formation of biofilm and pellicle. AbaR may be considered to be a target of anti-biofilm agents.
This study investigates the effects of soybean meal fermented by Enterococcus faecium as a replacement for soybean meal on growth performance, apparent total tract digestibility, blood profile and ...gut microbiota of weaned pigs. Eighty piglets (weaned at 21 days) (Landrace × Yorkshire) × Duroc with average body weight of 6.52 ± 0.59 kg) were selected and assigned to 4 treatments/4 replicate pens (3 barrows and 2 gilts). The four diets (SBM, 3, 6 and 9% FSBM) were formulated using fermented soybean meal to replace 0, 3, 6 and 9% of soybean meal, respectively. The trial lasted for 42 days phase 1, 2 and 3. Result showed that supplemental FSBM increased (P < 0.05) the body weight gain (BWG) of piglets at day 7, 21 and 42 and ADG at days 1-7, 8-21, 22-42 and 1-42, and ADFI at days 8-21, 22-42 and 1-42 and G: F at days 1-7, 8-21 and 1-42, and crude protein, dry matter, and gross energy digestibility at day 42, and lowered (P < 0.05) diarrhea at days 1-21 and 22-42. The concentration of glucose levels, WBC, RBC, and lymphocytes were increased while, concentration of BUN level in the serum was lowered in the FSBM treatment compared to the SBM group (P < 0.05). Microbiota sequencing found that FSBM supplementation increased the microbial Shannon, Simpsons and Chao indexs, (P < 0.05) and the abundances of the phylum Firmicutes, and genera prevotella, Lactobacillus, Lachnospiraceae and Lachnoclostridium (P < 0.05), lower in the abundances of the phylum bacteroidetes, Proteobacteria, genera Escherichia-Shigella, Clostridium sensu stricto1, Bacteroides and Parabacteroides (P < 0.05). Overall, FSBM replacing SBM improved the growth performance, apparent total tract digestibility, and blood profiles; perhaps via altering the faecal microbiota and its metabolites in weaned pigs. The present study provides theoretical support for applying FSBM at 6-9% to promote immune characteristics and regulate intestinal health in weaning piglets.
Transposable elements (TEs), also known as mobile elements (MEs), are interspersed repeats that constitute a major fraction of the genomes of higher organisms. As one of their important functional ...impacts on gene function and genome evolution, TEs participate in regulating the expression of genes nearby and even far away at transcriptional and post-transcriptional levels. There are two known principal ways by which TEs regulate the expression of genes. First, TEs provide cis-regulatory sequences in the genome with their intrinsic regulatory properties for their own expression, making them potential factors for regulating the expression of the host genes. TE-derived cis-regulatory sites are found in promoter and enhancer elements, providing binding sites for a wide range of trans-acting factors. Second, TEs encode for regulatory RNAs with their sequences showed to be present in a substantial fraction of miRNAs and long non-coding RNAs (lncRNAs), indicating the TE origin of these RNAs. Furthermore, TEs sequences were found to be critical for regulatory functions of these RNAs, including binding to the target mRNA. TEs thus provide crucial regulatory roles by being part of cis-regulatory and regulatory RNA sequences. Moreover, both TE-derived cis-regulatory sequences and TE-derived regulatory RNAs have been implicated in providing evolutionary novelty to gene regulation. These TE-derived regulatory mechanisms also tend to function in a tissue-specific fashion. In this review, we aim to comprehensively cover the studies regarding these two aspects of TE-mediated gene regulation, mainly focusing on the mechanisms, contribution of different types of TEs, differential roles among tissue types, and lineage-specificity, based on data mostly in humans.
Human endogenous retroviruses (HERVs) comprise a significant portion of the human genome, making up roughly 8%, a notable comparison to the 2-3% represented by coding sequences. Numerous studies have ...underscored the critical role and importance of HERVs, highlighting their diverse and extensive influence on the evolution of the human genome and establishing their complex correlation with various diseases. Among HERVs, the HERV-K (HML-2) subfamily has recently attracted significant attention, integrating into the human genome after the divergence between humans and chimpanzees. Its insertion in the human genome has received considerable attention due to its structural and functional characteristics and the time of insertion. Originating from ancient exogenous retroviruses, these elements succeeded in infecting germ cells, enabling vertical transmission and existing as proviruses within the genome. Remarkably, these sequences have retained the capacity to form complete viral sequences, exhibiting activity in transcription and translation. The HERV-K (HML-2) subfamily is the subject of active debate about its potential positive or negative effects on human genome evolution and various pathologies. This review summarizes the variation, regulation, and diseases in human genome evolution arising from the influence of HERV-K (HML-2).
is a host-adapted oral pathogen associated with chronic periodontitis that successfully survives and persists in the oral epithelium. Recent studies have positively correlated periodontitis with ...increased risk and severity of oral squamous cell carcinoma (OSCC). Intriguingly, the presence of
enhances tumorigenic properties independently of periodontitis and has therefore been proposed as a potential etiological agent for OSCC. However, the initial host molecular changes induced by
infection which promote predisposition to cancerous transformation through EMT (epithelial-mesenchymal-transition), has never been studied in human primary cells which more closely mimic the physiological state of cells
. In this study, we examine for the first time in primary oral epithelial cells (OECs) the expression and activation of key EMT mediators during long-term
infection
. We examined the inactive phosphorylated state of glycogen synthase kinase-3 beta (p-GSK3β) over 120 h
infection and found p-GSK3β, an important EMT regulator, significantly increases over the course of infection (
< 0.01). Furthermore, we examined the expression of EMT-associated transcription factors, Slug, Snail, and Zeb1 and found significant increases (
< 0.01) over long-term
infection in protein and mRNA expression. Additionally, the protein expression of mesenchymal intermediate filament, Vimentin, was substantially increased over 120 h of
infection. Analysis of adhesion molecule E-cadherin showed a significant decrease (
< 0.05) in expression and a loss of membrane localization along with β-catenin in OECs. Matrix metalloproteinases (MMPs) 2, 7, and 9 are all markedly increased with long-term
infection. Finally, migration of
infected cells was evaluated using scratch assay in which primary OEC monolayers were wounded and treated with proliferation inhibitor, Mitomycin C. The cellular movement was determined by microscopy. Results displayed
infection promoted cell migration which was slightly enhanced by co-infection with
, another oral opportunistic pathogen. Therefore, this study demonstrates human primary OECs acquire initial molecular/cellular changes that are consistent with EMT induction during long-term infection by
and provides a critically novel framework for future mechanistic studies.
Background
Reconstruction of amino acid sequences from assembled transcriptome is of interest in personalized medicine, for example, to predict drug-target (or protein-protein) interaction ...considering individual’s genomic variations. Most of the existing transcriptome assemblers, however, seems not well suited for this purpose.
Methods
In this work, we present StringFix, an annotation guided transcriptome assembly and protein sequence reconstruction software tool that takes genome-aligned reads and the annotations associated to the reference genome as input. The tool ‘fixes’ the pre-annotated transcript sequence by taking small variations into account, finally to produce possible amino acid sequences that are likely to exist in the test tissue.
Results
The results show that, using outputs from existing reference-based assemblers as the input GTF-guide, StringFix could reconstruct amino acid sequences more precisely with higher sensitivity than direct generation using the recovered transcripts from all the assemblers we tested.
Conclusion
By using StringFix with the existing reference-based assemblers, one can recover not only a novel transcripts and isoforms but also the possible amino acid sequence stemming from them.
Aeromonas spp. are the opportunistic pathogens that infect both aquatic and terrestrial homeotherms. They were commonly present in aquatic environments, including effluent, tap water, marine, river, ...and lake, where they are often isolated from aquatic animals, including fish, molluscs, and crustaceans. The Aeromonas infections can cause sepsis, ulcer, and other symptoms, resulting in the death of massive aquatic animals. Therefore, the prevention and control of Aeromonas is of great significance for the healthy development of aquaculture. In this study, we used modern molecular methods to enhance disease control of Aeromonas isolates from freshwater fish in Hebei Province. A total of 130 Aeromonas spp. isolates were isolated from freshwater fish farms in Hengshui, Handan, and Shijiazhuang and all 130 Aeromonas spp. isolates were sequenced for species identification. Of the 130 Aeromonas spp. isolates, 104 isolates were successfully sequenced, and BLAST analysis showed that Aeromonas veronii was predominant in freshwater fish farms in Hebei Province. In addition, 26 antibiotic resistance profiles were obtained from 102 fully cultured isolates among the 104 Aeromonas spp. isolates whose species was primarily identified, and 44 multidrug-resistant bacteria among the 102 isolates were identified using an antibiotic susceptibility test. Using the Multilocus Sequence Typing (MLST) method, 33 out of 44 multidrug-resistant isolates with 14 non-Aeromonas reference strains were selected for phylogenetic and MLST analysis, and all 33 multidrug-resistant isolates were A. veronii. A total of 30 new Sequence Types (STs) were obtained by comparing concatenated sequences (gyrB-groL-gltA-metG-ppsA-recA) on PubMLST website. Furthermore, recombination event analysis detected using RDP5 and ClonalFrameML software 42 and 49 recombination events, respectively, and 22 recombination events were validated by four or more algorithms. Since mutation and recombination events increase clonal diversity and single housekeeping gene sequence alignments are limited for identifying species, we propose the use of multiple concatenated sequence loci to increase discriminatory power. In addition, we propose that the MLST method is an appropriate technique to study and develop the resistance mechanisms of multidrug-resistant Aeromonas and to identify Aeromonas systematically in complex samples obtained from the environment.
The importance of probiotics in pig production is widely recognized. However, the precise role of probiotics in regulating the gut microbiota of piglets has not been assessed extensively. Therefore, ...we intend to examine whether suckling pigs ingesting with synthetic milk (SM) and probiotics along with mother milk has a carryover effect on its growth and gut health at the post-weaning stage. A total of 40 Duroc× (Yorkshire× Landrace) neonates with an initial BW of 1.49 ± 0.28 kg were assigned to one of two treatments groups: control (CON) and treatment (TRT). Control group piglets were nourished with synthetic milk, while TRT group piglets were nourished SM with (1 × 10
CFU/g)
sp. probiotics. The treatment group piglets showed higher (
< 0.05) body weight and daily gain at week 3 than the CON group piglets. 16S metagenome sequencing showed average demultiplexed reads and denoised reads counts of 157,399 and 74,945, respectively. The total ASV taxonomy number classified with a confidence threshold > 70% (default) on sequence alignment with the SILVA v138 reference database was 4,474. During week 1,
, and
were confirmed as the major dominant bacterial genera in both the groups at the genus level. However, during week 2, the relative proportion of
, and
was decreased, while that of
and
was increased in pigs receiving the probiotic supplement. During weeks 2 and 3,
, and
phyla were dominant in both groups. During week 6, the relative proportion of
was slightly increased in both groups. Furthermore,
was confirmed as the major dominant bacterial genus in both groups during weeks 3 and 6. This study suggests that nourishing neonatal piglets with synthetic milk and
sp. probiotics from birth to 21 days would be beneficial to enhance the gut health of piglets and to overcome post-weaning mortality.
The present study investigated the effect of topical application of
(EPI-7) ferment filtrate, which is a postbiotic product of a novel
on skin aging, by performing a prospective randomized split-face ...clinical study on Asian woman participants. The investigators measured skin biophysical parameters, including skin barrier function, elasticity, and dermal density, and revealed that the application of the EPI-7 ferment filtrate-including test product resulted in significantly higher improvements in barrier function, skin elasticity, and dermal density compared to the placebo group. This study also investigated the influence of EPI-7 ferment filtrate on skin microbiome diversity to access its potential beneficial effects and safety. EPI-7 ferment filtrate increased the abundance of commensal microbes belonging to
,
,
,
,
,
,
,
, and
. The abundance of
was significantly increased along with significant changes in
and
abundance. Therefore, EPI-7 postbiotics, which contain the metabolite called orotic acid, ameliorate the skin microbiota linked with the aging phenotype of the skin. This study provides preliminary evidence that postbiotic therapy may affect the signs of skin aging and microbial diversity. To confirm the positive effect of EPI-7 postbiotics and microbial interaction, additional clinical investigations and functional analyses are required.
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