Development and use of a multiplex real-time quantitative polymerase chain reaction assay for detection and differentiation of Porcine circovirus-2 genotypes 2a and 2b in an epidemiological survey.

By the end of 2004, the Canadian swine population had experienced a severe 2 increase in the incidence of Porcine circovirus-associated disease (PCVAD), a problem that was 3 associated with the emergence of a new Porcine circovirus-2 genotype (PCV-2b), previously 4 unrecovered in North America. Thus it became important to develop a diagnostic tool that could 5 differentiate between the old and new circulating genotypes (PCV-2a and -2b, respectively). 6 Consequently, a multiplex real-time quantitative polymerase chain reaction (mrtqPCR) assay that 7 could sensitively and specifically identify and differentiate PCV-2 genotypes was developed. A 8 retrospective epidemiological survey that used the mrtqPCR assay was performed to determine if 9 cofactors could affect the risk of PCVAD. From 121 PCV-2–positive cases gathered for this 10 study, 4.13%, 92.56% and 3.31% were positive for PCV-2a, PCV-2b, and both genotypes, 11 respectively. In a data analysis using univariate logistic regressions, PCVAD compatible 12 (PCVAD/c) score was significantly associated with the presence of Porcine reproductive and 13 respiratory syndrome virus (PRRSV), PRRSV viral load, PCV-2 viral load, and PCV-2 14 immunohistochemistry (IHC) results. Polytomous logistic regression analysis revealed that 15 PCVAD/c score was affected by PCV-2 viral load (P = 0.0161) and IHC (P = 0.0128), but not by 16 the PRRSV variables (P > 0.9); suggesting that mrtqPCR in tissue is a reliable alternative to IHC. 17 Logistic regression analyses revealed that PCV-2 increased the odds ratio of isolating 2 major 18 swine pathogens of the respiratory tract, Actinobacillus pleuropneumoniae and Streptococcus 19 suis serotypes 1/2, 1, 2, 3, 4, and 7, which are serotypes commonly associated with clinical 20 diseases.

Chicken Caecal Microbiome Modifications Induced by Campylobacter jejuni Colonization and by a Non-Antibiotic Feed Additive

Campylobacter jejuni is an important zoonotic foodborne pathogen causing acute gastroenteritis in humans. Chickens are often colonized at very high numbers by C. jejuni, up to 109 CFU per gram of caecal content, with no detrimental effects on their health. Farm control strategies are being developed to lower the C. jejuni contamination of chicken food products in an effort to reduce human campylobacteriosis incidence. It is believed that intestinal microbiome composition may affect gut colonization by such undesirable bacteria but, although the chicken microbiome is being increasingly characterized, information is lacking on the factors affecting its modulation, especially by foodborne pathogens. This study monitored the effects of C. jejuni chicken caecal colonization on the chicken microbiome in healthy chickens. It also evaluated the capacity of a feed additive to affect caecal bacterial populations and to lower C. jejuni colonization. From day-0, chickens received or not a microencapsulated feed additive and were inoculated or not with C. jejuni at 14 days of age. Fresh caecal content was harvested at 35 days of age. The caecal microbiome was characterized by real time quantitative PCR and Ion Torrent sequencing. We observed that the feed additive lowered C. jejuni caecal count by 0.7 log (p<0.05). Alpha-diversity of the caecal microbiome was not affected by C. jejuni colonization or by the feed additive. C. jejuni colonization modified the caecal beta-diversity while the feed additive did not. We observed that C. jejuni colonization was associated with an increase of Bifidobacterium and affected Clostridia and Mollicutes relative abundances. The feed additive was associated with a lower Streptococcus relative abundance. The caecal microbiome remained relatively unchanged despite high C. jejuni colonization. The feed additive was efficient in lowering C. jejuni colonization while not disturbing the caecal microbiome.

La tagatose-1,6-bisphosphate aldolase et la fructose-1,6-bisphosphate aldolase de classe I : mécanisme et stéréospécificité

La tagatose-1,6-biphosphate aldolase de Streptococcus pyogenes est une aldolase qui fait preuve d'un remarquable manque de spécificité vis à vis de ses substrats. En effet, elle catalyse le clivage réversible du tagatose-1,6-bisphosphate (TBP), mais également du fructose-1,6-bisphosphate (FBP), du sorbose-1,6-bisphosphate et du psicose-1,6-bisphosphate, quatre stéréoisomères, en dihydroxyacétone phosphate (DHAP) et en glycéraldéhyde-3-phosphate (G3P). Aldolase de classe I, qui donc catalyse sa réaction en formant un intermédiaire covalent obligatoire, ou base de Schiff, avec son susbtrat, la TBP aldolase de S. pyogenes partage 14 % d’identité avec l’enzyme modèle de cette famille, la FBP aldolase de muscle de mammifère. Bien que le mécanime catalytique de la FBP aldolase des mammifères ait été examiné en détails et qu’il soit approprié d’en tirer des renseignements quant à celui de la TBP aldolase, le manque singulier de stéréospécificité de cette dernière tant dans le sens du clivage que celui de la condensation n’est toujours pas éclairci. Afin de mettre à jour les caractéristiques du mécanisme enzymatique, une étude structurale de la TBP aldolase de S. pyogenes, un pathogène humain extrêmement versatile, a été entreprise. Elle a permis la résolution des structures de l’enzyme native et mutée, en complexe avec des subtrats et des inhibiteurs compétitifs, à des résolutions comprises entre 1.8 Å et 2.5 Å. Le trempage des cristaux de TBP aldolase native et mutante dans une solution saturante de FBP ou TBP a en outre permis de piéger un authentique intermédiaire covalent lié à la Lys205, la lysine catalytique. La determination des profils pH de la TBP aldolase native et mutée, entreprise afin d'évaluer l’influence du pH sur la réaction de clivage du FBP et TBP et ìdentifier le(s) résidu(s) impliqué(s), en conjonction avec les données structurales apportées par la cristallographie, ont permis d’identifier sans équivoque Glu163 comme résidu responsable du clivage. En effet, le mode de liaison sensiblement différent des ligands utilisés selon la stéréochimie en leur C3 et C4 permet à Glu163, équivalent à Glu187 dans la FBP aldolase de classe I, d’abstraire le proton sur l’hydroxyle du C4 et ainsi d’amorcer le clivage du lien C3-C4. L’étude du mécanimse inverse, celui de la condensation, grâce par exemple à la structure de l’enzyme native en complexe avec ses substrats à trois carbones le DHAP et le G3P, a en outre permis d’identifier un isomérisme du substrat G3P comme possible cause de la synthèse des isomères en C4 par cette enzyme. Ce résultat, ainsi que la decouverte d’un possible isomérisme cis-trans autour du lien C2-C3 de la base de Schiff formée avec le DHAP, identifié précedemment, permet de cerner presque complètement les particularités du mécanisme de cette enzyme et d’expliquer comment elle est capable de synthétiser les quatres stéréoisomères 3(S/R), 4(S/R). De plus, la résolution de ces structures a permis de mettre en évidence trois régions très mobiles de la protéine, ce qui pourrait être relié au rôle postulé de son isozyme chez S. pyogenes dans la régulation de l’expression génétique et de la virulence de la bactérie. Enfin, la résolution de la structure du mutant Lys229→Met de la FBP aldolase de muscle en complexe avec la forme cyclique du FBP, de même que des études cristallographiques sur le mutant équivalent Lys205→Met de la TBP aldolase de S. pyogenes et des expériences de calorimétrie ont permis d’identifier deux résidus particuliers, Ala31 et Asp33 chez la FBP aldolase, comme possible cause de la discrimination de cette enzyme contre les substrats 3(R) et 4(S), et ce par encombrement stérique des substrats cycliques. La cristallographie par rayons X et la cinétique enzymatique ont ainsi permis d'avancer dans l'élucidation du mécanisme et des propriétés structurales de cette enzyme aux caractéristiques particulières.

Probiotic Effects of Lactic Acid Bacteria Against Vibrio Alginolyticus in Penaeus (Fenneropenaeus) Indicus (H. Milne Edwards)

Cell free extracts of four strains of Lactic acid bacteria (LAB) viz. Lactobacillus. acidophilus, Streptococcus.cremoris, Lactobacillus bulgaricus –56 and Lactobacillus bulgaricus –57 inhibited growth of Vibrio alginolyticus in nutrient broth. The antagonism of LAB to Vibrio alginolyticus was further confirmed by streak plating wherein suppression of growth of Vibrio was obtained. Juveniles of Penaeus indicus (average weight 0.985 ± 0.1 g) on administering orally a moist feed base containing 5 × 106 cells·g of the four LAB probionts for a period of four weeks showed better survival (56 to 72%) when challenged with V. alginolyticus by intra-muscular injection of 0.1 ml containing 3 × 109 cells·ml. Animals maintained on a diet devoid of bacterial biomass exhibited 80% mortality. No external or internal pathological changes were observed in shrimp fed with the LAB incorporated diets. Results showed inhibition of V. alginolyticus by LAB and stimulation of the non-specific immune response resulting in resistance to disease in the shrimp fed on LAB incorporated diets.

Infección perinatal por estreptococo del Grupo B

Objetivo: Determinar la prevalencia de colonización vagino-rectal materna por Estreptococo Hemolítico del grupo B (SßG) entre la semana 35 y 37 de gestación, en la población obstétrica de la Clínica Universitaria Colombia, Bogotá, Colombia. Diseño: Estudio descriptivo de prevalencia Métodos: Entre abril y septiembre de 2008 se tomó la totalidad de pacientes obstétricas con parto atendido en la Clínica Universitaria Colombia y con tamizaje de colonización por SßG entre las semanas 35 y 37 de gestación, empleando cultivo vaginal y/o rectal. Se discriminó el sitio de toma del cultivo, se determinó la prevalencia de colonización vagino-rectal materna por SßG y se evaluó la presencia de infección neonatal temprana en la población estudio. Resultados: Se estudiaron 928 pacientes, encontrándose una prevalencia de colonización por SGB entre la semana 35 y 37 de gestación de 7,8%. Dentro de las pacientes colonizadas el 12,5% fueron detectadas por cultivo vaginal y el 87,5 % por cultivo vaginal – rectal. Conclusiones: La prevalencia de colonización vagino-rectal por SGB entre la semana 35 y 37 de gestación en las pacientes de la Clínica Universitaria Colombia, se encuentra en el rango reportado en Norteamérica y otras poblaciones latinas. La colonización por Streptococcus agalactiae encontrada con cultivo vaginal fue menor a la colonización encontrada por cultivo vaginal y rectal; lo cual está en relación con la importancia en la realización de cultivo vaginal y rectal reportada en la literatura, ya que el tracto gastrointestinal es un reservorio mayor de SGB.

Análisis económico de las vacunas 10-valente y 13-valente contra neumococo: revisión sistemática

Introducción: Las vacunas clásicamente han representado un método económico y eficaz para el control y prevención de múltiples enfermedades infecciosas. En los últimos años se han introducido nuevas vacunas contra neumococo a precios elevados, y los diferentes análisis económicos a nivel mundial de estas vacunas no muestran tendencias. El objetivo de este trabajo era resumir la evidencia existente a través de los diferentes estudios económicos evaluando las dos vacunas de segunda generación contra neumococo en la población a riesgo. Metodología: En este trabajo se realizo una revisión sistemática de la literatura en 8 bases de datos localizadas en diferentes partes del mundo y también que tuvieran literatura gris. Los artículos fueron inicialmente evaluados acorde a su titulo y resumen, posteriormente los elegidos se analizaron en su totalidad. Resultados: Se encontraron 404 artículos, de los cuales 20 fueron incluidos en el análisis final. Se encontró que la mayoría de los estudios se realizaron en áreas donde la enfermedad tiene una carga baja, como es Norte América y Europa, mientras que en los lugares del mundo donde la carga es mas alta, se realizaron pocos estudios. De igual manera se observo que la mayoría de los estudios mostraron por los menos ser costo efectivos respecto a la no vacunación, y en su totalidad las dos vacunas de segunda generación mostraron costo efectividad respecto a la vacunación con PCV-7. Los resultados de los estudios son muy heterogéneos, hasta dentro del mismo país, señalando la necesidad de guías para la conducción de este tipo de estudios. De igual manera, la mayoría de los estudios fueron financiados por farmacéuticas, mientras en un numero muy reducido por entes gubernamentales. Conclusiones: La mayoría de los estudios económicos sobre las vacunas de segunda generación contra neumococo han sido realizados en países con un alto índice de desarrollo económico y patrocinados por farmacéuticas. Dado que la mayoría de la carga de la enfermedad se encuentran en regiones con un menor nivel de desarrollo económico se deberían realizar mas en estas zonas. De igual manera, al ser la vacunación un asunto de salud publica y con un importante impacto económico los gobiernos deberían estar mas involucrados en los mismos.

Evaluación muticéntrica de la actividad antimicrobiana in vitro de tigeciclina en aislados obtenidos de pacientes hospitalizados en Colombia

El aumento en la resistencia bacteriana es un problema global que afecta también a nuestro país y que puede llevar a fracasos terapéuticos, peores desenlaces clínicos, uso de terapia combinada, mayor riesgo de interacciones medicamentosas y de reacciones adversas asi como a aumento de los costos del tratamiento. Tigeciclina, un nuevo antibiótico de la clase de las glicilciclinas ha mostrado una promisoria actividad antibacteriana in vitro contra bacterias comunes incluyendo multiresistentes que cada vez son más prevalentes en nuestro país especialmente a nivel hospitalario. Este estudio fue desarrollado para determinar la actividad de tigeciclina en nuestro medio y conocer su potencial utilidad.

Discoespondilite Canina : Estudo Retrospectivo de 10 Casos Clínicos

A discoespondilite é uma doença infecciosa rara que afecta, de forma crónica, os discos intervertebrais e as extremidades adjacentes dos corpos vertebrais. Geralmente advém de uma infecção disseminada por via hematógena e os agentes mais frequentes são bacterianos e são principalmente Staphylococcus spp., Streptococcus spp., E. Coli e Brucella spp. Também pode ser devida a infecções fúngicas, parasitárias ou migração de corpos estranhos. É caracterizada pela degenerescência do disco intervertebral e lesões escleróticas e proliferativas das extremidades dos corpos vertebrais. O principal sinal clínico desta doença é a hiperestesia paravertebral e alterações da marcha ou relutância ao movimento. Febre e anorexia são menos frequentes do que seria de esperar e os sinais neurológicos são considerados raros. O diagnóstico desta doença é geralmente radiográfico e a determinação do agente pode ser conseguida por cultura de material discal, hemocultura ou urocultura. Podem ser usados meios de imagiologia avançada como TAC e RM para melhor avaliar a extensão das lesões e o envolvimento dos tecidos circunvizinhos. A realização de hemogramas raramente revela alterações significativas embora possa existir leucocitose. O tratamento médico é eficaz em aproximadamente 76% dos casos e deve ser feito com base em cultura e TSA mas, de forma empírica, as cefalosporinas de primeira geração são frequentemente utilizadas. Em alguns casos pode ser necessária a estabilização ou desbridamento cirúrgicos. O estudo retrospectivo realizado no âmbito deste trabalho, teve como objectivo avaliar os sinais clínicos, radiográficos e laboratoriais , assim como o maneio médico e cirúrgico de 10 casos de discoespondilite confirmada radiográfica e clinicamente, num período de 2 anos. Observou-se maior prevalência da doença em machos, em cães jovens e adultos, e raças de grande porte. A região mais afectada foi a junção lombossagrada, e o sinal mais observado foi a dor paraespinhal. No entanto os sinais neurológicos foram mais frequentes do que o descrito. Os agentes isolados em cultura de material discal não foram os mais comuns. O tratamento médico instituído pelos veterinários foi eficaz em 6 dos casos, Foi necessária intervenção cirúrgica em 3 e 1 animal não recuperou totalmente até à conclusão deste estudo.

Avaliação da relação entre contagens de células somáticas e os agentes mais prevalentes de mastite em explorações leiteiras da região de entre Douro e Vouga

Quando um microrganismo patogénico invade a glândula mamária, através do canal do teto, pode ocorrer infecção intramamária, desencadeando uma resposta inflamatória – a mastite. Esta possui diversas etiologias, sendo normalmente de origem bacteriana. Na resposta inflamatória, actuam as células somáticas presentes no leite. O presente estudo teve como principal objectivo avaliar a relação entre as contagens de células somáticas e os agentes causadores de mastite em amostras de leite. Foram utilizados dados referentes aos resultados de análises de leite para diagnóstico de mastite realizadas em amostras de explorações de Entre Douro e Vouga. Os resultados consistem em identificação dos agentes e respectivo antibiograma, CCS, sendo ainda registado o objectivo da análise (Secagem ou Tratamento). Determinaram-se as prevalências dos agentes, avaliando de seguida a relação entre as seguintes variáveis: agentes e CCS; CCS e objectivo da análise; e entre agentes e objectivo da análise. Concluiu-se que os Staphylococcus coagulase-negativa são os mais prevalentes, 14,5%, seguindo, Streptococcus uberis, 7,6%; Escherichia coli, 6,3%; Lactococcus garviae, 5,8% e Staphylococcus aureus, 4,1%. Concluiu-se ainda, a existência de diferenças estatisticamente significativas nas análises realizadas, confirmando a relação entre as demais variáveis.

Allobaculum stercoricanis gen. nov., sp nov., isolated from canine feces

Morphological, biochemical, and molecular genetic studies were performed on an unknown anaerobic, catalase-negative, nonspore-forming, rod-shaped bacterium isolated from dog feces. The unknown bacterium was tentatively identified as a Eubacterium species, based on cellular morphological and biochemical tests. 16S rRNA gene sequencing studies, however, revealed that it was phylogenetically distant from Eubacterium limosum, the type species of the genus Eubacterium. Phylogenetically, the unknown species forms a hitherto unknown sub-line proximal to the base of a cluster of organisms (designated rRNA cluster XVI), which includes Clostridium innocuum, Streptococcus pleomorphus, and some Eubacterium species. Based on both phenotypic and phylogenetic criteria, it is proposed that the unknown bacterium be classified as a new genus and species, Allobaculum stercoricanis. Using a specific rRNA-targeted probe designed to identify Allobacultan stercoricanis, in situ hybridisation showed this novel species represents a significant organism in canine feces comprising between 0.1% and 3.7% of total cells stained with DAPI (21 dog fecal samples). The type strain of Allobaculum stereoricanis is DSM 13633(T) = CCUG 45212(T). (C) 2004 Elsevier Ltd. All rights reserved.

Antigenotoxicity of probiotics and prebiotics on faecal water-induced DNA damage in human colon adenocarcinoma cells

Six strains of lactic acid producing bacteria (LAB) were incubated (1 x 10(8)cfu/ml) with genotoxic faecal water from a human subject. HT29 human adenocarcinoma cells were then challenged with the resultant samples and DNA damage measured using the single cell gel electrophoresis (comet) assay. The LAB strains investigated were Bifidobacterium sp. 420, Bifidobacterium Bb12, Lactobacillus plantarum, Streptococcus thermophilus, Lactobacillus bulgaricus and Enterococcus faecium. DNA damage was significantly decreased by all bacteria used with the exception of Strep. thermophilus. Bif. Bb12 and Lact. plantarum showed the greatest protective effect against DNA damage. Incubation of faecal water with different concentrations of Bif. Bb12 and Lact. plantarum revealed that the decrease in genotoxicity was related to cell density. Non-viable (heat treated) probiotic cells had no effect on faecal water genotoxicity. In a second study, HT29 cells were cultured in the presence of supernatants of incubations of probiotics with various carbohydrates including known prebiotics; the HT29 cells were then exposed to faecal water. Overall, incubations involving Lact. plantarum with the fructooligosaccharide (FOS)-based prebiotics Inulin, Raftiline, Raftilose and Actilight were the most effective in increasing the cellular resistance to faecal water genotoxicity, whereas fermentations with Elixor (a galactooligosaccharide) and Fibersol (a maltodextrin) were less effective. Substantial reductions in faecal water-induced DNA damage were also seen with supernatants from incubation of prebiotics with Bif. Bb12. The supernatant of fermentations involving Ent. faecium and Bif. sp. 420 generally had less potent effects on genotoxicity although some reductions with Raftiline and Elixor fermentations were apparent.

In vitro evaluation of the antimicrobial activity of a range of probiotics against pathogens: Evidence for the effects of organic acids

The aim of this study was to investigate the antimicrobial properties of fifteen selected strains belonging to the Lactobacillus, Bifidobacterium, Lactococcus, Streptococcus and Bacillus genera against Gram-positive and Gram-negative pathogenic bacteria. In vitro antibacterial activity was initially investigated by an agar spot method. Results from the agar spot test showed that most of the selected strains were able to produce active compounds on solid media with antagonistic properties against Salmonella Typhimurium, Escherichia coli, Enterococcus faecalis, Staphylococcus aureus and Clostridium difficile. These results were also confirmed when cell-free culture supernatants (CFCS) from the putative probiotics were used in an agar well diffusion assay. Neutralization of the culture supernatants with alkali reduced the antagonistic effects. These experiments are able to confirm the capacity of potential probiotics to inhibit selected pathogens. One of the main inhibitory mechanisms may result from the production of organic acids from glucose fermentation and consequent lowering of culture pH. This observation was confirmed when the profile of organic acids was analysed demonstrating that lactic and acetic acid were the principal end products of probiotic metabolism. Furthermore, the assessment of the haemolytic activity and the susceptibility of the strains to the most commonly used antimicrobials, considered as basic safety aspects, were also studied. The observed antimicrobial activity was mainly genus-specific, additionally significant differences could be observed among species.

Genetic relatedness and phenotypic characteristics of Treponema associated with human periodontal tissues and ruminant foot disease

Treponema have been implicated recently in the pathogenesis of digital dermatitis (DID) and contagious ovine digital dermatitis (CODD) that are infectious diseases of bovine and ovine foot tissues, respectively. Previous analyses of treponemal 16S rDNA sequences, PCR-amplified directly from DID or CODD lesions, have suggested relatedness of animal Treponema to some human oral Treponema species isolated from periodontal tissues. In this study a range of adhesion and virulence-related properties of three animal Treponema isolates have been compared with representative human oral strains of Treponema denticola and Treponema vincentii. In adhesion assays using biotinylated treponemal cells, T denticola cells bound in consistently higher numbers to fibronectin, laminin, collagen type 1, gelatin, keratin and lactoferrin than did T. vincentii or animal Treponema isolates. However, animal DID strains adhered to fibrinogen at equivalent or greater levels than T denticola. All Treponema strains bound to the amino-terminal heparin l/fibrin I domain of fibronectin. 16S rDNA sequence analyses placed ovine strain UB1090 and bovine strain UB1467 within a cluster that was phylogenetically related to T vincentii, while ovine strain UB1466 appeared more closely related to T denticola. These observations correlated with phenotypic properties. Thus, T denticola ATCC 35405, GM-1, and Treponema UB1466 had similar outer-membrane protein profiles, produced chymotrypsin-like protease (CTLP), trypsin-like protease and high levels of proline iminopeptidase, and co-aggregated with human oral bacteria Porphyromonas gingivalis and Streptococcus crista. Conversely, T vincentii ATCC 35580, D2A-2, and animal strains UB1090 and UB1467 did not express CTLP or trypsin-like protease and did not co-aggregate with P. gingivalis or S. crista. Taken collectively, these results suggest that human oral-related Treponema have broad host specificity and that similar control or preventive strategies might be developed for human and animal Treponema-associated infections.

Antipathogenic activity of probiotics against Salmonella Typhimurium and Clostridium difficile in anaerobic batch culture systems: is it due to synergies in probiotic mixtures or the specificity of single strains?

Probiotics are currently being investigated for prevention of infections caused by enteric pathogens. The aim of this in vitro study was to evaluate the influence of three single probiotics: Lactobacillus casei NCIMB 30185 (PXN 37), Lactobacillus acidophilus NCIMB 30184 (PXN 35), Bifidobacterium breve NCIMB 30180 (PXN 25) and a probiotic mixture containing the above strains plus twelve other strains belonging to the Lactobacillus, Bifidobacterium, Lactococcus, Streptococcus and Bacillus genera on the survival of Salmonella Typhimurium and Clostridium difficile using pH-controlled anaerobic batch cultures containing mixed fecal bacteria. Changes in relevant bacterial groups and effects of probiotic addition on survival of the two pathogens were assessed over 24 h. Quantitative analysis of bacterial populations revealed that there was a significant increase in lactobacilli and/or bifidobacteria numbers, depending on probiotic addition, compared with the control (no added probiotic). There was also a significant reduction in S. Typhimurium and C. difficile numbers in the presence of certain probiotics compared with controls. Of the probiotic treatments, two single strains namely L. casei NCIMB 30185 (PXN 37), and B. breve NCIMB 30180 (PXN 25) were the most potent in reducing the numbers of S. Typhimurium and C. difficile. In addition, the supplementation with probiotics into the systems influenced some fermentations parameters. Acetate was found in the largest concentrations in all vessels and lactate and formate were generally detected in higher amounts in vessels with probiotic addition compared to controls.

Metaproteomics analysis reveals the adaptation process for the chicken gut microbiota

The animal gastrointestinal tract houses a large microbial community, the gut microbiota, that confers many benefits to its host, such as protection from pathogens and provision of essential metabolites. Metagenomic approaches have defined the chicken fecal microbiota in other studies, but here, we wished to assess the correlation between the metagenome and the bacterial proteome in order to better understand the healthy chicken gut microbiota. Here, we performed high-throughput sequencing of 16S rRNA gene amplicons and metaproteomics analysis of fecal samples to determine microbial gut composition and protein expression. 16 rRNA gene sequencing analysis identified Clostridiales, Bacteroidaceae, and Lactobacillaceae species as the most abundant species in the gut. For metaproteomics analysis, peptides were generated by using the Fasp method and subsequently fractionated by strong anion exchanges. Metaproteomics analysis identified 3,673 proteins. Among the most frequently identified proteins, 380 proteins belonged to Lactobacillus spp., 155 belonged to Clostridium spp., and 66 belonged to Streptococcus spp. The most frequently identified proteins were heat shock chaperones, including 349 GroEL proteins, from many bacterial species, whereas the most abundant enzymes were pyruvate kinases, as judged by the number of peptides identified per protein (spectral counting). Gene ontology and KEGG pathway analyses revealed the functions and locations of the identified proteins. The findings of both metaproteomics and 16S rRNA sequencing analyses are discussed.