16S rRNA Sequencing Research Articles

Detection and characterization of pathogenic Bacillus haynesii from Tribulus terrestris extract: ways to reduce its levels.

Plant parts such as roots, bark, leaves, flowers, and fruits that hold ethnopharmacological significance are naturally prone to microbial contamination, influenced by environmental factors like moisture and humidity. This study focuses on assessing the microbial load in the raw material of Tribulus terrestris (TT). The primary bacterium isolated from the pulverized raw material was identified as Bacillus haynesii through 16S rRNA sequencing. Biochemical assays revealed the organism's ability to utilize lysine and ornithine, produce urease, and generate hydrogen sulfide. The bacterium exhibited resistance to multiple antibiotics and caused 21.5% hemolysis in RBC lysis assays. To reduce microbial contamination, Glutaraldehyde (GA) and polyhexamethylene biguanide (PHMB) were tested, with GA at 1% reducing the microbial load by 99% without affecting the yield (0.5%) or bioactive saponin content. High-Performance Liquid Chromatography (HPLC) confirmed the absence of residual GA, ensuring an eco-friendly and safe process. This highlights the importance of quality control measures, including Hazard Analysis and Critical Control Points (HACCP) regulations, in maintaining the integrity of herbal extracts.

The Gut Bacteria of Gampsocleis gratiosa (Orthoptera: Tettigoniidae) by Culturomics

Gampsocleis gratiosa Brunner von Wattenwyl, 1862, is a type of omnivorous chirping insect with a long history of artificial breeding. It has high economic value and is also an excellent orthopteran model organism. In this study, 12 types of culture media combined with 16S rRNA sequencing were employed to isolate 838 bacterial strains from the gut of G. gratiosa. After sequence comparison, a total of 98 species of bacteria were identified, belonging to 3 phyla, 5 classes, 11 orders, 20 families, and 45 genera. Firmicutes and Proteobacteria accounted for the majority (92.86%). At the order level, Enterobacteriaceae, Bacillales, and Lactobacillales predominated (79.59%). At the genus level, Klebsiella (11.22%) and Enterococcus (7.14%) predominated. This study also enumerated the strain morphological, physiological and biochemical properties of 98 species of bacteria, including colony morphology, Gram staining, bacterial motility test, temperature gradient growth, pH gradient growth, citrate utilization test, temperature oxidase test, contact enzyme test, methyl red test, V-P test, indole test, gelatin liquefaction test, nitrate reduction test, hydrogen sulfide test, starch hydrolysis test, cellulose decomposition test, esterase (corn oil) test and antibiotic susceptibility testing. Additionally, 16 antibiotics were utilized to test the bacterial susceptibility of the strains. This study explored the types and community structure of some culturable microorganisms in the intestinal tract of G. gratiosa and recorded their physiological characteristics. These data reflect the physiological functions of the intestinal microorganisms of G. gratiosa and provide support for subsequent research on the interaction mechanism between microorganisms and their hosts.

Effects of vaginal microbiota on in vitro fertilization outcomes in women with different infertility causes.

Many studies suggest that vaginal microbiota (VMB) may affect in vitro fertilization-embryo transfer (IVF-ET) outcomes. Assessing VMB before embryo transfer can optimize timing for better assisted reproductive technology (ART) results. This study examined VMB distribution in infertile women undergoing ART using 16S rRNA sequencing. Results revealed that VMB structure impacted ART outcomes in women with polycystic ovary syndrome (PCOS) and tubal factor infertility (TFI) before embryo transfer ([less than or equal to] 24 hours). Lactobacillus iners and Pseudomonas spp. were identified as adverse factors for post-ET pregnancy. The study also showed differences in pre-ET VMB between normal women and women with PCOS and TFI during the ovulatory window. These findings highlight the importance of considering VMB composition to optimize embryo transfer timing and personalize ART treatment based on infertility type, improving the chances of success.

Genome drafting of nosocomial infection CRE Klebsiella pneumoniae confirming resistance to colistin and eravacycline, carrying blaNDM-1, mcr-1, and blaKPC-2, in neonatology from November to December 2023

BackgroundCarbapenem-resistant Klebsiella pneumoniae (CRKP) is a critical pathogen in healthcare settings, associated with high mortality due to its extensive antibiotic resistance. In this study, we report an outbreak of CRKP in a neonatal intensive care unit (NICU) within a 200-bed tertiary hospital. The main goal of this study was to characterize the phenotypic and genomic profiles of the CRKP isolates involved in the outbreak and to gain insights into their resistance mechanisms and transmission dynamics within the NICU.MethodsThe study was conducted between November and December 2023 in a 5-bed NICU. Monthly surveillance cultures were performed to monitor colonization and infection with multidrug-resistant organisms. CRKP isolates were obtained from blood and nasal swabs of affected neonates. Identification and antimicrobial susceptibility testing were initially conducted using the Vitek®2 system with an N-395 card and further confirmed by 16S rRNA sequencing. Whole-genome sequencing (WGS) and antimicrobial resistance (AMR) profiling were performed to identify resistance genes and virulence factors. For genetic analysis, both Illumina short-read and Nanopore long-read sequencing were used, followed by hybrid assembly for enhanced genome resolution. Plasmid and resistance gene profiles were determined using AMRFinder and PlasmidFinder databases.ResultsA total of three CRKP isolates (designated Kp1, Kp2, and Kp3) were identified. Kp1 and Kp2 belonged to sequence type (ST) ST23 and were genetically near-identical, differing by a single allele, while Kp3 was of a distinct sequence type, ST2096, with 245 allelic differences from Kp1 and Kp2. All isolates were resistant to colistin and carried resistance genes, including mcr-1 and blaNDM-1,blaKPC2 confirming carbapenem resistance. Efflux pump genes and aminoglycoside resistance genes were also detected, providing a multifaceted defence against antibiotics. Plasmid analysis identified several incompatibility groups (IncFI, IncHI, IncFIB, IncX), indicating the potential for horizontal gene transfer of resistance determinants.ConclusionThis study highlights the complexity of CRKP outbreaks in neonatal care, with isolates exhibiting resistance mechanisms that complicate treatment. The plasmid profiles suggest these strains are reservoirs for multidrug-resistant genes, emphasizing the need for strict infection control and ongoing genomic surveillance. For neonatal care, these resistance challenges increase the risk of treatment failures and mortality, underscoring the importance of enhanced infection prevention and novel therapeutic strategies.

Effects of rumen fluid transplantation on the fecal flora of yaks

IntroductionThere are few studies on the effect of rumen fluid transplantation on the fecal flora of yaks. Yak fecal flora is closely related to their health. This study aimed to evaluate the effects of rumen fluid transplantation on growth performance and fecal flora indicators.MethodsTwenty 6-month healthy male yaks (weight: 57.20 ± 7.80 kg) were selected from grazing yaks in an alpine meadow pasture at an altitude of approximately 3,400 m. They were then transferred to a farm and randomly divided into a control group (CON; n = 10) and a rumen fluid transplantation group (RT; n = 10). Separate single-pen rearing was performed in two pens using the same rearing environment and feeding method, and all yaks were earmarked for identification. In addition, 10 yaks that had been adapted to stall fattening feed in 1 month were selected as the rumen fluid donor group to provide fresh rumen fluid. Ruminal fluid transplantation trials were conducted on the 1st, 3rd, and 5th weeks. Overall, 1 L of ruminal fluid was transplanted to each yak in the RT and CON groups. The formal trial then began with both groups fed the same diet. After this, yak feed intake was recorded daily; yaks were weighed on days 1, 30, and 60 of the formal trial; and yak feces were collected directly from the ground on days 1, 4, 7, 14, 30, and 60 to compare the microbial composition of the feces using 16S rRNA sequencing data.ResultsThe results showed that rumen fluid transplantation significantly increased the alpha diversity of fecal microflora (P < 0.05), and on day 30 of the experiment, both the operational taxonomic unit (OTU) and Shannon index were significantly higher in the RT group than the CON group (P < 0.05). In the principal coordinate analysis (PCoA) plot, the intestinal flora of the RT group was significantly different (P < 0.05) on days 1–7 but not significantly different after day 14. In contrast, the intestinal flora of the CON group was significantly different (P < 0.05) on days 1–14 but not significantly different after day 30. Compared with the CON group, the relative abundance of Firmicutes in the RT group was significantly lower on days 1, 4, 7, and 14 (P < 0.05); the relative abundance of Bacteroidetes in the RT group was significantly higher on days 1, 4, 14, and 30 and significantly lower on day 7 (P < 0.05); the relative abundance of Tenericutes in the RT group was significantly higher on day 30 (P < 0.05); the relative abundance of Actinobacteria in the RT group was significantly higher on day 60 (P < 0.05); the relative abundance of Ruminococcaceae_UCG-005 in the RT group was significantly lower on days 4, 7, 14, and 60 (P < 0.05); the relative abundance of Unidentified in the RT group was significantly higher on days 1, 4, and 7 days (P < 0.05); and the relative abundance of Rikenellaceae_RC9_gut_group, Bacteroides, and Christensenellaceae_R-7_group in the RT group was significantly higher on day 1 (P < 0.05). Moreover, Actinobacteria was positively correlated with ADG and negatively correlated with DMI; Tenericutes was positively correlated with weight and negatively correlated with F/G. Metabolism of terpenes and polyketones, metabolism of other amino acids, and energy metabolism were higher in the RT group than in the CON group. LEfSe analysis showed that 32 species were more abundant in the RT group and 11 in the CON group. In conclusion, our findings suggest that rumen fluid transplantation improved the stability of the intestinal tract of yaks, improved the immunity of yaks, and reduced the occurrence of intestinal diseases; rumen fluid transplantation remodeled the structure of the intestinal flora, shortened the time of remodeling the intestinal flora of yaks during the transition period, and accelerated yak adaptation to digest housed rations, reducing the DMI. The findings of this study provide new insights into yak microbial community transplantation and a reference for improving feed efficiency in the yak industry.

Paludibacillus litoralis gen. nov., sp. nov.: a novel species of a novel genus in the family Paracoccaceae, isolated from the sediment of a tidal flat located in Zhoushan, China.

A Gram-stain-negative, aerobic and rod-shaped bacterium, designated as HZG-20T, was isolated from a tidal flat in Zhoushan, Zhejiang Province, China. The 16S rRNA sequence similarities between strain HZG-20T and Pikeienuella piscinae RR4-56T, Coraliihabitans acroporae NNCM2T, Parvibaculum indicum P31T and Zhengella mangrovi X9-2-2T were 98.9, 91.7, 91.0 and 91.0%, respectively. Colonies of strain HZG-20T were 1.4 mm in diameter, milky white, round, smooth and convex after cultivating on marine agar at 30 °C for 48 h. Cells were catalase and oxidase-negative. Growth occurred at 15-37 ℃ (optimum, 28 ℃), pH 5.0-9.0 (optimum, pH 6.0-8.0) and with 0-8% (w/v) NaCl (optimum, 1-3%). It contained Menaquinone-8 (H2) as the sole respiratory quinone, and C16:0 (11.8-13.6%), C18:1 ω9c (6.8-13.3%) and C15:0 anteiso (10.9-27.7%) as the major cellular fatty acids. The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid, one unidentified aminolipid, one unidentified phosphoglycolipid, two unidentified glycolipids (GL1-GL2) and three unidentified lipids (L1-L3). The genome of strain HZG-20T was 3 835 886 bp in length, comprised 3746 protein-coding genes, with DNA G+C content of 67.1 mol%. The phylogenetic and phylogenomic trees indicated that strain HZG-20T formed an independent and stable clade with P. piscinae RR4-56T. However, the average nucleotide identity, digit DNA-DNA hybridization and average amino acid identity values between strain HZG-20T and P. piscinae RR4-56T, C. acroporae NNCM2T, P. indicum P31T and Z. mangrovi X9-2-2T were 81.6, 71.1, 68.7 and 69.5%; 23.0, 18.5, 17.9 and 17.5%; and 78.2, 56.8, 56.5 and 61.9%, respectively, together with distinct chemotaxonomic features, indicating strain HZG-20T should not be assigned to known genera. As a result, a novel species of a novel genus within the family Paracoccaceae, designated as Paludibacillus litoralis gen. nov., sp. nov., was proposed. The type strain is HZG-20T (MCCC 1K08468T=KCTC 82692T).

A timescale for the evolutionary history of sea spiders (Arthropoda: Pycnogonida)

Abstract Sea spiders (Arthropoda: Pycnogonida) are an ancient lineage of chelicerates represented by a single living order, Pantopoda, and a patchy fossil record that provides limited information of their evolutionary timescale. The sudden appearance of Pantopoda in the Middle Jurassic has led several authors to propose a recent (Early Jurassic) origin and rapid diversification of modern pycnogonids. In contrast, a recent molecular clock study suggested Pantopoda originated before the Devonian, and diversified slowly, though the calibrations on which it was based have since been revised. Here, we conduct timetree inference analyses using a set of 13 mitochondrial protein-coding genes, 18S rRNA sequences and 98 Ultra Conserved Elements from 198 pycnogonid taxa, with calibrations reflecting the most recent interpretations of the sea spider fossil record. Our analyses estimate that pycnogonids diverged from other arthropods during the Cambrian (539-510 Ma), indicating about 100 Myr between Pycnogonida origin and pantopod diversification. The pycnogonid crown group (=Pantopoda) diversified during the Late Palaeozoic, in an interval spanning the Early Silurian and the Late Devonian (435-367 Ma), preceding the appearance of the first pantopod fossil by ~206.5 Myr. Our analysis also implies that pantopod families originated between the Late Devonian and the Late Jurassic (378-154 Ma). This leads to very different estimates to previous studies based on the fossil record. However, previous molecular divergence time analyses yielded a similar evolutionary timescale, despite a notably different set of calibrations. This effective corroboration of previous evidence indicates that the underpinning molecular evidence is informative and that the inferred long ghost lineages faithfully reflect the patchy nature of the pycnogonid fossil record which results from their low fossilisation potential. Regardless, our results predict further fossil discoveries from different environments and periods, which might at least partially rewrite pycnogonid history.

Unveiling the Dark Side of Flavonoid: Rutin Provokes Hepatotoxicity in Low-Dose 2-Amino-3-methylimidazo [4,5-f] Quinoline-Exposed Mice via Regulating Gut Microbiota and Liver Metabolism.

2-Amino-3-methylimidazole [4,5-f] quinoline (IQ) is a kind of heterocyclic amine (HCAs) with high carcinogenicity in hot processed meat. Rutin (Ru) is a flavonoid compound with anti-inflammatory and antioxidant properties. However, whether Ru is scatheless under IQ-stimulated potential unhealthy conditions, especially liver function, in vivo, is unknown. In this study, we explored the effects and underlying mechanism of Ru on liver injury induced by a low dose of IQ in mice. Results showed that Ru supplement led to liver injury upon low-dose IQ alone administration, as shown by histological analysis, inflammatory, and serum biochemical indexes. Additionally, nontargeted metabolomics analysis revealed that coexposure of Ru and IQ disrupted liver metabolic balance, leading to significant changes in metabolites and metabolic pathways, hinting at a possible relationship with intestinal microbiota. Furthermore, the 16S rRNA sequencing data indicated that a combination of Ru and IQ caused gut microbiota dysbiosis and decreased the level of short-chain fatty acids (SCFAs). Correlation analysis between gut microbiota, SCFAs, liver metabolites, and liver damage markers highlighted the crucial role of the gut-liver axis in IQ and Ru coexposure-induced liver injury in vivo. In general, this study offers a valuable perspective on flavones and HCA compounds in the realms of food safety and human health.

Shenmai injection revives cardiac function in rats with hypertensive heart failure: involvement of microbial-host co-metabolism

Heart failure (HF) is a complex syndrome marked by considerable expenditures and elevated mortality and morbidity rates globally. Shenmai injection (SMI), a form of Traditional Chinese Medicine-based therapy, has demonstrated effectiveness in treating HF. Recent research suggests that Traditional Chinese Medicine (TCM) may induce beneficial changes in microbial-host co-metabolism, potentially providing cardiovascular protection. This study used a rat model of hypertensive heart failure (H-HF) to explore the mechanism of SMI. The possible compounds and key targets of SMI against H-HF were investigated using network pharmacology. The pharmacodynamics of SMI were validated using the H-HF animal model, with analysis of fecal gut microbiota integrating metabolomics and 16S rRNA sequencing. Metorigin metabolite traceability analysis and the MetaboAnalyst platform were utilized to explore the action mechanism. To evaluate changes in serum TMAO levels, targeted metabolomics was performed. Finally, the study looked at the intrinsic relationships among modifications in the intestinal flora, metabolite profile changes, and the targets of SMI compounds to clarify how they might be used to treat H-HF. According to metabolomics and 16S rRNA sequencing, by reestablishing homeostasis in the gut microbiota, SMI affects vital metabolic pathways, such as energy metabolism, amino acid metabolism, and bile acid metabolism. Increased serum TMAO levels were identified to be a risk factor for H-HF, and SMI was able to downregulate the levels of TMAO-related metabolites. Network pharmacology analysis identified 13 active components of SMI targeting 46 proteins, resulting in differential expression changes in 8 metabolites and 24 gut microbes. In conclusion, this study highlights the effectiveness of SMI in alleviating H-HF and its potential to modulate microbial-host co-metabolism. Through a comprehensive discussion of the interconnected relationships among the components, targets, metabolites, and gut microbiota, it provided fresh light on the therapeutic mechanism of SMI on H-HF.

Role of Ribosomal Protein bS1 in Orthogonal mRNA Start Codon Selection.

In many bacteria, the location of the mRNA start codon is determined by a short ribosome binding site sequence that base pairs with the 3'-end of 16S rRNA (rRNA) in the 30S subunit. Many groups have changed these short sequences, termed the Shine-Dalgarno (SD) sequence in the mRNA and the anti-Shine-Dalgarno (ASD) sequence in 16S rRNA, to create "orthogonal" ribosomes to enable the synthesis of orthogonal polymers in the presence of the endogenous translation machinery. However, orthogonal ribosomes are prone to SD-independent translation. Ribosomal protein bS1, which binds to the 30S ribosomal subunit, is thought to promote translation initiation by shuttling the mRNA to the ribosome. Thus, a better understanding of how the SD and bS1 contribute to start codon selection could help efforts to improve the orthogonality of ribosomes. Here, we engineered the Escherichia coli ribosome to prevent binding of bS1 to the 30S subunit and separate the activity of bS1 binding to the ribosome from the role of the mRNA SD sequence in start codon selection. We find that ribosomes lacking bS1 are slightly less active than wild-type ribosomes in vitro. Furthermore, orthogonal 30S subunits lacking bS1 do not have an improved orthogonality. Our findings suggest that mRNA features outside the SD sequence and independent of binding of bS1 to the ribosome likely contribute to start codon selection and the lack of orthogonality of present orthogonal ribosomes.

Extended-spectrum β-lactamase-producing, multidrug-resistant bacteria in fish pond water threaten public health

ABSTRACT Extensive use of antibiotics leads to the appearance of multi-drug resistant (MDR) ESBL-producing bacteria across various sectors, however, little is known about their emergence from fish ponds. This study investigates the isolation of MDR ESBL-producing bacteria from three fish ponds in Ibadan, Nigeria, where water samples (n = 72) were collected and analysed for Gram-negative bacteria. Antibiotic susceptibility testing and ESBL phenotypic detection were performed using the Kirby-Bauer disc diffusion method and the double disc synergy test, respectively. Polymerase chain reaction identified ESBL bla SHV, bla TEM, and bla CTX-M genes. MDR ESBL-producers were confirmed through 16S rRNA sequencing. Pseudomonas species (n = 52), Plesiomonas species (n = 24), and Morganella species (n = 6) were isolated from the fish ponds, whereas Pseudomonas monteilii (n = 2), and one isolate each of Pseudomonas viridiflava and Plesiomonas shigelloides, were MDR. Morganella morganii (n = 1) was MDR-ESBL and harboured bla SHV and bla CTX-M. The presence of MDR ESBL-producing bacteria in fish pond water suggests aquaculture may threaten public health unless overuse of antibiotics can be prevented.

Prevalence and pathogenic potential of Shewanella species in oysters and seawater collected from the Chesapeake Bay and Maryland Coastal Bays

Shewanella is a genus of Gram-negative marine bacteria with some species associated with human and shellfish illnesses. This study evaluated the abundance of Shewanella species in oysters and seawater from the Chesapeake and Maryland Coastal Bays at four sites between 2019 and 2021. Physicochemical parameters such as temperature, salinity, dissolved oxygen, turbidity, pH, chlorophyll-a, rainfall within the last 48 h, total dissolved solids, and atmospheric pressure were also recorded to evaluate if there was a correlation between environmental parameters and the level of Shewanella. The highest total Shewanella counts were 1.8 × 107 CFU/g in oysters and 4.0 × 102 CFU/mL in seawater. 16S rRNA sequencing was performed on 1,344 representative isolates of which 890 (713 oyster, 177 seawater) were confirmed as Shewanella within 16 species. The top four species isolated from oysters and seawater were S. khirikhana a known shrimp pathogen (49%), S. marisflavi (19%), S. loihica (11%), and S. algae (8%). Testing for alpha and beta hemolysis were performed on all confirmed Shewanella isolates. Beta hemolysis was observed in 405 (46%) of the isolates of which 313 were in oysters and 92 in seawater. In oysters, beta-hemolysis was most prevalent in S. khirikhana (233 of 344 isolates, 68%), while in seawater 64 of 92 isolates (70%) were beta-hemolytic strains. Beta-hemolysis suggests that these could be potentially pathogenic strains. Correlations were performed between physicochemical attributes of the seawater and Shewanella counts. Only seawater temperature and dissolved oxygen correlated with Shewanella counts (r = 0.45 and − 0.41), respectively. No correlations were observed between the physicochemical parameters and Shewanella abundances in oysters. Results suggest that virulent strains of Shewanella may be present in oysters and seawater from the Chesapeake and Maryland Coastal Bays, perhaps as a consequence of rising seawater temperatures.

Studies on the alleviating effect of Bifidobacterium lactis V9 on dextran sodium sulfate-induced colitis in mice

BackgroundInflammatory bowel disease (IBD) has become a global public health problem with complex pathogenesis and limited therapeutic options. We aimed to investigate the potential mechanisms by which Bifidobacterium lactis V9 (V9) alleviated colitis in a dextran sodium sulfate-induced colitis model mice.MethodsMice were induced to develop colitis by drinking DSS solution to induce colitis. The expression of the relevant factors in the blood supernatant of the mice was determined by ELISA. RT-qPCR and Western blotting were used to detect mRNA and protein expression of target genes. The fecal microbiota was analyzed by 16S rRNA sequencing. Intestinal metabolites were analyzed by untargeted metabolomics;ResultsV9 effectively improved the overall symptoms of the colitis model mice. H&E showed that V9 re-stored the intestinal tissue structure. ELISA showed that V9 decreased the levels of IL-6, IL-22, and TNF-α and increased IL-10, SP, VIP, and 5-HT. V9 increased the expression of AHR, CYP1A1, MUC2, Claudin-3, Occludin, and ZO-1, and decreased 5-hydroxytryptamine transporter and Claudin-2. V9 increased the abundance of gut microbiota in colitis mice to promote the growth of beneficial bacteria. V9 increased tryptophan metabolites, and short-chain fatty acids, and improved gut inflammation.ConclusionV9 attenuates intestinal inflammation, improves the mucosal barrier, modulates intestinal microecology and exerts a protective effect in a mouse model of DSS-induced colitis.

Hypertrophic heart failure promotes gut dysbiosis and gut leakage in interleukin 10-deficient mice.

Heart failure (HF) is a leading cause of death worldwide. We have shown that pressure overload (PO)-induced inflammatory cell recruitment leads to heart failure in IL-10 knockout (KO) mice. However, it's unclear if PO-induced inflammatory cells also target the gut mucosa, causing gut dysbiosis and leakage. We hypothesized that TAC (transverse aortic constriction) exacerbates immune cell homing to the gut (small intestine and colon), promoting dysbiosis and gut leakage in IL-10 KO mice. HF was induced in 8-10 weeks old C57BL/6J wild-type (WT) and B6.129P2-Il10tm1Cgn/J mutant (IL-10 KO) male and female mice by TAC and cardiac function was measured using visual sonics VEVO 3100. Fourteen days post-TAC, levels of monocytes, macrophages, neutrophils, and proinflammatory cytokines were measured in blood and gut. Gut dysbiosis was assessed via 16S rRNA sequencing in feces at 56 days post-TAC. IL-10 KO mice showed worsened cardiac dysfunction post-TAC. TAC worsened monocytes, and neutrophils infiltration in systemic circulation and facilitated their homing to the gut in IL-10 KO mice. Intriguingly, proinflammatory cytokines level was increased in blood, and gut of IL-10 KO mice following TAC. Furthermore, IL-10 expression was reduced in the colon of WT mice post-TAC. Moreover, TAC exacerbated gut dysbiosis in IL-10 KO mice. Finally, an impaired intestinal permeability was noted in IL-10 KO mice post-TAC. In conclusion, TAC-induced systemic inflammation leads to gut dysbiosis and impaired gut permeability in IL-10 KO mice, indicating IL-10's potential role in regulating intestinal integrity and microbiota balance during heart failure.

No rumen fermentation profiles and associated microbial diversities difference were found between Hu sheep and Karakul sheep fed a cottonseed hull diet

BackgroundThis research aimed to investigate differences in rumen fermentation characteristics between Karakul sheep and Hu sheep reared under identical conditions. The test subjects included newborn Hu and Karakul sheep, which were monitored across three stages: stage I (Weaning period: 15 ~ 30 days), stage II (Supplementary feeding period: 31 ~ 90 days), and stage III (Complete feeding period: 91 ~ 150 days). During the supplementary feeding period, cottonseed hulls were the main roughage source. To analyze the dynamics of rumen fermentation, 16S rRNA sequencing and metabolomics methods were employed, alongside measurements of rumen fermentation parameters and cellulase activity. This comprehensive approach aimed to investigate the potential impact of breed on rumen fermentation indicators, microbial community structure, and metabolites in Hu and Karakul sheep.ResultsThe 16S rRNA sequencing analysis revealed no significant differences in the relative abundance or dominant bacterial communities in the rumen across all stages. In stage II, rumen bacteria in both Hu and Karakul sheep were relatively stable. However, the Simpson index of Hu sheep in stage II was substantially greater than that of Karakul sheep, demonstrating similarities in the rumen microbial structure between stages II and III. Dynamic variations in fermentation parameters and cellulase activity in the rumen revealed that the indicators in both sheep breeds stabilized at 150 days. Metabolomic results revealed that the metabolic pathways in stage I were mainly concentrated in purine metabolism and lipid metabolism, while stage II was dominated by amino acid metabolism. Stage III involved mainly in pyrimidine and purine metabolism. An exploration of the relationships among rumen microbial biomarkers, key differentially abundant metabolites and rumen characteristics indicated that Karakul sheep exhibited superior lipid metabolism compared to Hu sheep.ConclusionThese findings reveal that there were no interbreed differences in the rumen characteristics of Hu and Karakul sheep when fed the same cottonseed hull diet, despite differences in their metabolic pathways. The findings also indicate that the first 20 days represent the initial stage of rumen bacteria in Hu sheep, followed by a transition phase between 20 and 90 days, and a relatively stable stage from 90 to 150 days. These results provide a scientific basis for further understanding the rumen function of sheep and for optimizing their feeding strategies.D2CHRS7zryw_AWg9hJmKX2Video

Brain Tumors and Beyond: Multi-Compartment Microbiome and Mycobiome Analysis

Brain tumors are frequently diagnosed diseases in which etiology and progression largely depend on mutations and genetic factors. Additionally, recent reports document that the microbiome may influence tumor growth, tumor microenvironment, and response to therapy. Our goal was to examine the extent to which the bacterial composition—microbiota—and fungal composition—mycobiota—characteristic of the tumor and its microenvironment correlate with the composition of the gut and blood microbiota and mycobiota in five randomly selected brain tumor patients. The bacterial composition of the tumor, tumor-adjacent tissue (TAT), blood, and gut samples of the five patients were analyzed by 16S rRNA and ITS-based sequencing in order to determine the bacterial and fungal composition. The gut microbiome and mycobiome composition showed individual and tissue-specific signatures in each patient. The microbiome composition of the blood, TAT, and tumor tissue was very similar in each patient, dominated by Klebsiella, Enterococcus, Blautia, and Lactobacillus spp. In contrast, the mycobiome composition of the blood, TAT, and tumor showed a diverse, individual picture. The most common fungal species in the blood and TAT were Tomentella, Didymosphaeria, Alternaria, Penicillium, Mycosphaerella, and Discosia. The blood and TAT mycobiome were similar to each other but unique and characteristic of the patients. In contrast, in the tumor tissues, Alternaria, Malassezia, Schizophyllum, and Tomentella genus were the most common fungi genus. Our results showed that the presence of fungi in tumors shows a unique pattern that is independent of the pattern observed in the gut, blood, and tumor environment and that the effects of the mycobiome are distinct and cannot be associated with those of the microbiome. Elucidating the role of fungi in tumors and exploring the relationship between fungi and brain tumor types may open up further therapeutic options.

Associations between the gut microbiome, inflammation and cardiovascular profiles in people with HIV.

Inflammation and innate immune activation are associated with chronic HIV infection, despite effective treatment. Although gut microbiota alterations are linked to systemic inflammation, the relationships between the gut microbiome, inflammation and HIV remain unclear. The UPBEAT-CAD sub-study, examining cardiovascular disease (CVD) risk in HIV, enrolled participants matched on HIV status and traditional CVD risk factors. Subclinical CVD was assessed using coronary computed tomography angiography (CCTA). 34 biomarkers were measured using quantitative immunoassays. Microbiota composition was analysed by 16S rRNA sequencing of stool samples, with taxonomic assignment via the SPINGO pipeline. Differentially abundant species were identified by Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) and correlated to biomarkers, diet and CCTA outcomes using Spearman correlation. Among 81 participants (median age 51 years, 73% male), people with HIV (n=44 , 54%) had a higher prevalence of hypercholesterolaemia (p <0.025) and statin use (p <0.001). A significant separation in gut microbiome β-diversity was observed between people with and without HIV. ANCOM-BC analysis identified 42 differentially abundant species and 10 genera in those with HIV. Enrichment of Bifidobacterium pseudocatenulatum, Megamonas hypermegale and Selenomonas ruminantium and depletion of Fusicatenenibacter correlated with lower plaque burden. Depletion of SCFA-producing Ruminococcus bromii correlated with higher plaque burden and fat intake, while depletion of Bacteroides spp and Alistepes spp correlated with elevated inflammatory biomarkers (D-dimer, CD40-ligand, CRP and IFN-γ). Significant gut microbiota differences in people with HIV were linked to subclinical CVD, diet, and inflammation, suggesting a role for the microbiome in cardiovascular risk in HIV infection.

The impact of different gastrointestinal reconstruction techniques on gut microbiota after gastric cancer surgery

IntroductionGastric cancer is one of the common malignant tumors in the digestive tract, characterized by high incidence and mortality rates. This is particularly significant in China, where a large proportion of global new cases of gastric cancer and related deaths occur. In recent years, with the continuous development of molecular biology technology, people have gained a deeper understanding of the gastrointestinal microbiome, and studies have shown that it is closely related to the occurrence, development, and therapeutic response of gastric cancer. Although surgical intervention is crucial in significantly extending the survival of gastric cancer patients, the disruption of the balance of the intestinal microbiota caused by surgery itself should not be overlooked, as it may affect postoperative recovery.MethodsThis study was approved by the Biomedical Ethics Committee of Sichuan Mianyang 404 Hospital. A random sampling method was used to select patients who underwent gastric cancer surgery at the hospital from January 2023 to December 2023. All patients signed written informed consent forms. Standardized perioperative management was conducted for the patients in the study, including preoperative preparation, intraoperative handling, and postoperative treatment. Fecal samples were collected from patients before surgery (before bowel preparation) and around one week after surgery for 16S rRNA sequencing analysis, through which differential biomarkers and related functional genes were sought.ResultsThe study results indicated that there was no significant difference in the diversity of the gut microbiota between the two groups. Compared with the R-Y group, the DTR surgical method significantly altered the structure of the gut microbiota, affecting the types, quantities, and proportions of intestinal bacteria. Furthermore, the DTR group exhibited poorer postoperative nutritional absorption capacity compared to the R-Y group, as indicated by a lower F/B ratio. The R-Y group showed a richer abundance of Bacteroidetes and a lower abundance of Proteobacteria, as well as a higher F/B ratio after surgery. These findings provide new insights into the changes in the gut microbiota following gastric cancer surgery, which may be of significant importance for postoperative recovery and long-term health management.DiscussionThis study reveals the impact of different gastrointestinal reconstruction techniques on the postoperative gut microbiota of gastric cancer patients, providing new insights into the physiological changes during the postoperative recovery period. Although there was no significant difference in microbial diversity between the DTR group and the R-Y group, the DTR group showed more pronounced changes in microbial structure postoperatively, which may be associated with an increased risk of postoperative infection. These findings emphasize the importance of considering the impact on the gut microbiota when selecting gastric cancer surgery methods. However, the study had a limited sample size and did not delve into changes in metabolites. Future studies should expand the sample size and conduct metabolomic analyses to further validate these preliminary findings.

Characterization, Identification, and Biosafety Evaluation of Multifaceted Traits of Plant Growth-Promoting Endophytes for Ameliorating Productivity of Forage Sorghum.

Endophytes are bacteria that inhabit host plants for most of their life cycle without causing harm. In the study, 15 endophytic bacteria were isolated from 30 forage Sorghum plants and assessed for various plant growth-promoting (PGP) traits, such as phosphate solubilization, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, ammonia production, siderophore production, gibberellic acid production, Indole-3-acetic acid (IAA) production, and zinc solubilization. One isolate, JJG_Zn, demonstrated multiple PGP activities and was identified as Enterobacter sp. through 16S rRNA sequencing. Considering the concept of 'One health,' a comprehensive biosafety analysis for any plant growth-promoting bacteria (PGP bacteria) is essential, thus, Enterobacter sp. (JJG_Zn), along with two other standard cultures, Burkholderia seminalis and Stenotrophomonas maltophilia, were evaluated for biosafety tests-including sheep blood agar assay, E.coli sensitivity assay, and pathogenicity tests on albino mice. The results indicated that all three PGP bacteria were potentially innocuous and compatible with each other. Furthermore, the field experiments were conducted at Punjab Agricultural University, Regional Research Station, Bathinda, and School of Organic Farming, IFS, Punjab Agricultural University, Ludhiana during Kharif 2022 employing a randomized complete block design (RCBD) with nine treatment combinations. The treatments included liquid bacterial inoculants (LBIs) of Stenotrophomonas maltophilia, Burkholderia seminalis, and Enterobacter sp. (JJG_Zn) applied in combination with 100% and 75% of the recommended dose of fertilizer (RDF), with each treatment replicated thrice. The treatment T9 (75% RDF + dual inoculation with B. seminalis and S. maltophilia) resulted in the highest productivity, showing a 10.23% increase in pooled green fodder yield (GFY) compared to the control. The treatment T8 (75% RDF + Enterobacter sp. (JJG_Zn)) showed a 5.14% increase in productivity over the control. Thus, liquid bacterial inoculants (LBIs) present a promising approach to enhance the productivity of forage Sorghum.

Exploring Microbial Signatures in Endometrial Tissues with Endometriosis.

The endometrial microbiota exerts a crucial role in maintaining the health of the female reproductive system. As such, in this study, we have examined the composition of the microbiota in endometrium tissues with and without endometriosis, with the objective of identifying key species that may potentially contribute to the progression of endometriosis. We obtained endometrial tissues from 43 women diagnosed as either having endometriosis or not. Subsequently, we utilized a diverse array of techniques, including fluorescence in situ hybridization (FISH), immunohistochemistry (utilizing anti-LPS and anti-LTA antibodies), transmission electron microscopy (TEM), and 16S rRNA sequencing, to undertake a comprehensive examination of the presence of microorganisms in the endometrium and their potential role in endometriosis. Our findings consistently indicated the existence of bacteria in both normal endometrium tissues and those affected by endometriosis. By employing the fluorescent co-staining technique, we observed the colocalization of macrophages and bacteria in both tissue types. Notably, we discovered a significant increase in microbial diversity in endometrial tissue from women with endometriosis compared to normal endometrial tissues. Additionally, we identified 13 species that were more abundant in the normal group, such as Acinetobacter guillouiae. In contrast, seven species were prominent in the endometriosis group, with Faecalibacterium prausnitzii being a notable one. Finally, our results suggest that Faecalibacterium prausnitzii may play an essential role in the progression of endometriosis. We carried out a comprehensive analysis of the endometrial microbial landscape in endometriosis tissue and revealed that Faecalibacterium prausnitzii is a pivotal species that may potentially play a crucial role in the pathogenesis of endometriosis.