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Frontiers in Microbiology 2020Microbiota coexists in true symbiosis with the host playing pivotal roles as a key element for well-being and health. Exopolysaccharides from lactic acid bacteria are an...
Microbiota coexists in true symbiosis with the host playing pivotal roles as a key element for well-being and health. Exopolysaccharides from lactic acid bacteria are an alternative as novel potential prebiotics that increase microbiota diversity. Considering this, the aim of the present work was to evaluate the capacity of the EPS produced by two strains isolated from kefir grains, to be metabolized by fecal microbiota producing short chain fatty acids. For this purpose, fecal samples from healthy children were inoculated in a basal medium with EPS and incubated in anaerobiosis at 37°C for 24, 48, and 72 h. DGGE profiles and the production of SCFA after fermentation were analyzed. Additionally, three selected samples were sequenced by mass sequencing analysis using Ion Torrent PGM. EPS produced by CIDCA 8339 (EPS) and CIDCA 83124 (EPS) are metabolized by fecal microbiota producing a significant increase in SCFA. EPS fermentation led to an increment of propionate and butyrate, while fermentation of EPS increased butyrate levels. Both EPS led to a profile of SCFA different from the ones obtained with inulin or glucose fermentation. DGGE profiles of 72 h fermentation demonstrated that both EPS showed a different band profile when compared to the controls; EPS profiles grouped in a cluster that have only 65% similarity with glucose or inulin profiles. Mass sequencing analysis demonstrated that the fermentation of EPS leads to an increase in the proportion of the genera , and and a significant drop in the proportion of enterobacteria. In the same direction, the fermentation of EPS also resulted in a marked reduction of Enterobacteriaceae with a significant increase in the genus . It was observed that the changes in fecal microbiota and SCFA profile exerted by both polymers are different probably due to differences in their structural characteristics. It can be concluded that EPS synthesized by both strains, could be potentially used as bioactive compound that modify the microbiota increasing the production of propionic and butyric acid, two metabolites highly associated with beneficial effects both at the gastrointestinal and extra-intestinal level.
PubMed: 33178165
DOI: 10.3389/fmicb.2020.583254 -
Frontiers in Veterinary Science 2022The fermented feed has been used extensively as a growth promoter in agricultural animal production. However, the effects of fermented feed on swine gut microbiota are...
The fermented feed has been used extensively as a growth promoter in agricultural animal production. However, the effects of fermented feed on swine gut microbiota are still largely unknown. The work presented here aimed to investigate the growth performance and gut microbiota of nursery pigs receiving the LPF diet (10% and co-fermented feed + basal diet) compared with pigs receiving the NC diet (basal diet). The data showed LPF diet numerically improved average daily gain and significantly increased fecal acetate, butyrate, and total short-chain fatty acid (SCFA) concentrations. Furthermore, gut microbiota structure and membership significantly changed in response to the addition of fermented feed in the diet. Gut microbiota results indicated that LPF treatment significantly enriched SCFA-producing bacteria such as , and . Some of these bacteria also had anti-inflammatory and other beneficial functions. Overall, these findings suggested that and co-fermented feed benefited growth performance and established potential health impacts on the gut microbiota of nursery pigs.
PubMed: 36578437
DOI: 10.3389/fvets.2022.1076906 -
Nutrients Nov 2022Pre-clinical studies suggest that circulating oxylipins, i.e., the oxidation products of polyunsaturated fatty acids (PUFAs), modulate gut microbiota composition in...
Pre-clinical studies suggest that circulating oxylipins, i.e., the oxidation products of polyunsaturated fatty acids (PUFAs), modulate gut microbiota composition in mice, but there is no information available in humans. Therefore, this study aimed to investigate the relationship between omega-3 and omega-6 derived oxylipins plasma levels and fecal microbiota composition in a cohort of young adults. 80 young adults (74% women; 21.9 ± 2.2 years old) were included in this cross-sectional study. Plasma levels of oxylipins were measured using liquid chromatography-tandem mass spectrometry. Fecal microbiota composition was analyzed by V3-V4 16S rRNA gene sequencing. We observed that plasma levels of omega-3 derived oxylipins were positively associated with the relative abundance of genus ( phylum; rho ≥ 0.415, ≤ 0.009) and negatively associated with the relative abundance of genus (Proteobacteria phylum; rho ≥ -0.270, ≤ 0.041), respectively. Moreover, plasma levels of omega-6 derived oxylipins were negatively associated with the relative abundance of and genera ( phylum; all rho ≥ -0.263, ≤ 0.024), as well as , , and genera ( phylum; all rho ≥ -0.263, ≤ 0.024). Lastly, the ratio between omega-6 and omega-3 oxylipins plasma levels was negatively associated with the relative abundance of cluster IV genus ( phylum; rho = -0.334, = 0.004) and genus ( phylum; rho = -0.292, = 0.014). In conclusion, our results show that the plasma levels of omega-3 and omega-6 derived oxylipins are associated with the relative abundance of specific fecal bacteria genera.
Topics: Young Adult; Humans; Female; Mice; Animals; Adult; Male; RNA, Ribosomal, 16S; Cross-Sectional Studies; Oxylipins; Feces; Microbiota; Firmicutes; Bacteroidetes; Proteobacteria; Fatty Acids, Omega-3
PubMed: 36501021
DOI: 10.3390/nu14234991 -
Frontiers in Physiology 2021Carotid atherosclerosis (CAS) is an important cause of stroke. Although interactions between the gut microbiome and metabolome have been widely investigated with respect...
BACKGROUND
Carotid atherosclerosis (CAS) is an important cause of stroke. Although interactions between the gut microbiome and metabolome have been widely investigated with respect to the pathogenesis of cardiovascular diseases, information regarding CAS remains limited.
MATERIALS AND METHODS
We utilized 16S ribosomal DNA sequencing and untargeted metabolomics to investigate the alterations in the gut microbiota and plasma metabolites of 32 CAS patients and 32 healthy controls. The compositions of the gut microbiota differed significantly between the two groups, and a total of 11 differentially enriched genera were identified. In the metabolomic analysis, 11 and 12 significantly changed metabolites were screened in positive (POS) and negative (NEG) modes, respectively. α-N-Phenylacetyl-L-glutamine was an upregulated metabolite in CAS patients detected in both POS and NEG modes and had the highest | log(fold change)| in POS mode. In addition, transcriptomic analysis was performed using the GSE43292 dataset.
RESULTS
A total of 132 differentially expressed genes (DEGs) were screened. Among the upregulated DEGs in CAS patients, FABP4 exhibited the highest | log(fold change)|. Furthermore, FABP4 was positively associated with and had the highest Spearman's correlation coefficient and the most significant -value among the microbiota-DEG pairs.
CONCLUSION
In this study, we investigated the potential "microbiota-metabolite-gene" regulatory axis that may act on CAS, and our results may help to establish a theoretical basis for further specialized study of this disease.
PubMed: 34108883
DOI: 10.3389/fphys.2021.645212 -
International Journal of Molecular... Aug 2022Type V Cas12a nucleases are DNA editors working in a wide temperature range and using expanded protospacer-adjacent motifs (PAMs). Though they are widely used, there is...
Type V Cas12a nucleases are DNA editors working in a wide temperature range and using expanded protospacer-adjacent motifs (PAMs). Though they are widely used, there is still a demand for discovering new ones. Here, we demonstrate a novel ortholog from sp. entitled RbCas12a, which is able to efficiently cleave target DNA templates, using the particularly high accessibility of PAM 5'-YYN and a relatively wide temperature range from 20 °C to 42 °C. In comparison to sp. (AsCas12a) nuclease, RbCas12a is capable of processing DNA more efficiently, and can be active upon being charged by spacer-only RNA at lower concentrations in vitro. We show that the human-optimized RbCas12a nuclease is also active in mammalian cells, and can be applied for efficient deletion incorporation into the human genome. Given the advantageous properties of RbCas12a, this enzyme shows potential for clinical and biotechnological applications within the field of genome editing.
Topics: Acidaminococcus; Animals; CRISPR-Cas Systems; DNA; Endonucleases; Gene Editing; Humans; Mammals; Ruminococcus
PubMed: 36012553
DOI: 10.3390/ijms23169289 -
Diabetes, Metabolic Syndrome and... 2022Emerging evidence has revealed that gut microbiota plays a pivotal role in the pathogenesis of type 2 diabetes mellitus (TDM) and diabetic kidney disease (DKD). However,...
PURPOSE
Emerging evidence has revealed that gut microbiota plays a pivotal role in the pathogenesis of type 2 diabetes mellitus (TDM) and diabetic kidney disease (DKD). However, few studies have used metagenomic sequencing to analyze the alterations of gut microbiota community in patients with early-stage DKD.
METHODS
We carried out metagenomic sequencing in fecal samples of 10 DKD patients (DKD group) and 10 TDM patients who appeared to be less prone to DKD (non-DKD group), aiming to compare the composition and function of gut microbiota between the DKD and non-DKD groups.
RESULTS
The gut microbial community of the DKD group was significantly different from that of the non-DKD group, characterized by a marked increase in phylum Proteobacteria, genus , species, unclassified, and . The amounts of species and were significantly and positively correlated with the urinary albumin creatinine ratio in the DKD group. Furthermore, functional analysis based on dbCAN and KEGG databases showed aberrant lipopolysaccharide (LPS) biosynthesis and carbohydrate metabolism in the gut microbiome of the DKD group.
CONCLUSION
Our findings provided evidence for alterations in the composition and function of gut microbiota in patients with DKD versus the non-DKD group. These data may contribute to a more comprehensive understanding of the pathological mechanisms of DKD.
PubMed: 35280499
DOI: 10.2147/DMSO.S347805 -
Journal of Animal Science and Technology Sep 2021Short-chain fatty acids (SCFAs) are metabolic products produced during the microbial fermentation of non-digestible fibers and play an important role in metabolic...
Short-chain fatty acids (SCFAs) are metabolic products produced during the microbial fermentation of non-digestible fibers and play an important role in metabolic homeostasis and overall gut health. In this study, we investigated the effects of supplementation with multispecies probiotics (MSPs) containing , , and on the gut microbiota, and fecal SCFAs and lactate levels of weaned pigs. A total of 38 pigs weaned at 4 weeks of age were fed either a basal diet or a diet supplemented with MSPs for 6 weeks. MSP administration significantly increased the fecal concentrations of lactate (2.3-fold; < 0.01), acetate (1.8-fold; < 0.05), and formate (1.4-fold; < 0.05). Moreover, MSP supplementation altered the gut microbiota of the pigs by significantly increasing the population of potentially beneficial bacteria such as , , , , and . MSP supplementation also decreased the abundance of pathogenic bacteria such as Escherichia and . The modulation of the gut microbiota was observed to be strongly correlated with the changes in fecal SCFAs and lactate levels. Furthermore, we found changes in the functional pathways present within the gut, which supports our findings that MSP modulates the gut microbiota and SCFAs levels in pigs. The results support the potential use of MSPs to improve the gut health of animals by modulating SCFAs production.
PubMed: 34796353
DOI: 10.5187/jast.2021.e94 -
Frontiers in Oral Health 2021Inflammation is a driven force in modulating microbial communities, but little is known about the interplay between colonizing microorganisms and the immune response in...
Inflammation is a driven force in modulating microbial communities, but little is known about the interplay between colonizing microorganisms and the immune response in periodontitis. Since local and systemic inflammation may play a whole role in disease, we aimed to evaluate the oral and fecal microbiome of patients with periodontitis and to correlate the oral microbiome data with levels of inflammatory mediator in saliva. Nine patients with periodontitis (P) in Stage 3/Grade B and nine age-matched non-affected controls (H) were evaluated. Microbial communities of oral biofilms (the supra and subgingival from affected and non-affected sites) and feces were determined by sequencing analysis of the V3-V4 region. Salivary levels of 40 chemokines and cytokines were correlated with oral microbiome data. Supragingival microbial communities of P differed from H (Pielou's evenness index, and Beta diversity, and weighted UniFrac), since relative abundance (RA) of was higher in P, whereas and were more abundant in H. Subgingival non-affected sites of P did not differ from H, except for a lower abundance of . The microbiome of affected periodontitis sites (PD ≥ 4 mm) clustered apart from the subgingival sites of H. Oral pathobionts was more abundant in sub and supragingival biofilms of P than H. Fecal samples of P were enriched with when compared to H. The salivary levels of interleukin 6 (IL-6) and inflammatory chemokines were positively correlated with the RA of several recognized and putative pathobionts, whereas the RA of beneficial species, such as and was negatively correlated with the levels of Chemokine C-C motif Ligand 2 (CCL2), which is considered protective. Dysbiosis in patients with periodontitis was not restricted to periodontal pockets but was also seen in the supragingival and subgingival non-affected sites and feces. Subgingival dysbiosis revealed microbial signatures characteristic of different immune profiles, suggesting a role for candidate pathogens and beneficial organisms in the inflammatory process of periodontitis.
PubMed: 35048045
DOI: 10.3389/froh.2021.722495 -
The Journals of Gerontology. Series A,... Jun 2020Determining the role of gut microbial communities in aging-related phenotypes, including weight loss, is an emerging gerontology research priority. Gut microbiome... (Comparative Study)
Comparative Study
Determining the role of gut microbial communities in aging-related phenotypes, including weight loss, is an emerging gerontology research priority. Gut microbiome datasets comprise relative abundances of microbial taxa that necessarily sum to 1; analysis ignoring this feature may produce misleading results. Using data from the Osteoporotic Fractures in Men (MrOS) study (n = 530; mean [SD] age = 84.3 [4.1] years), we assessed 163 genera from stool samples and body weight. We compared conventional analysis, which does not address the sum-to-1 constraint, to compositional analysis, which does. Specifically, we compared elastic net regression (for variable selection) and conventional Bayesian linear regression (BLR) and network analysis to compositional BLR and network analysis; adjusting for past weight, height, and other covariates. Conventional BLR identified Roseburia and Dialister (higher weight) and Coprococcus-1 (lower weight) after multiple comparisons adjustment (p < .0125); plus Sutterella and Ruminococcus-1 (p < .05). No conventional network module was associated with weight. Using compositional BLR, Coprococcus-2 and Acidaminococcus were most strongly associated with higher adjusted weight; Coprococcus-1 and Ruminococcus-1 were most strongly associated with lower adjusted weight (p < .05), but nonsignificant after multiple comparisons adjustment. Two compositional network modules with respective hub taxa Blautia and Faecalibacterium were associated with adjusted weight (p < .01). Findings depended on analytical workflow. Compositional analysis is advocated to appropriately handle the sum-to-1 constraint.
Topics: Age Factors; Aged; Aged, 80 and over; Aging; Bayes Theorem; Body Weight; Cohort Studies; Gastrointestinal Microbiome; Humans; Linear Models; Male; Osteoporotic Fractures; Sex Factors
PubMed: 32025711
DOI: 10.1093/gerona/glaa034 -
Nucleic Acids Research Jan 2022The adoption of CRISPR systems for the generation of synthetic transcription factors has greatly simplified the process for upregulating endogenous gene expression, with...
The adoption of CRISPR systems for the generation of synthetic transcription factors has greatly simplified the process for upregulating endogenous gene expression, with a plethora of applications in cell biology, bioproduction and cell reprogramming. The recently discovered CRISPR/Cas12a (Cas12a) systems offer extended potential, as Cas12a is capable of processing its own crRNA array, to provide multiple individual crRNAs for subsequent targeting from a single transcript. Here we show the application of dFnCas12a-VPR in mammalian cells, with the Francisella novicida Cas12a (FnCas12a) possessing a shorter PAM sequence than Acidaminococcus sp. (As) or Lachnospiraceae bacterium (Lb) variants, enabling denser targeting of genomic loci, while performing just as well or even better than the other variants. We observe that synergistic activation and multiplexing can be achieved using crRNA arrays but also show that crRNAs expressed towards the 5' of 6-crRNA arrays show evidence of enhanced activity. This not only represents a more flexible tool for transcriptional modulation but further expands our understanding of the design capabilities and limitations when considering longer crRNA arrays for multiplexed targeting.
Topics: Bacterial Proteins; CRISPR-Associated Proteins; CRISPR-Cas Systems; Endodeoxyribonucleases; Gene Editing; HEK293 Cells; Humans; Protein Splicing
PubMed: 34908140
DOI: 10.1093/nar/gkab1191