Search Results (40)

Viral infections have been associated with multiple sclerosis (MS), an immune-mediated disease in the central nervous system (CNS). Since Theiler’s murine encephalomyelitis virus (TMEV) can induce MS-like demyelination, TMEV infection is the most widely used viral model for MS. Although the precise pathophysiology is unknown, altered fecal bacterial populations were associated with distinct immune gene expressions in the CNS. We aimed to determine the role of gut microbiota in TMEV infection by administering an antibiotic cocktail in drinking water before (prophylactic administration) or after (therapeutic administration) TMEV infection. The antibiotic administration reduced total eubacteria, including the phyla Bacillota and Bacteroidota, but increased the phylum Pseudomonadata in feces. Prophylactic administration did not alter TMEV-induced inflammatory demyelination clinically or histologically, without changes in anti-viral IgG1/IgG2c levels or lymphoproliferative responses; therapeutic administration temporarily suppressed the neurological signs. Although antibiotic treatment had minimal effects on TMEV infection, adding metronidazole and ampicillin in drinking water substantially reduced water intake in the antibiotic group of mice, resulting in significant body weight loss. Since dehydration and stress could affect immune responses and gut microbiota, caution should be exercised when planning or evaluating the oral antibiotic cocktail treatment in experimental animals. Full article

Trans-kingdom conjugation (TKC)/inter-domain conjugation is a horizontal gene transfer phenomenon that transfers DNA from eubacteria to eukaryotes and archaebacteria via a type IV secretion system encoded in IncP1-type broad-host-range plasmids. Although TKC is considered a potential gene introduction tool, donor chromosomal genes that influence TKC efficiency have rarely been analyzed, hindering targeted donor breeding. To identify potential TKC-related genes on a donor chromosome, a genome-wide screening of TKC-deficient mutants was performed using a comprehensive collection of Escherichia coli gene knockout mutants (Keio collection) as donors and a Saccharomyces cerevisiae strain as a recipient. Out of 3884 mutants, two mutants (∆aceE, ∆priA) showed a severe decrease in TKC efficiency by more than two orders of magnitude but not in bacterial conjugation. The effect on TKC efficiency by the two mutants was partly recovered by a preculture with a fresh culture medium before the TKC reaction, regardless of the presence of antibiotics. These results suggest that no single chromosomal target gene is solely responsible for universally blocking IncP1-type conjugation by impeding its function. The results also suggest the existence of an unidentified recognition or transfer mechanism distinct from bacterial conjugation, highlighting the novel roles of aceE and priA. Full article

An estimated 10% of COVID-19 survivors have been reported to suffer from complaints after at least three months. The intestinal microbiome has been shown to impact long COVID through the gut–lung axis and impact the severity. We aimed to investigate the relationship between the gut microbiome and clinical characteristics, exploring microbiome heterogeneity through clustering. Seventy-nine patients with long COVID evaluated at 3 to 6 months after infection were sampled for fecal metagenome analysis. Patients were divided into two distinct hierarchical clusters, based solely on the microbiome composition. Compared to cluster 1 (n = 67), patients in cluster 2 (n = 12) showed a significantly reduced lung function (FEV₁, FVC, and DLCO) and during acute COVID-19 showed a longer duration of hospital admissions (48 compared to 7 days) and higher rates of ICU admissions (92% compared to 22%). Additionally, the microbiome composition showed a reduced alpha diversity and lower proportion of butyrate-producing bacteria in cluster 2 together with higher abundances of Ruminococcus gnavus, Escherichia coli, Veillonella spp. and Streptococcus spp. and reduced abundances of Faecalibacterium prausnitzii and Eubacteria spp. Further research could explore the effect of pre- and pro-biotic supplementation and its impact on lung function and societal participation in long COVID. Full article

The impact of ZnO as a feed additive on growth-performance and intestinal function of Enterotoxigenic Escherichia coli (ETEC) K88-infected piglets remains unclear. Fecal scores of piglets in ETEC group were significantly increased compared to control group. ETEC K88 significantly damages the small intestine, including a reduction in villus height in the jejunum, duodenum, and ileum, and a decrease in total superoxide dismutase activity in the jejunum and catalase activity in the ileum and jejunum. Compared to control group, ETEC K88 infection significantly elevated the mRNA level of gene IL-1β and the level of ileal epithelial cell apoptosis. ZnO administration significantly alleviated these negative effects and improved the antioxidative capability of the ileum. Moreover, ZnO supplementation alleviated the imbalance of gut microbiota by restoring the reduced amount of Enterococcus and Lactobacillus in the jejunum, Clostridium in the ileum, and Lactobacillus in the cecum, as well as the increased amount of total eubacteria in the ileum and Enterococcus in the cecum induced by the ETEC K88 infection. In conclusion, ZnO administration can reduce the diarrhea of piglets infected with ETEC K88 by reducing the structural damage of the intestine, attenuating intestinal oxidative stress and epithelial cell apoptosis, and modulating the gut microbiota. Full article

Essential genes are crucial for microbial viability, playing key roles in both the primary and secondary metabolism. Since mutations in these genes can threaten organism viability, identifying them is challenging. Conditionally essential genes are required only under specific conditions and are important for functions such as virulence, immunity, stress survival, and antibiotic resistance. Transposon-directed sequencing (Tn-Seq) has emerged as a powerful method for identifying both essential and conditionally essential genes. In this review, we explored Tn-Seq workflows, focusing on eubacterial species and some yeast species. A comparison of 14 eubacteria species revealed 133 conserved essential genes, including those involved in cell division (e.g., ftsA, ftsZ), DNA replication (e.g., dnaA, dnaE), ribosomal function, cell wall synthesis (e.g., murB, murC), and amino acid synthesis (e.g., alaS, argS). Many other essential genes lack clear orthologues across different microorganisms, making them specific to each organism studied. Conditionally essential genes were identified in 18 bacterial species grown under various conditions, but their conservation was low, reflecting dependence on specific environments and microorganisms. Advances in Tn-Seq are expected to reveal more essential genes in the near future, deepening our understanding of microbial biology and enhancing our ability to manipulate microbial growth, as well as both the primary and secondary metabolism. Full article

Loewi’s discovery of acetylcholine (ACh) release from the frog vagus nerve and the discovery by Dale and Dudley of ACh in ox spleen led to the demonstration of chemical transmission of nerve impulses. ACh is now well-known to function as a neurotransmitter. However, advances in the techniques for ACh detection have led to its discovery in many lifeforms lacking a nervous system, including eubacteria, archaea, fungi, and plants. Notably, mRNAs encoding choline acetyltransferase and muscarinic and nicotinic ACh receptors (nAChRs) have been found in uninnervated mammalian cells, including immune cells, keratinocytes, vascular endothelial cells, cardiac myocytes, respiratory, and digestive epithelial cells. It thus appears that non-neuronal cholinergic systems are expressed in a variety of mammalian cells, and that ACh should now be recognized not only as a neurotransmitter, but also as a local regulator of non-neuronal cholinergic systems. Here, we discuss the role of non-neuronal cholinergic systems, with a focus on immune cells. A current focus of much research on non-neuronal cholinergic systems in immune cells is α7 nAChRs, as these receptors expressed on macrophages and T cells are involved in regulating inflammatory and immune responses. This makes α7 nAChRs an attractive potential therapeutic target. Full article

As methane fermentation is inhibited by ammonia derived from organic waste, anaerobic microbial communities tolerant to enriched wastewater with high concentrations of ammonia and salt must be obtained for methane fermentation. Therefore, acclimation cultures were prepared in bottles for 60–80 weeks with artificial wastewater medium added every 2 weeks, using three types of sludge from wastewater treatment plants in food factories. These cultures were maintained without substantially decreasing methanogenesis and gradually increasing NH₄-N and salt concentrations to 5 and 34 g/L, respectively, via the accumulation of ammonia and salt through anaerobic digestion and direct addition. The culture did not show the severe inhibition of methanogenesis or the accumulation of volatile fatty acids (VFAs) such as acetic and propionic acids. The analysis of bacterial consortia in the acclimated sludge based on the 16S rRNA sequence showed that hydrogenotrophic methanogenic bacteria of the genus Methanoculleus were dominant among archaea, whereas bacteria from the orders Clostridiales and Bacteroidales were dominant among eubacteria. Further, VFA-assimilating bacteria, including synthetic acetate-oxidizing bacteria coupled with hydrogenotrophic Methanoculleus to convert methane from acetate, were present to prevent the excessive accumulation of VFAs in the acclimation culture. The proposed acclimation process can enhance the anaerobic digestion of wastewater for methane production. Full article

The production of Volatile Fatty Acids (VFAs) from wastewater holds significant importance in the context of biorefinery concepts due to their potential as valuable precursors for various bio-based processes. Therefore, the primary objective of this research is to investigate the fermentation of Winery Wastewater (WW) in an Upflow Anaerobic Sludge Blanket (UASB) reactor to generate VFAs, with particular emphasis on Caproic Acid (HCa) production and the dynamics of the microbiota, under varying Hydraulic Retention Time (HRT) periods (8, 5, and 2.5 h). The change from an 8 h to a 5 h HRT period resulted in an approximately 20% increase in total VFA production. However, when the HRT was further reduced to 2.5 h, total VFA production decreased by approximately 50%. Concerning the specific production of HCa, expressed in grams of Chemical Oxygen Demand (gCOD), the maximum yield was observed at around 0.9 gCOD/L for a 5-h HRT. Microbial population analysis revealed that Eubacteria outnumbered Archaea across all HRTs. Population dynamics analysis indicated that the Firmicutes Phylum was predominant in all cases. Within this phylum, bacteria such as Clostridium kluyveri and Clostridium sp., known for their ability to produce HCa, were identified. Based on the results obtained, the application of the UASB reactor for WW treatment, within the biorefinery framework, has the potential to provide a practical alternative for HCa production when operated with a 5 h HRT. Full article

Post-transcriptional modifications of tRNA are crucial for their core function. The inosine (I; 6-deaminated adenosine) at the first position in the anticodon of tRNA^Arg(ICG) modulates the decoding capability and is generally considered essential for reading CGU, CGC, and CGA codons in eubacteria. We report here that the Bacillus subtilis yaaJ gene encodes tRNA-specific adenosine deaminase and is non-essential for viability. A β−galactosidase reporter assay revealed that the translational activity of CGN codons was not impaired in the yaaJ-deletion mutant. Furthermore, tRNA^Arg(CCG) responsible for decoding the CGG codon was dispensable, even in the presence or absence of yaaJ. These results strongly suggest that tRNA^Arg with either the anticodon ICG or ACG has an intrinsic ability to recognize all four CGN codons, providing a fundamental concept of non-canonical wobbling mediated by adenosine and inosine nucleotides in the anticodon. This is the first example of the four-way wobbling by inosine nucleotide in bacterial cells. On the other hand, the absence of inosine modification induced +1 frameshifting, especially at the CGA codon. Additionally, the yaaJ deletion affected growth and competency. Therefore, the inosine modification is beneficial for translational fidelity and proper growth-phase control, and that is why yaaJ has been actually conserved in B. subtilis. Full article

The cpdB gene is pro-virulent in avian pathogenic Escherichia coli and in Salmonella enterica, where it encodes a periplasmic protein named CpdB. It is structurally related to cell wall-anchored proteins, CdnP and SntA, encoded by the also pro-virulent cdnP and sntA genes of Streptococcus agalactiae and Streptococcus suis, respectively. CdnP and SntA effects are due to extrabacterial hydrolysis of cyclic-di-AMP, and to complement action interference. The mechanism of CpdB pro-virulence is unknown, although the protein from non-pathogenic E. coli hydrolyzes cyclic dinucleotides. Considering that the pro-virulence of streptococcal CpdB-like proteins is mediated by c-di-AMP hydrolysis, S. enterica CpdB activity was tested as a phosphohydrolase of 3′-nucleotides, 2′,3′-cyclic mononucleotides, linear and cyclic dinucleotides, and cyclic tetra- and hexanucleotides. The results help to understand cpdB pro-virulence in S. enterica and are compared with E. coli CpdB and S. suis SntA, including the activity of the latter on cyclic-tetra- and hexanucleotides reported here for the first time. On the other hand, since CpdB-like proteins are relevant to host-pathogen interactions, the presence of cpdB-like genes was probed in eubacterial taxa by TblastN analysis. The non-homogeneous genomic distribution revealed taxa with cpdB-like genes present or absent, identifying eubacteria and plasmids where they can be relevant. Full article

A common genome composition pattern in eubacteria is an asymmetry between the leading and lagging strands resulting in opposite skew patterns in the two replichores that lie between the origin and terminus of replication. Although this pattern has been reported for a couple of isolated plastid genomes, it is not clear how widespread it is overall in this chromosome. Using a random walk approach, we examine plastid genomes outside of the land plants, which are excluded since they are known not to initiate replication at a single site, for such a pattern of asymmetry. Although it is not a common feature, we find that it is detectable in the plastid genome of species from several diverse lineages. The euglenozoa in particular show a strong skew pattern as do several rhodophytes. There is a weaker pattern in some chlorophytes but it is not apparent in other lineages. The ramifications of this for analyses of plastid evolution are discussed. Full article

Objective: The detection of special bacterial species in patients with periodontitis is considered useful for clinical diagnosis and treatment. The aim of this study was to investigate the presence of specific periopathogens and investigate whether there is a correlation between the results of different bacterial species in whole saliva and pooled subgingival plaque samples (healthy and diseased sites) from individuals with periodontitis and periodontally healthy subjects. Materials and methods: In total, 52 patients were recruited and divided into two groups: non-periodontitis and periodontitis patients. For each group, the following periodontal pathogens were detected using real-time polymerase chain reaction: A. actinomycetemcomitans JP2 clone, A. actinomycetemcomitans non JP2 clone, Porphyromonasgingivalis, and total eubacteria. Results: Higher levels of the various studied bacteria were present in both saliva and plaque samples from the periodontitis group in comparison to non-periodontitis subjects. There were significant differences in P. gingivalis and A. actinomycetemcomitans JP2 clones in the saliva of periodontitis patient compared to the control group. Subgingival plaque of diseased sites presented a significant and strong positive correlation between A. actinomycetemcomitans and P. gingivalis. In saliva samples, there was a significant positive correlation between A. actinomycetemcomitans JP2 clone and P. gingivalis (p ≤ 0.002). Conclusion: Quantifying and differentiating these periodontal species from subgingival plaque and saliva samples showed a good potential as diagnostic markers for periodontal disease. Regarding the prevalence of the studied bacteria, specifically A. actinomycetemcomitans JP2 clone, found in this work, and the high rate of susceptibility to periodontal species in Africa, future larger studies are recommended. Full article

To address the continued rise of multi-drug-resistant microorganisms, the development of novel drugs with new modes of action is urgently required. While humans biosynthesize the essential isoprenoid precursors isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) via the established mevalonate pathway, pathogenic protozoa and certain pathogenic eubacteria use the less well-known methylerythritol phosphate pathway for this purpose. Important pathogens using the MEP pathway are, for example, Plasmodium falciparum, Mycobacterium tuberculosis, Pseudomonas aeruginosa and Escherichia coli. The enzymes of that pathway are targets for antiinfective drugs that are exempt from target-related toxicity. 2C-Methyl-D-erythritol 4-phosphate (MEP), the second enzyme of the non-mevalonate pathway, has been established as the molecular target of fosmidomycin, an antibiotic that has so far failed to be approved as an anti-infective drug. This review describes the development and anti-infective properties of a wide range of fosmidomycin derivatives synthesized over the last four decades. Here we discuss the DXR inhibitor pharmacophore, which comprises a metal-binding group, a phosphate or phosphonate moiety and a connecting linker. Furthermore, non-fosmidomycin-based DXRi, bisubstrate inhibitors and several prodrug concepts are described. A comprehensive structure–activity relationship (SAR) of nearly all inhibitor types is presented and some novel opportunities for further drug development of DXR inhibitors are discussed. Full article

Daqu provides functional microbiota and various nutrients for artificial pit mud (APM) cultivation. However, little is known about whether its attributes affect the microbiome and metabolome of APM. Here, two types of APM were manufactured by adding fortified Daqu (FD) and conventional Daqu (CD); they were comprehensively compared by polyphasic detection methods after being used for two years. The results showed that FD altered the prokaryotic communities rather than the fungal ones, resulting in increased archaea and Clostridium_sensu_stricto_12 and decreased eubacteria and Lactobacillus. Correlation analysis suggested that these variations in community structure promoted the formation of hexanoic acid, butyric acid, and the corresponding ethyl esters, whereas they inhibited that of lactic acid and ethyl lactate and thus improved the flavor quality of the APM. Notably, pH was the main driving factor for the bacterial community variation, and the total acid mediated the balance between the stochastic and the deterministic processes. Furthermore, the results of the network analysis and PICRUSt2 indicated that FD also enhanced the modularity and robustness of the co-occurrence network and the abundance of enzymes related to hexanoic acid and butyric acid production. Our study highlights the importance of Daqu attributes in APM cultivation, which are of great significance for the production of high-quality strong-flavor Baijiu. Full article

Short chain fatty acid (SCFA) butyrate has various beneficial effects on the gut microbiota as well as on the overall health status and metabolism of the host organism. The modulatory role of butyrate on gut barrier integrity reflected by tight junction protein expression has been already described in mammalian species. However, there is limited information available regarding chickens. Therefore, the main aim of this study was to monitor the effects of protected butyrate on claudin barrier protein and monocarboxylate transporter 1 abundance in different gastrointestinal segments of chickens as well as the growth performance of broiler chickens. The effect of protected butyrate on the caecal microbiota was monitored by quantifying the concentrations of total eubacteria and key enzymes of butyrate production. Furthermore, intestinal SCFA concentrations were also measured. Based on the data obtained, protected butyrate increased the overall performance as well as the barrier integrity of various gut segments. Protected butyrate also positively affected the SCFA concentration and composition. These findings provide valuable insight into the complex effects of protected butyrate on broiler gut health, highlighting the beneficial effects in improving intestinal barrier integrity and performance parameters. Full article