Ruminococcin C, a promising antibiotic produced by a human gut symbiont

A major public health challenge today is the resurgence of microbial infections caused by multidrug-resistant strains. Consequently, novel antimicrobial molecules are actively sought for development. In this context, the human gut microbiome is an under-explored potential trove of valuable natural molecules, such as the ribosomally-synthesized and post-translationally modified peptides (RiPPs). The biological activity of the sactipeptide subclass of RiPPs remains under-characterized. Here, we characterize an antimicrobial sactipeptide, Ruminococcin C1, purified from the caecal contents of rats mono-associated with Ruminococcus gnavus E1, a human symbiont. Its heterologous expression and post-translational maturation involving a specific sactisynthase establish a thioether network, which creates a double-hairpin folding. This original structure confers activity against pathogenic Clostridia and multidrug-resistant strains but no toxicity towards eukaryotic cells. Therefore, the Ruminococcin C1 should be considered as a valuable candidate for drug development and its producer strain R. gnavus E1 as a relevant probiotic for gut health enhancement.

Effects of Diets Supplemented with Ensiled Mulberry Leaves and Sun-Dried Mulberry Fruit Pomace on the Ruminal Bacterial and Archaeal Community Composition of Finishing Steers

This study investigated the effects of ensiled mulberry leaves (EML) and sun-dried mulberry fruit pomace (SMFP) on the ruminal bacterial and archaeal community composition of finishing steers. Corn grain- and cotton meal-based concentrate was partially replaced with EML or SMFP. The diets had similar crude protein (CP), neutral detergent fiber (NDF), and metabolizable energy. Following the feeding trial, the steers were slaughtered and ruminal liquid samples were collected to study the ruminal microbiome. Extraction of DNA, amplification of the V4 region of the 16S rRNA gene, and Illumina MiSeq pyrosequencing were performed for each sample. Following sequence de-noising, chimera checking, and quality trimming, an average of 209,610 sequences were generated per sample. Quantitative real-time PCR was performed to examine the selected bacterial species in the rumen. Our results showed that the predominant phyla were Bacteroidetes (43.90%), Firmicutes (39.06%), Proteobacteria (4.31%), and Tenericutes (2.04%), and the predominant genera included Prevotella (13.82%), Ruminococcus (2.51%), Butyrivibrio (2.38%), and Succiniclasticum (2.26%). Compared to the control group, EML and SMFP groups had a higher abundance of total bacteria (p < 0.001); however, the bacterial community composition was similar among the three groups. At the phylum level, there were no significant differences in Firmicutes (p = 0.7932), Bacteroidetes (p = 0.2330), Tenericutes (p = 0.2811), or Proteobacteria (p = 0.0680) levels among the three groups; however, Fibrobacteres decreased in EML (p = 0.0431). At the genus level, there were no differences in Prevotella (p = 0.4280), Ruminococcus (p = 0.2639), Butyrivibrio (p = 0.4433), or Succiniclasticum (p = 0.0431) levels among the groups. Additionally, the dietary treatments had no significant effects on the archaeal community composition in the rumen. Therefore, EML and SMFP supplementation had no significant effects on the ruminal bacterial or archaeal community composition of finishing steers.

Effects of extracts of Humulus lupulus (hops) and Yucca schidigera applied alone or in combination with monensin on rumen fermentation and microbial populations in vitro

BACKGROUND

β-Acids in hops (Humulus lupulus) and saponins in yucca (Yucca schidigera) have been found to possess antimicrobial properties similar to that of monensin and could be an alternative to in-feed antibiotics. The effects of monensin (MON) and ethanol extracts of hops (HE) and Y. schidigera (YE) alone and in combination with MON were assessed on ruminal microbial composition and fermentation in vitro of a barley-based diet.

RESULTS

All treatments decreased (P < 0.05) CH4 production (per unit of dry matter), microbial protein (mg), and NH3 -N accumulation. All treatments reduced (P < 0.01) the acetate:propionate (A:P) ratio and molar proportions of butyrate, but increased (P < 0.01) those of propionate, whereas those of acetate decreased (P < 0.001) with addition of MON (10 µg mL(-1)) and combined with HE or YE. Methane produced per unit of true digested dry matter decreased (P < 0.001) with all treatments except YE. Monensin reduced (P < 0.001) proportions of 16S rRNA copies of Ruminococcus flavefaciens, but increased (P < 0.01) those of Selenomonas ruminantium. Hops extract alone or combined with MON reduced (P < 0.01) proportions of R. flavefaciens but combined with MON tended (P < 0.1) to increase those of S. ruminantium. Yucca extract combined with MON increased (P < 0.01) the proportions of R. flavefaciens and S. ruminantium. All treatments except MON (2.5 µg mL(-1)) reduced (P < 0.01) the relative abundance of methanogens.

CONCLUSION

Hops extract and YE altered rumen microbes and fermentation in a manner similar to MON with many responses being additive when applied in combination.

vanD and vanG-like gene clusters in a Ruminococcus species isolated from human bowel flora

A vancomycin-resistant, anaerobic, gram-positive coccus containing the vanD and vanG-like genes (strain CCRI-16110) was isolated from a human fecal specimen during a hospital surveillance program to detect carriers of vancomycin-resistant enterococci. Comparison of the 16S rRNA gene sequence of strain CCRI-16110 with databases revealed a potentially novel Ruminococcus species that was most similar (<94% identity) to Clostridium and Ruminococcus species. Strain CCRI-16110 was highly resistant to vancomycin and teicoplanin (MICs of >256 microg/ml). The complete DNA sequence of the vanD cluster was most similar (98.2% identity) to that of Enterococcus faecium BM4339, containing the vanD1 allele. An intD gene with 99% identity with that of this E. faecium strain was found to be associated with the vanD gene cluster of this novel anaerobic bacterium. Strain CCRI-16110 also harbors genes encoding putative VanS(G), VanG, and VanT(G) proteins displaying 56, 73.6, and 55% amino acid sequence identity, respectively, compared to the corresponding proteins encoded by the vanG1 and vanG2 operons of Enterococcus faecalis BM4518 and N03-0233. This study reports for the first time an anaerobic bacterium containing the vanD gene cluster. This strain also harbors a partial vanG-like gene cluster. The presence of vanD- and vanG-containing anaerobic bacteria in the human bowel flora suggests that these bacteria may serve as a reservoir for the vanD and vanG vancomycin resistance genes.

[Liver abscess and infective endocarditis cases caused by Ruminococcus productus]

The genus Ruminococcus which are anaerobe Gram positive cocci, previously classified as Peptostreptococcus, may colonize the upper respiratory tract, gastrointestinal tract, vagina and skin of humans and animals. In this report a case of liver abscess and a case of infective endocarditis caused by Ruminoccocus productus, which is very rarely encountered in the clinical practice were presented. The first case was a 32 years old male who was admitted to the hospital in 2002, with the complaints of fever lasting for 20 days and pain while breathing. The abdominal ultrasonography revealed the presence of a liver abscess, and the drainage material from the abscess yielded Ruminococcus productus, identified in BACTEC 9200 (Becton Dickinson, Sparks, Md) anaerobe system. As the isolate was found to be sensitive to penicilin, the empirical gentamicin and ampicillin/sulbactam therapy was continued. The second case was a 25 years old male who was admitted to the hospital in 2005, with the signs of fever lasting for 3-4 months, chills, bone and joint pains. As multiple vegetations were detected in echocardiography, blood cultures were collected and empirical therapy with ceftriaxone and gentamicin was initiated with the preliminary diagnosis of infective endocarditis. Bacteria which were isolated from blood cultures by BACTEC 9200 system have been identified as R. productus. As this strain was also sensitive to penicillin, the empirical therapy was changed to penicilin and gentamicin. These two cases indicated that R. productus should be considered in complicated infections even if it is a rarely isolated species from the clinical samples.

Effects of difructose anhydride III (DFA III) administration on bile acids and growth of DFA III-assimilating bacterium Ruminococcus productus on rat intestine

The growth of DFA III-assimilating bacteria in the intestines of rats fed 3% DFA III for 2 weeks was examined. Sixty-four percent of the DFA III intake had been assimilated on day 3 of ingestion, and almost all of the DFA III was assimilated at the end of the experiment. The DFA III-assimilating bacterium, Ruminococcus productus, in DFA III-fed rats was in the stationary state of 10(8)-10(9) cells/g dry feces within a week from 10(6) cells/g dry feces on day 1 of DFA III ingestion. The number of R. productus cells was associated with the amount of DFA III excreted in the feces. The acetic acid produced from DFA III by R. productus lowered the cecal pH to 5.8. In control-fed rats and DFA III-fed rats, 94% of secondary bile acids and 94% of primary bile acids, respectively, were accounted for in the total bile acids analyzed. DFA III ingestion increased the ratio of primary bile acids and changed the composition of fecal bile acids. In conclusion, R. productus assimilated DFA III, produced short chain fatty acids, and the cecal pH was lowered. The acidification of rat intestine perhaps inhibited secondary bile acid formation and decreased the ratio of secondary bile acids. Therefore, it is expected that DFA III may prevent colorectal cancer and be a new prebiotic candidate.

Effects of difructose anhydride III (DFA III) administration on rat intestinal microbiota

The effects of difructose anhydride III (di-D-fructofuranose-1,2':2,3'-dianhydride; DFA III) administration (3% DFA III for 4 weeks) on rat intestinal microbiota were examined using denaturing gradient gel electrophoresis (DGGE). According to DGGE profiles, the number of bacteria related to Bacteroides acidofaciens and uncultured bacteria within the Clostridium lituseburense group decreased, while that of bacteria related to Bacteroides vulgatus, Bacteroides uniformis and Ruminococcus productus increased in DFA III-fed rat cecum. In the cecal contents of DFA III-fed rats, a lowering of pH and an increase in short chain fatty acids (SCFAs), especially acetic acid, were observed. The DFA III-assimilating bacterium, Ruminococcus sp. M-1, was isolated from the cecal contents of DFA III-fed rats. The strain had 98% similarity with R. productus ATCC 27340T (L76595), and mainly produced acetic acid. These results confirmed that the bacteria harmful to host health were not increased by DFA III administration. Moreover, DFA III stimulated the growth of Ruminococcus sp. M-1 producing acetic acid, which may alter the intestinal microbiota towards a healthier composition. It is expected that DFA III would be a new candidate as a prebiotic.

Use of community genome arrays (CGAs) to assess the effects of Acacia angustissima on rumen ecology

This research developed a community genome array (CGA) to assess the effects of Acacia angustissima on rumen microbiology. A. angustissima produces non-protein amino acids as well as tannins, which may be toxic to animals, and CGA was used to assess the effects of this plant on the ecology of the rumen. CGAs were developed using a 7·5 cm×2·5 cm nylon membrane format that included up to 96 bacterial genomes. It was possible to separately hybridize large numbers of membranes at once using this mini-membrane format. Pair-wise cross-hybridization experiments were conducted to determine the degree of cross-hybridization between strains; cross-hybridization occurred between strains of the same species, but little cross-reactivity was observed among different species. CGAs were successfully used to survey the microbial communities of animals consuming an A. angustissima containing diet but quantification was not precise. To properly quantify and validate the CGA, Fibrobacter and Ruminococcus populations were independently assessed using 16S rDNA probes to extracted rRNA. The CGA detected an increase in these populations as acacia increased in the diet, which was confirmed by rRNA analysis. There was a great deal of variation among strains of the same species in how they responded to A. angustissima. However, in general Selenomonas strains tended to be resistant to the tannins in the acacia while Butyrivibrio fibrisolvens was sensitive. On the other hand some species, like streptococci, varied. Streptococcus bovis-like strains were sensitive to an increase in acacia in the diet while Streptococcus gallolyticus-like strains were resistant. Strep. gallolyticus has independently been shown to be resistant to tannins. It is concluded that there is significant variation in tannin resistance between strains of the same species. This implies that there are specific molecular mechanisms at play that are independent of the phylogenetic position of the organism.

Variation in antimicrobial action of proanthocyanidins from Dorycnium rectum against rumen bacteria

The proanthocyanidin polymer fractions of the leaves of the forage legume Dorycnium rectum were analysed by acid catalysis with benzyl mercaptan, NMR and ES-MS. The results showed that D. rectum differs from other temperate proanthocyanidin-containing forage legumes in that the range of polymers extends up to very high degrees of polymerisation. Three fractions were characterised as low, medium, and high molecular weight proanthocyanidin fractions with mean degree of polymerisations of 10.3, 41 and 127, respectively. Epigallocatechin was the most abundant extension unit and the terminating flavan-3-ols comprised largely catechin and gallocatechin units in equal proportions. Formation of thiolyated dimer products showed the interflavan-linkages of the lower molecular weight proanthocyanidins to be predominantly C4-->C8 with a small amount of C4-->C6. ES-MS spectra distinguished lower from higher polymeric proanthocyanidins from M2- to M8(2)-. The antibacterial activity of proanthocyanidin fractions against pure cultures of microbes selected from the ruminal population to represent fibre degrading, proteolytic and hyper ammonia producing bacteria in broth culture was evaluated. The activity of proanthocyanidin fractions against Clostridium aminophilum, Butyrivibrio fibrisolvens and Clostridium proteoclasticum was significantly dependent on their structure but not so against Ruminococcus albus and Peptostreptococcus anaerobius. The latter observation was unique in that they were sensitive to all proanthocyanidin fractions evaluated, even at the lowest concentration (100 microg/ml). The results suggest the effects of the extractable proanthocyanidins on rumen microbes should be considered when evaluating an alternative proanthocyanidin-containing forage source for ruminants, such as D. rectum.

Albusin B, a bacteriocin from the ruminal bacterium Ruminococcus albus 7 that inhibits growth of Ruminococcus flavefaciens

An approximately 32-kDa protein (albusin B) that inhibited growth of Ruminococcus flavefaciens FD-1 was isolated from culture supernatants of Ruminococcus albus 7. Traditional cloning and gene-walking PCR techniques revealed an open reading frame (albB) encoding a protein with a predicted molecular mass of 32,168 Da. A BLAST search revealed two homologs of AlbB from the unfinished genome of R. albus 8 and moderate similarity to LlpA, a recently described 30-kDa bacteriocin from Pseudomonas sp. strain BW11M1.