Type IV pili (T4P) are bacterial surface-exposed appendages that have been extensively studied in Gram-negative pathogenic bacteria. Despite recent sequencing efforts, little is known regarding these structures in non-pathogenic anaerobic Gram-positive species, particularly commensals of the mammalian gut. Early studies revealed that T4P in two ruminal Gram-positive species are associated with growth on cellulose, suggesting possible associations of T4P with substrate utilization patterns. In the present study, genome sequences of 118 taxonomically diverse, mainly Gram-positive, bacterial strains isolated from anaerobic (gastrointestinal) environments, have been analysed for T4P biogenesis genes and genes encoding Carbohydrate Active enZYmes (CAZymes) to predict carbohydrate utilization abilities of selected strains. The predictive power of this approach was confirmed by experimental assessment of substrate-related growth patterns of selected strains. Our analysis revealed that T4P systems with diverse genetic organization are widespread among Gram-positive anaerobic non-pathogenic bacteria isolated from different environments, belonging to two phylogenetically distantly related phyla: Firmicutes and Actinobacteria.
COBISS.SI-ID: 43459331
The aim of the present study was to characterize human milk microbiota (HMM) with 16S rRNA gene amplicon next-generation sequencing and cultivation/matrix-assisted laser desorption/ionization (MALDI)-time of flight (TOF) mass spectrometry (MS) identification approaches. We analyzed 31 human milk samples from healthy Slovenian mothers. To check the accuracy of MALDI-TOF MS identification, several colonies representing most abundant genera and those, which could not be reliably identified by MALDI-TOF, were subjected to Sanger sequencing of their 16S rRNA gene. We showed that cultivation/MALDI-TOF MS was a suitable tool for culture-dependent determination of HMM. With both approaches, Staphylococcus and Streptococcus were found as predominant genera in HMM and the abundance of Staphylococcus was associated with decreased microbial diversity. In addition, we characterized factors that might influence HMM. The use of a breast pump was significantly associated with composition of HMM, higher microbial load, and lower abundance of cultivable staphylococci. Moreover, our study suggests that administration of probiotics to the suckling infant might influence HMM by increased abundance of lactobacilli and the presence of viable probiotic bacteria in human milk. However, since our study was observational with relatively small sample size, more targeted studies are needed to study possible transfer of probiotics to the mammary gland via an external route and the physiological relevance of these events.
COBISS.SI-ID: 4326792
Lactic acid bacteria (LAB) and bifidobacteria deliberately introduced into the food chain may act as a reservoir of antimicrobial resistance (AR), which is considered a safety concern. In the present study, resistance to antimicrobials of own and commercial probiotic and starter culture lactobacilli and bifidobacteria (n=20) was characterized based on integration of phenotypic and in silico data. Minimum inhibitory concentrations (MICs) were determined using broth microdilution and/or E-test. Antimicrobial resistance genes (ARG), mutations, genomic islands (GIs), and mobile genetic elements (MGE) were predicted in whole genome sequences (WGS) using different databases and tools (CARD, Resfams, ResFinder, ARG-ANNOT, FARME DB, IslandViewer4, PlasmidFinder, PointFinder, BLAST, HMMER3). In addition, a comprehensive in silico analysis of the prevalence of the tetW gene and its flanking sequences (FStetWs) across lactobacilli and bifidobacteria (n =1423) was conducted. Several strains exhibited phenotypic resistance to kanamycin, tetracycline, chloramphenicol, quinupristin-dalfopristin, ciprofloxacin, and neomycin. These resistances, however, did not always correspond to the presence of ARG and vice versa. We detected an acquired tetW gene in four probiotic strains of Bifidobacterium animalis subsp. lactis, whereas no acquired ARG were identified in genomes of lactobacilli. Nevertheless, homologs of AR proteins were predicted in all 20 proteomes. The prevalence of tetW, which is often flanked by MGE, was higher in analysed bifidobacteria (31.9 %) than lactobacilli (6.3 %). Results suggest that FStetWs may be associated with GIs and were conserved in several strains, including potential pathogens. Our findings provide an insight into AR of probiotic and starter cultures with an emphasis on tetracycline and into the safety of these strains in context of AR.
COBISS.SI-ID: 4320904
In the present study, we investigated the effect of supplementation with supranutritional concentrations of vitamin E, vitamin C, and selenium in broilers exposed to oxidative stress caused by the addition of polyunsaturated fatty acids (PUFA) to the feed. We monitored markers of oxidative stress and antioxidant defence in samples of fresh and cooked meat. Similar to our previous study on in vivo oxidative stress parameters, we showed that in all meat samples the only consistently effective antioxidant that protects animals from oxidative stress caused by PUFA is vitamin E, and that vitamin C and selenium do not possess clear synergistic effects, although they may partially accumulate in tissues.
COBISS.SI-ID: 4204936
Although the Prevotella are commonly observed in high shares in the mammalian hindgut and rumen studies using NGS approach, the knowledge on their actual role, though postulated to lie in soluble fibre degradation, is scarce. Here we analyse in total 23, more than threefold of hitherto known rumen and hindgut Prevotella species and show that rumen/hindgut Prevotella generally possess extensive repertoires of polysaccharide utilization loci (PULs) and carbohydrate active enzymes targeting various plant polysaccharides. These PUL repertoires separate analysed Prevotella into generalists and specialists yet a finer diversity among generalists is evident too, both in range of substrates targeted and in PUL combinations targeting the same broad substrate classes. Upon evaluation of the shares of species analysed in this study in rumen metagenomes we found firstly, that they contributed significantly to total Prevotella abundance though much of rumen Prevotella diversity may still be unknown. Secondly, the hindgut Prevotella species originally isolated in pigs and humans occasionally dominated among the Prevotella with surprisingly high metagenome read shares and were consistently found in rumen metagenome samples from sites as apart as New Zealand and Scotland. This may indicate frequent passage between different hosts and relatively low barriers to their successful establishment in rumen versus the hindgut.
COBISS.SI-ID: 4149384