RESUMEN
Genome sequencing of Clostridium clostridioforme strain LM41 revealed the presence of an atypically high proportion of mobile genetic elements for this species, with a particularly high abundance of prophages. Bioinformatic analysis of prophage sequences sought to characterize these elements and identify prophage-linked genes contributing to enhanced fitness of the host bacteria in the dysbiotic gut. Using PHASTER, PhageScope and manual curation, this work has identified 15 prophages: 4 predicted to be intact, 2 predicted to be defective and 9 which are unclassified. Quantitative PCR (qPCR) analysis revealed spontaneous release of four of the LM41 prophages (φ1, φ2, φ4 and φ10) into the culture supernatant, with virion-like particles visualized using transmission electron microscopy. The majority (12/14) of these particles had morphology akin to podoviruses, which is consistent with morphology predictions for φ1 and φ4. We observed diversity in the lysogeny mechanisms utilized by the prophages, with examples of the classical λ-like CI/Cro system, the ICEBs1 ImmR/ImmA-like system and the Mu-like C/Ner system. Classical morons, such as toxins or immune evasion factors, were not observed. We did, however, identify a variety of genes with roles in mediating restriction modification and genetic diversity, as well as some candidate genes with potential roles in host adaptation. Despite being the most abundant entities in the intestine, there is a dearth of information about phages associated with members of the microbiome. This work begins to shed light on the contribution of these elements to the lifestyle of C. clostridioforme LM41.
Asunto(s)
Clostridium , Microbioma Gastrointestinal , Profagos , Profagos/genética , Clostridium/virología , Clostridium/genética , Lisogenia , Genoma Bacteriano , Genoma Viral , Genómica , Biología ComputacionalRESUMEN
The genus Clostridium consists of a diverse group of pathogenic and non-pathogenic bacteria. The non-pathogenic clostridia contain several solventogenic members of industrial importance, such as Clostridium acetobutylicum or C. beijerinckii. In the process of acetone-butanol-ethanol (ABE) fermentation, these strains are used in large scale fermentation plants since almost 100 years. Soon after establishment of the first plants, the fermentation processes suffered from different bacteriophage infections worldwide. A limited set of studies addressing bacteriophages in solventogenic clostridia have been conducted since then. In this study, we present the genome sequence of the temperate bacteriophage TBP2 of the solventogenic strain C. saccharoperbutylacetonicum N1-4 (HMT) that is used for ABE fermentation. The phage genome consists of 38 039 bp and includes 48 open reading frames. Sequence analysis indicates that the genome encloses random parts of the bacterial genome in addition to its own DNA. It represents the first fully sequenced genome of a temperate bacteriophage infecting solventogenic clostridia.
Asunto(s)
Bacteriófagos/genética , Bacteriófagos/aislamiento & purificación , Clostridium/virología , Genoma Viral , Acetona/metabolismo , Bacteriófagos/clasificación , Butanoles/metabolismo , Clostridium/metabolismo , Etanol/metabolismo , Fermentación , Microbiología Industrial , Sistemas de Lectura Abierta , Proteínas Virales/genéticaRESUMEN
During the history of the solventogenic clostridia fermentation industry, bacteriophages have been a recurrent problem. This study reports that HM2, a lytic bacteriophage for solventogenic Clostridium saccharoperbutylacetonicum N1-4 (N1-4), has a genome size of 17 470 bp with 22 open reading frames, including replication, lysis, integration and structural modules. To understand HM2 infection and resistance in N1-4, bacteriophage insensitive mutants (BIMs) were isolated and characterized. These eight independent BIMs included four adsorption mediated and four non-adsorption types. Adsorption mediated BIMs had increased exopolysaccharide (EPS) production and decreased attachment of HM2 to the cell surface. Non-adsorption mediated BIMs had a moderate increase in EPS production, which did not affect HM2 attachment. Absorption mediated BIMs had reduced fermentation performance, whereas the non-absorption mediated BIMs were indistinguishable from N1-4. Consequently, non-adsorption mediated BIMs would be more useful in a fermentation since they couple good fermentation performance with phage resistance.
Asunto(s)
Bacteriófagos/fisiología , Clostridium/metabolismo , Clostridium/virología , Polisacáridos/biosíntesis , Bacteriófagos/genética , Clostridium/genética , Fermentación , Tamaño del GenomaRESUMEN
This study was conducted to investigate the effects of bacteriophages in different environments on growth performance, digestibility, ileal and caecal microbiota, gut morphology and immunity of weanling pigs. Two hundred piglets were randomly assigned to four treatment groups with five replicate pens with 10 pigs per pen. A 2 × 2 factorial arrangement of treatments was used to investigate the response of weanling pigs to supplemental bacteriophages (0 and 1.0 g/kg of diet) in contaminated or hygienic environments. Bacteriophages supplementation did not affect average daily gain (ADG), average daily feed intake (ADFI) and gain:feed in phases I and III; however, there was a significant improvement in ADG and gain:feed in phase II. The supplementation of bacteriophages increased the overall gain:feed of pigs. The overall result showed a greater ADG and ADFI in hygienic room. There were reductions in population of both ileal (p < 0.05) and caecal (p < 0.01) Clostridium spp. and ileal coliforms (p < 0.01) with the inclusion of bacteriophages in the diet. Bacteriophages increased ileal Lactobacillus and caecal Bifidobacterium and tended to increase ileal Bifidobacterium (p = 0.08). Contaminated environment decreased ileal Lactobacillus and caecal Bifidobacterium and tended to increase ileal Clostridium (p = 0.08) and coliforms (p = 0.08). Total anaerobic bacteria was tended to decrease (p = 0.06) in contaminated environment. Jejunal villus height increased in pigs received bacteriophages, but they did not affect other morphological items. The interaction between bacteriophages and environment tended to be significant (p = 0.06) for ileal villus height and ileal villus height to crypt depth ratio. The overall faecal score was significantly greater in hygienic environment and bacteriophages groups. The present findings indicate that there is an interactive effect on feed efficiency between bacteriophages and contaminated environment. In addition, bacteriophages improve jejunum morphology, and intestinal microbiota of pigs.
Asunto(s)
Bacteriófagos , Clostridium/virología , Enterobacteriaceae/virología , Porcinos/crecimiento & desarrollo , Alimentación Animal , Crianza de Animales Domésticos , Animales , Derrame de Bacterias , Dieta , Heces/microbiología , Femenino , Vivienda para Animales , Higiene , MasculinoRESUMEN
Clostridium pasteurianum is emerging as a prospective host for the production of biofuels and chemicals, and has recently been shown to directly consume electric current. Despite this growing biotechnological appeal, the organism's genetics and central metabolism remain poorly understood. Here we present a concurrent genome sequence for the C. pasteurianum type strain and provide extensive genomic analysis of the organism's defence mechanisms and central fermentative metabolism. Next generation genome sequencing produced reads corresponding to spontaneous excision of a novel phage, designated φ6013, which could be induced using mitomycin C and detected using PCR and transmission electron microscopy. Methylome analysis of sequencing reads provided a near-complete glimpse into the organism's restriction-modification systems. We also unveiled the chief C. pasteurianum Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) locus, which was found to exemplify a Type I-B system. Finally, we show that C. pasteurianum possesses a highly complex fermentative metabolism whereby the metabolic pathways enlisted by the cell is governed by the degree of reductance of the substrate. Four distinct fermentation profiles, ranging from exclusively acidogenic to predominantly alcohologenic, were observed through redox consideration of the substrate. A detailed discussion of the organism's central metabolism within the context of metabolic engineering is provided.
Asunto(s)
Clostridium/metabolismo , Clostridium/virología , Redes y Vías Metabólicas/genética , Análisis de Secuencia de ADN , Activación Viral , Secuenciación Completa del Genoma , Clostridium/efectos de los fármacos , Clostridium/genética , Repeticiones Palindrómicas Cortas Agrupadas y Regularmente Espaciadas , Enzimas de Restricción-Modificación del ADN , Fermentación , Secuenciación de Nucleótidos de Alto Rendimiento , Microbiología Industrial , Microscopía Electrónica de Transmisión , Mitomicina/metabolismo , Reacción en Cadena de la Polimerasa , Profagos/genética , Profagos/fisiología , Virión/ultraestructuraRESUMEN
Lytic bacteriophage ATCC 8074-B1 produces large plaques on its host Clostridium sporogenes. Sequencing of the 47,595-bp genome allowed the identification of 82 putative open reading frames, including those encoding proteins for head and tail morphogenesis and lysis. However, sequences commonly associated with lysogeny were absent. ORF 22 encodes an endolysin, CS74L, that shows homology to N-acetylmuramoyl-L-alanine amidases, and when expressed in Escherichia coli, the protein causes effective lysis of C. sporogenes cells when added externally. CS74L was also active on Clostridium tyrobutyricum and Clostridium acetobutylicum. The catalytic domain expressed alone (CS74L(1-177)) exhibited a similar activity and the same host range as the full-length endolysin. A chimeric endolysin consisting of the CS74L catalytic domain fused to the C-terminal domain of endolysin CD27L, derived from Clostridium difficile bacteriophage ΦCD27, was produced. This chimera (CSCD) lysed C. sporogenes cells with an activity equivalent to that of the catalytic domain alone. In contrast, the CD27L C-terminal domain reduced the efficacy of the CS74L catalytic domain when tested against C. tyrobutyricum. The addition of the CD27L C-terminal domain did not enable the lysin to target C. difficile or other CD27L-sensitive bacteria.
Asunto(s)
Bacteriófagos/enzimología , Bacteriófagos/genética , Clostridium/virología , ADN Viral/química , Endopeptidasas/metabolismo , Genoma Viral , Análisis de Secuencia de ADN , ADN Viral/genética , Endopeptidasas/genética , Genes Virales , Datos de Secuencia Molecular , Proteínas Mutantes/genética , Proteínas Mutantes/metabolismo , Sistemas de Lectura Abierta , Esporas Bacterianas/virologíaRESUMEN
Descreve-se a aplicabilidade de uma técnica de imunofluorescência direta, para o diagnóstico de mionecroses causadas por clostrídios, a partir de tecidos fixados em formol e incluídos em parafina. Essa técnica pode auxiliar no diagnóstico do carbúnculo sintomático e da gangrena gasosa, contribuindo para determinar a real prevalência dessas doenças no país
Asunto(s)
Ántrax/diagnóstico , Ántrax/veterinaria , Clostridium/virología , Gangrena Gaseosa/diagnóstico , Gangrena Gaseosa/veterinaria , Infecciones por Clostridium/veterinaria , Porcinos/microbiología , Técnica del Anticuerpo Fluorescente Directa/métodos , Técnica del Anticuerpo Fluorescente Directa/veterinariaRESUMEN
An examination of the replication origin and stability determinant associated with the CAK1 filamentous viruslike particle recovered from Clostridium beijerinckii NCIMB 6444 was carried out. Seven deletion derivatives, pCKE, pCEP1, pDT5, pCKP, pDTH102, pYL102E and pYL102, were constructed and transformed into C. beijerinckii NCIMB 8052. The successful transformation of pCKE, pDT5, pCKP, pDTH102, pYL102E and pYL102 into C. beijerinckii 8052, together with the corresponding recovery of single-stranded DNA from Escherichia coli indicated that the double- and single-stranded replication origins are located on a 0.4-kb CAK1 DNA fragment. Sequence analysis of the putative 0.4-kb replication origin region of CAK1 reveals a nick site containing 22 base pairs that has homology with plasmids pC194 and pUB110 and suggests the presence of a 2.0-kb DNA region involved in stability. The putative Rep protein of CAK1 contains three conserved motifs and three essential residues of the catalytic site in agreement with Rep proteins associated with the pC194 family. The utility of the developed CAK1-derived phagemid designated pYL102E was evaluated by using it to examine heterologous expression of: (1) the manA gene derived from Thermoanaerobacterium polysaccharolyticum in E. coli and C. beijerinckii NCIMB 8052 and (2) the sol operon derived from Clostridium acetobutylicum DSM 792 in C. beijerinckii SA-2.
Asunto(s)
Clostridium/virología , Vectores Genéticos , Virión/genética , Secuencia de Aminoácidos , Clostridium/genética , Replicación del ADN , ADN Viral/química , Escherichia coli/genética , Datos de Secuencia MolecularRESUMEN
The reported incidence and effects of bacteriophage infections occurring in the industrial acetone butanol (AB) fermentation processes operated in the USA, Japan, and Puerto Rico during the earlier part of the twentieth century is reviewed. The growth characteristics and solvent-producing ability of a lysogenic strain of Clostridium madisonii isolated from a phage infection in Puerto Rico was determined in molasses fermentation medium. The host strain harbours a large lysogenic phage belonging to the Siphoviridae and the growth rate of the lysogenic strain was found to be slower than the non-lysogenic parent strain and exhibited reduced solvent production. The history of phage infections that occurred in the South African AB process is documented along with the various remedial actions that were taken to restore production. A more detailed account of the last phage infection that occurred in 1980 involving a small pseudo-lysogenic phage belonging to the Podoviridae is given. This phage infected Clostridium beijerinckii P260 and a number of closely related industrial strains. Factory-scale fermentations contaminated by this phage were compared with equivalent laboratory-scale control fermentations. The effect of the phage infection in the full-scale and laboratory-scale fermentations were monitored. Results obtained in laboratory-based studies included an assessment of the effect of the multiplicity of infection and the timing of phage infection. The general effects and symptoms of phage infections in the industrial AB fermentation are reviewed including gross changes in the fermentation and changes in cell morphology. Common techniques used for the diagnosis of phage infections and approaches for controlling phage contamination in the AB fermentation are discussed. Prevention strategies included good factory hygiene, sterilisation, decontamination and disinfection, and the use of resistant strains immunised against specific phages.
Asunto(s)
Acetona/metabolismo , Bacteriófagos/patogenicidad , Butanoles/metabolismo , Clostridium/virología , Fermentación , Clostridium/metabolismo , Melaza , SudáfricaRESUMEN
Cellulosomes prepared by the cellulose affinity digestion method from Clostridium thermocellum culture supernatant hydrolysed carob galactomannan during incubation at 60 degrees C and pH 6.5. A recombinant phage expressing mannanase activity was isolated from a library of C. thermocellum genomic DNA constructed in lambdaZAPII. The cloned fragment of DNA containing a putative mannanase gene (manA) was sequenced, revealing an ORF of 1767 nt, encoding a protein (mannanase A; Man26A) of 589 aa with a molecular mass of 66816 Da. The putative catalytic domain (CD) of Man26A, identified by gene sectioning and sequence comparisons, displayed up to 32% identity with other mannanases belonging to family 26. Immediately downstream of the CD and separated from it by a short proline/threonine linker was a duplicated 24-residue dockerin motif, which is conserved in all C. thermocellum cellulosomal enzymes described thus far and mediates their attachment to the cellulosome-integrating protein (CipA). Man26A consisting of the CD alone (Man26A") was hyperexpressed in Escherichia coli BL21(DE3) and purified. The truncated enzyme hydrolysed soluble and insoluble mannan, displaying a temperature optimum of 65 degrees C and a pH optimum of 6.5, but exhibited no activity against other plant cell wall polysaccharides. Antiserum raised against Man26A" cross-reacted with a polypeptide with a molecular mass of 70000 Da that is part of the C. thermocellum cellulosome. A second variant of Man26A containing the N-terminal segment of 130 residues and the CD (Man26A") bound to ivory-nut mannan and weakly to soluble Carob galactomannan and insoluble cellulose. Man26A" consisting of the CD alone did not bind to these polysaccharides. These results indicate that the N-terminal 130 residues of mature Man26A may constitute a weak mannan-binding domain. Sequence comparisons revealed a lack of identity between this region of Man26A and other polysaccharide-binding domains, but significant identity with a region conserved in the three family 26 mannanases from the anaerobic fungus Piromyces equi.