Metaproteomic Analysis of Gut Resistome in the Cecal Microbiota of Fattening Pigs Raised without Antibiotics

Improper use of antibiotics in swine could reduce commensal bacteria and possibly increase pathogen infections via the gut resistome. This study aimed to compare the metaproteomic profiles of the gut resistome and related metabolism in the cecal microbiota of fattening pigs raised under antibiotic-free (ABF) conditions with those of ordinary industrial pigs (controls [CTRL]). The top three relatively abundant microbes in both groups were Escherichia coli, Ruminococcus, and Lactobacillus, followed by Bacteroides and Bifidobacterium. E. coli, Lactobacillus, and Bacteroides were found to be increased in the CTRL group, whereas Ruminococcus and Clostridium were greater in the ABF group. The highest abundances of antibiotic resistance proteins (log2 expression levels [ELs] of >10) were found to be for tetracycline resistance (Tetr) and aminoglycoside resistance (AMGr) proteins found in Bacteroides, with a significant increase in the CTRL group. High Tetr (ELs of 5.32) was found in Ruminococcus in the CTRL group, although pigs in both groups had never received tetracycline, possibly reflecting the influence of environments in farms. In E. coli, AMGr and β-lactamase family proteins were observed in both groups (ELs of 3 to 6), whereas multidrug resistance protein MdtL was significantly expressed in the CTRL group (ELs of around 3). In the ABF group, CRISPR-associated endonucleases Cas1 and Cas9, which function to defend against viruses, were markedly observed in Ruminococcus and Lactobacillus, respectively, with ELs of 8.6 and 4.15, respectively. In conclusion, this study demonstrated that CRISPR-associated endonucleases were markedly observed in the ABF group, whereas higher levels of Tetr, AMGr, and multidrug resistance protein MdtL was markedly observed in dominant bacterial species in the CTRL group. IMPORTANCE In order to control and reduce antibiotic use in animals, the Department of Livestock Development, Thailand, has launched a campaign for antibiotic-free livestock production. The present study has shown for the first time that CRISPR-associated endonucleases Cas1 and Cas9, which function to defend against viruses, were markedly observed in Ruminococcus and Lactobacillus, respectively, in ceca of pigs raised without antibiotics (ABF). The highest abundances of antibiotic resistance proteins were for tetracycline (Tetr) and aminoglycoside resistance (AMGr) proteins found in Bacteroides, with a significant increase in the controls. In E. coli, the microbe with the highest relative abundance, AMGr and β-lactamase family proteins were observed in both groups, whereas multidrug resistance protein MdtL was significantly expressed in the controls. Pigs in both ABF and control groups had never received tetracycline, possibly reflecting the influence of farm environments. We suggest that pigs raised without antibiotics may have more beneficial microorganisms for the gut than pigs raised with antibiotics.

Efficacy of Triphala extracts on the changes of obese fecal microbiome and metabolome in the human gut model

Triphala is a mixture of tree fruits obtained from Terminalia chebula, Terminalia bellerica, and Phyllanthus emblica. It is one of the Ayurveda medicinal recipes used to treat health diseases such as obesity. The chemical composition analysis of Triphala extracts obtained from an equal portion of three fruits was performed. The contents of total phenolic compounds (62.87 ± 0.21 mg gallic acid equivalent/mL), total flavonoids (0.24 ± 0.01 mg catechin equivalent/mL), hydrolyzable tannins (177.27 ± 10.09 mg gallotannin equivalent/mL), and condensed tannins (0.62 ± 0.11 mg catechin equivalent/mL) were observed in Triphala extracts. The 1 mg/mL of Triphala extracts was applied to batch culture fermentation which contained the feces from voluntarily obese female adults (body mass index of 35.0-40.0 kg/m²) for 24 h. The extraction of DNA and metabolites was each conducted on the samples obtained from batch culture fermentation within and without Triphala extracts treatment. The 16S rRNA gene sequencing and untargeted metabolomic analysis were carried out. There was no statistically significant difference between Triphala extracts and control treatments on the changes in microbial profiles (p-value <0.05). While the metabolomic analysis showed statistically significant differences of 305 up-regulated and 23 down-regulated metabolites in the treatment of Triphala extracts when compared with the control (p-value <0.05 and fold-change ≥2) belonging to 60 pathways. The pathway analysis revealed that Triphala extracts play an important role in the activation of phenylalanine, tyrosine and tryptophan biosynthesis. In this study, phenylalanine and tyrosine were identified metabolites which involve in the regulation of energy metabolism. The treatment of Triphala extracts possesses the induction of phenylalanine, tyrosine and tryptophan biosynthesis in fecal batch culture fermentation of obese adults and therefore it can be suggested as a probable herbal medicinal recipe for obesity treatment.

Efficacy of cyclic lipopeptides obtained from Bacillus subtilis to inhibit the growth of Microsporum canis isolated from cats

Background and aim

Microsporum canis (M. canis) is a dermatophyte fungal pathogen that causes ringworms. Cats are considered to be a dominant reservoir host enabling M. canis transmission to humans. The concerns of dermatophyte resistance were raised among the usage of antifungal drugs to treat the ringworm. This study aimed to evaluate the fungal activity of cyclic lipopeptides (CLPs) obtained from Bacillus subtilis (B. subtilis) as an alternative method for the inhibition of M. canis growth.

Materials and methods

The culture plate of M. canis from confirmed cats with ringworm infection was provided. The purification of CLP extract, fengycin, iturin A, and surfactin was carried out from B. subtilis by preparative thin-layer chromatography (PTLC) coupled with solid-phase extraction (SPE) methods. Half-maximal effective concentration (EC₅₀) and agar well diffusion assays were performed to determine the efficacy of Bacillus CLP extract, fengycin, iturin A, and surfactin to inhibit the growth of M. canis isolated from cats.

Results

All purified Bacillus substances displayed antifungal activity to control the growth of M. canis when compared with 80% ethanol (control). EC₅₀ values for CLP extract, fengycin, iturin A, and surfactin were 0.23, 0.05, 0.17, and 0.08 mg/mL, respectively. In agar well diffusion assay, the ability of CLP extract, fengycin, iturin A, and surfactin on fungal inhibition had no statistically significant difference at 24 and 48 h after treatment (p < 0.05). However, CLP extract showed a statistically significant difference on M. canis inhibition at 62.21% followed by surfactin with 59.04% at 72 h after treatment.

Conclusion

In vitro, Bacillus CLPs revealed an inhibitory effect on M. canis growth which is a zoonotic pathogen that causes ringworms. This study suggests an alternative approach to control the growth of M. canis using substances obtained from B. subtilis as a biomedicine agent with antifungal activity.

Selection of potential probiotics with cholesterol-lowering properties for probiotic yoghurt production

From 61 lactic acid bacteria (LAB) isolates, three had good cholesterol-lowering properties, with Limosilactobacillus fermentum KUB-D18 having the highest cholesterol assimilation (68.75%) (51 µg/10⁹ CFU). In addition, Lactiplantibacillus pentosus HM04-25 and L. pentosus HM04-3 had the two highest levels of bile salt hydrolase (BSH) activity (22.60 and 21.45 U/mL, respectively). These three strains could resist four antibiotics (aztreonam, vancomycin, teicoplanin, and nalidixic). However, fortunately, they contained no mobile antibiotic resistance genes. To evaluate the influence of probiotic strains in yoghurt production, L. fermentum KUB-D18, L. pentosus HM04-25, or L. pentosus HM04-3 were simultaneously cultured with commercial yoghurt starter (YF-L812) and incubated at 43 °C for 6 h. During yoghurt fermentation, the total bacteria in the yoghurt tended to increase from 7.39 to 8.90 log CFU/mL. The growth rates of two probiotic strains (L. pentosus HM04-25 and L. pentosus HM04-3) were stable at 6.06 to 6.62 log CFU/mL. Only the rate for L. fermentum KUB-D18 increased (to 7.5 log CFU/mL). These three probiotics did not affect the physical characteristics of yoghurt. The total soluble solids, pH, and titratable acidity values of the probiotic yoghurts were similar to the control yoghurt at 30°Brix, 4.91, and 0.90%, respectively. The firmness values of the probiotic yoghurts and the control were not significantly different (p > 0.05). Differentiation of the appearance of color, odor, flavor, and texture between the control yoghurt and the probiotic yoghurts was investigated using 56 volunteers and no significant differences were identified. Additionally, sensory evolution revealed that the acceptability of the probiotic yoghurts was higher than for the control (p ≤ 0.05). Therefore, the three probiotic strains with cholesterol-lowering properties had potential in future yoghurt production.

Insights into stress responses in mandarins triggered by Bacillus subtilis cyclic lipopeptides and exogenous plant hormones upon Penicillium digitatum infection

Bacillus subtilis CLP extract activates defense gene expression and increases the unique protein production involving in pathways of ISR, SAR, ubiquitin-proteasome system, and glycolysis for stress responses in flavedo tissues. Cyclic lipopeptides (CLPs) of Bacillus subtilis ABS-S14 had ability to activate plant defensive pathways, increase resistance and control green mold rot caused by Penicillium digitatum in mandarin fruit. The current study investigated transcriptional and proteomic data to highlight the unique induction effect of CLPs produced by B. subtilis ABS-S14 on the defense mechanism of mandarins in response to P. digitatum attack, and their differences from those following the exogenous plant hormone application. The proteomic patterns of the flavedo tissues as affected by Bacillus CLP extract, salicylic acid (SA), methyl jasmonate (MeJA), and ethephon (Et) were explored. qPCR analysis revealed the great effects of CLP extract in enhancing the transcription of PAL, ACS1, GLU, POD, and PR1. Tryptic peptides by LC-MS analysis between treatments with and without fungal infection were compared. B. subtilis CLP extract empowered the plant's immune response to wound stress by the significant production of calmodulin-binding receptor-like cytoplasmic kinase 2, molybdenum cofactor sulfurase, and NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase. Ubiquitin carrier protein abundance was developed only in the treated flavedo with CLP extract coupled with P. digitatum infection. The gene expression and overall proteome findings involving pathways of ubiquitin proteasome system, ISR, SAR, and energy production provide a new insight into the molecular mechanisms of the antagonist B. subtilis ABS-S14 inducing resistance against green mold in mandarins.