A organização molecular do Celulossoma: caracterização estrutural da proteína CipA e estudo da diversidade das interações coesina-doquerina

A celulose, principal componente da parede celular vegetal e o composto orgânico mais abundante da biosfera, possui inúmeras aplicações biotecnológicas. O microrganismo anaeróbio Clostridium thermocellum (C.thermocellum) tem sido alvo de grande interesse pela sua capacidade em degradar eficientemente a celulose e outros componentes da parede celular vegetal, por meio de um complexo multi-enzimático altamente eficiente, denominado de celulossoma. A montagem deste complexo ocorre através de uma proteína multi-modular denominada CipA. Esta proteína estrutural possui módulos não catalíticos (coesinas tipo I) que se ligam a módulos complementares (doquerinas tipo I) presentes nas enzimas celulolíticas modulares. A CipA possui ainda um módulo doquerina de tipo II que permite a ancoragem deste complexo multi-enzimático à parede celular da bactéria. Na presente dissertação foram utilizadas as metodologias de Cristalografia de Raios-X, para caracterizar a interação coesina-doquerina a nível atómico e molecular, e de Microarrays, com o intuito de estudar as possíveis especifidades e afinidades dessas interações. Com base na primeira técnica foram elucidadas as estruturas do módulo coesina C4 da CipA em complexo com a doquerina da enzima modular Xyn10B e do módulo coesina C9 isolado. As estruturas foram comparadas com o complexo do módulo coesina C2-doquerina Xyn10B já publicado. Esta análise encontra-se descrita no capítulo 3. Por último, a técnica de Microarrays, associada à eletroforese em gel de poliacrilamida em condições nativas, permitiu a caracterização das diferenças de afinidade e especificidade entre os vários pares coesina-doquerina dos celulossomas de C. thermocellum e de Rumminococcus flavefaciens (R. flavefaciens). As especificidades e afinidades dos módulos doquerina, dos celulossomas mencionados anteriormente estão descritas no capítulo 4.

Efeito dos taninos condensados de forrageiras nativas do semi-árido nordestino sobre o crescimento e atividade celulolítica de Ruminococcus flavefaciens FD1

Avaliaram-se o crescimento da população, a atividade in vitro da enzima 1,4-b-endoglucanase e a taxa de digestão de celulose em culturas de Ruminococcus flavefaciens FD1 na presença de 50, 100, 200 e 400µg/ml de taninos purificado das leguminosas Mimosa hostilis (Jurema Preta), Mimosa caesalpinifolia (Sabiá) e Bauhinia cheilantha (Mororó). O crescimento bacteriano, a atividade da endoglucanase e a digestão de celulose foram fortemente inibidos pela presença dos taninos condensados purificados das três espécies, entretanto, a intensidade da inibição foi variável em função da espécie da leguminosa e da concentração de tanino.

Potential of novel dextran oligosaccharides as prebiotics for obesity management through in vitro experimentation.

The energy-salvaging capacity of the gut microbiota from dietary ingredients has been proposed as a contributing factor for the development of obesity. This knowledge generated interest in the use of non-digestible dietary ingredients such as prebiotics to manipulate host energy homeostasis. In the present study, the in vitro response of obese human faecal microbiota to novel oligosaccharides was investigated. Dextrans of various molecular weights and degrees of branching were fermented with the faecal microbiota of healthy obese adults in pH-controlled batch cultures. Changes in bacterial populations were monitored using fluorescent in situ hybridisation and SCFA concentrations were analysed by HPLC. The rate of gas production and total volume of gas produced were also determined. In general, the novel dextrans and inulin increased the counts of bifidobacteria. Some of the dextrans were able to alter the composition of the obese human microbiota by increasing the counts of Bacteroides–Prevotella and decreasing those of Faecalibacterium prausnitzii and Ruminococcus bromii/R. flavefaciens. Considerable increases in SCFA concentrations were observed in response to all substrates. Gas production rates were similar during the fermentation of all dextrans, but significantly lower than those during the fermentation of inulin. Lower total gas production and shorter time to attain maximal gas production were observed during the fermentation of the linear 1 kDa dextran than during the fermentation of the other dextrans. The efficacy of bifidobacteria to ferment dextrans relied on the molecular weight and not on the degree of branching. In conclusion, there are no differences in the profiles between the obese and lean human faecal fermentations of dextrans.

Impact of increasing fruit and vegetables and flavonoid intake on the human gut microbiota

Epidemiological studies have shown protective effects of fruits and vegetables (F&V) in lowering the risk of developing cardiovascular diseases (CVD) and cancers. Plant-derived dietary fibre (non-digestible polysaccharides) and/or flavonoids may mediate the observed protective effects particularly through their interaction with the gut microbiota. The aim of this study was to assess the impact of fruit and vegetable (F&V) intake on gut microbiota, with an emphasis on the role of flavonoids, and further to explore relationships between microbiota and factors associated with CVD risk. In the study, a parallel design with 3 study groups, participants in the two intervention groups representing high-flavonoid (HF) and low flavonoid (LF) intakes were asked to increase their daily F&V intake by 2, 4 and 6 portions for a duration of 6 weeks each, while a third (control) group continued with their habitual diet. Faecal samples were collected at baseline and after each dose from 122 subjects. Faecal bacteria enumeration was performed by fluorescence in situ hybridisation (FISH). Correlations of dietary components, flavonoid intake and markers of CVD with bacterial numbers were also performed. A significant dose X treatment interaction was only found for Clostidium leptum-Ruminococcus bromii/flavefaciens with a significant increase after intake of 6 additional portions in the LF group. Correlation analysis of the data from all 122 subjects independent from dietary intervention indicated an inhibitory role of F&V intake, flavonoid content and sugars against the growth of potentially pathogenic clostridia. Additionally, we observed associations between certain bacterial populations and CVD risk factors including plasma TNF-α, plasma lipids and BMI/waist circumference.

Quantificação molecular de bactérias ruminais, parâmetros ruminais e digestibilidade de dietas de novilhos alimentados com diferentes relações de volumoso: concentrado na dieta

Pós-graduação em Zootecnia - FCAV

Quantificação de microrganismos ruminais de novilhos alimentados com cana-de-açúcar ou feno de tifton com diferentes relações volumoso:concentrado

Pós-graduação em Zootecnia - FCAV

In vitro fermentation parameters and biohydrogenation of vegetable oils without glycerol

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Different sources of forage with crude glycerin in diets with higher percentage of concentrate to beef cattle

Pós-graduação em Zootecnia - FCAV

Glycerol combined with oils did not limit biohydrogenation of unsaturated fatty acid but reduced methane production in vitro

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Feeding increasing concentrate to Tifton 85 hay ratios modulated rumen fermentation and microbiota in Nellore feedlot steers

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Virginiamycin via mineral supplementation and sward height in growing Nelore young bulls

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Energy sources in the supplementation of beef cattle grazing Brachiaria brizantha cv. Xaraés

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Use of tomato and cucumber horticulture by-products in goat diets: effects o nrumen fermentation and microbial communities in batch and continuous cultures

Two in vitro experiments were conducted to analyse the effects of replacing dietary barley grain with wastes of tomato and cucumber fruits and a 1 : 1 tomato : cucumber mixture on rumen fermentation characteristics and microbial abundance. The control (CON) substrate contained 250 g/kg of barley grain on a dry matter (DM) basis, and another 15 substrates were formulated by replacing 50, 100, 150, 200 or 250 g of barley grain/kg with the same amount (DM basis) of tomato or cucumber fruits or 1 : 1 tomato : cucumber mixture. In Expt 1, all substrates were incubated in batch cultures with rumen micro-organisms from goats for 24 h. Increasing amounts of tomato, cucumber and the mixture of both fruits in the substrate increased final pH and gas production, without changes in final ammonia-nitrogen (NH3-N) concentrations, substrate degradability and total volatile fatty acid (VFA) production, indicating that there were no detrimental effects of any waste fruits on rumen fermentation. Therefore, in Expt 2 the substrates including 250 g of waste fruits (T250, C250 and M250 for tomato, cucumber and the mixture of both fruits, respectively) and the CON substrate were incubated in single-flow continuous-culture fermenters for 8 days. Total VFA production did not differ among substrates, but there were differences in VFA profile. Molar proportions of propionate, isobutyrate and isovalerate were lower and acetate : propionate ratio was greater for T250 compared with CON substrate. Fermentation of substrates containing cucumber (C250 and M250) resulted in lower proportions of acetate, isobutyrate and isovalerate and acetate : propionate ratio, but greater butyrate proportions than the CON substrate. Carbohydrate degradability and microbial N synthesis tended to be lower for substrates containing cucumber than for the CON substrate, but there were no differences between CON and T250 substrates. Abundance of total bacteria, Fibrobacter succinogenes and Ruminococcus flavefaciens, fungi, methanogenic archaea and protozoa were similar in fermenters fed T250 and CON substrates, but fermenters fed C250 and M250 substrates had lower abundances of R. flavefaciens, fungi and protozoa than those fed the CON substrate. Results indicated that tomato fruits could replace dietary barley grain up to 250 g/kg of substrate DM without noticeable effects on rumen fermentation and microbial populations, but the inclusion of cucumber fruits at 250 g/kg of substrate DM negatively affected some microbial populations as it tended to reduce microbial N synthesis and changed the VFA profile. More studies are needed to identify the dietary inclusion level of cucumber which produces no detrimental effects on rumen fermentation and microbial growth.

Influencia del tipo de filtrado y tratamiento con Stomacher del fluido ruminal de ovejas en las poblaciones microbianas del inóculo

Four rumen-fistulated sheep fed a 66:34 alfalfa hay:concentrate diet were used as donors to investigate the effect of rumen contents’ treatment on microbial populations in the resulting fluid. Rumen contents were sampled from each individual sheep and subjected to the following treatments: SQ: squeezed through 4 layers of cheesecloth; FIL: SQ treatment and further filtration through a 100-μm nylon cloth; STO: reated with a Stomacher® for 3 min at 230 rev min-1 and followed by SQ. Microbial populations in the fluid were analysed by real-time PCR and bacterial diversity was assessed by the automated ribosomal intergenic spacer analysis (ARISA) of the 16S ribosomal DNA. Bacterial DNA concentrations and relative abundance of Ruminococcus flavefaciens, arqueal and fungal DNA did not differ (P>0.05) between treatments. In contrast, STO treatment decreased (P<0.05) protozoal DNA concentrations and increased (P<0.05) the relative abundance of Fibrobacter succinogenes compared with SQ method. There were no differences (P>0.05) between treatments either in the Shannon index or in the number of peaks in the ARISA electropherograms, indicating no effect on bacterial diversity. Studies analyzing the influence on the tested methods on fermentation characteristics of different substrates when the fluid is used as inoculum is required.

Comparative genomic approaches for investigating evolution in the microbial and viral populations of the rumen

The rumen is home to a diverse population of microorganisms encompassing all three domains of life: Bacteria, Archaea, and Eukarya. Viruses have also been documented to be present in large numbers; however, little is currently known about their role in the dynamics of the rumen ecosystem. This research aimed to use a comparative genomics approach in order to assess the potential evolutionary mechanisms at work in the rumen environment. We proposed to do this by first assessing the diversity and potential for horizontal gene transfer (HGT) of multiple strains of the cellulolytic rumen bacterium, Ruminococcus flavefaciens, and then by conducting a survey of rumen viral metagenome (virome) and subsequent comparison of the virome and microbiome sequences to ascertain if there was genetic information shared between these populations. We hypothesize that the bacteriophages play an integral role in the community dynamics of the rumen, as well as driving the evolution of the rumen microbiome through HGT. In our analysis of the Ruminococcus flavefaciens genomes, there were several mobile elements and clustered regularly interspaced short palindromic repeat (CRISPR) sequences detected, both of which indicate interactions with bacteriophages. The rumen virome sequences revealed a great deal of diversity in the viral populations. Additionally, the microbial and viral populations appeared to be closely associated; the dominant viral types were those that infect the dominant microbial phyla. The correlation between the distribution of taxa in the microbiome and virome sequences as well as the presence of CRISPR loci in the R. flavefaciens genomes, suggested that there is a “kill-the-winner” community dynamic between the viral and microbial populations in the rumen. Additionally, upon comparison of the rumen microbiome and rumen virome sequences, we found that there are many sequence similarities between these populations indicating a potential for phage-mediated HGT. These results suggest that the phages represent a gene pool in the rumen that could potentially contain genes that are important for adaptation and survival in the rumen environment, as well as serving as a molecular ‘fingerprint’ of the rumen ecosystem.