Avaliação da eficácia da desinfecção de instrumentos usados durante o período transoperatório do tratamento endodôntico

Esta investigação objetivou a eficácia antimicrobiana de agentes desinfetantes utilizados na desinfecção dos instrumentos endodônticos, durante o período transoperatório do tratamento endodôntico. A atividade antimicrobiana dos desinfetantes álcool isopropílico, acetona e ácido peracético (PAA) foi avaliada sobre microrganismos planctônicos através de teste de contato (time kill assay), utilizando inóculo de 9,9 X 109 a 1,2 X 1012 unidades formadoras de colônia (UFC) e por determinação da concentração bactericida mínima (CBM), usando inóculo de aproximadamente 106 UFC. Os agentes químicos também foram avaliados sobre Enterococcus faecalis (E. faecalis) ATCC 29212 cultivada em matriz de dentina (ex vivo) visando a formação de biofilme. O biofilme (organismos sésseis) microbiano foi removido com limas tipo Kerr (LK), até as lâminas estarem visualmente preenchidas. As LK contaminadas foram usadas como carreadores (logo após a contaminação ou secas dentro de uma câmara de fluxo laminar por 10 minutos). As LK carreadoras foram imersas em álcool isopropílico ou acetona ambos a 80%, ou em Ácido peracético 2%, por 30 ou 60 segundos. As limas foram posteriormente colocadas em tubos de ensaio contendo caldo Enterococcosel para observar o crescimento dos enterococos viáveis. Depois, os experimentos in vivo foram realizados com LK contaminadas por material necrótico pulpar da região cervical de dentes indicados para tratamento endodôntico. As LK contaminadas foram imersas, por 30 ou 60 segundos, em 80% de acetona ou 80% de álcool isopropílico ou 2% de PAA. As limas foram então inoculadas em tubos de ensaio contendo meio tioglicolato. Os organismos que cresceram, foram identificados após o tratamento com PAA. A corrosão mediada pelos agentes químicos também foi testada, após a incubação de LK de aço inoxidável e de NiTi por 60 minutos, medindo o peso das LK antes e depois da imersão e por microscopia eletrônica de varredura (MEV). Todos os agentes químicos foram capazes de eliminar ou reduzir a viabilidade das bactérias de espécies planctônicas Gram-negativas e Gram-positivas, embora a atividade dos produtos químicos sobre E. faecalis sésseis em testes de carreadores de LK demonstrou que o álcool isopropílico ou acetona foram incapazes de eliminar a contaminação bacteriana, especialmente, quando as limas foram secas previamente à exposição aos produtos químicos, por 15 ou 30 segundos. O PAA demonstrou a melhor atividade antimicrobiana e eliminou a viabilidade das células sésseis E. faecalis de ambas as limas endodônticas tipo K úmidas ou secas, após exposição por 15 segundos (100% de eliminação). Os experimentos desenvolvidos in vivo demonstraram que o PAA foi o agente mais eficaz (p<0,05), capaz de eliminar a viabilidade dos organismos em 92% das LK imersas depois de 60 segundos, quando comparado com acetona (64%) ou com álcool isopropílico (50%). O crescimento microbiano após o contato com o PAA demonstrou que somente o grupo dos Lactobacillus sp foi resistente a essa substância química. Os agentes químicos não demonstraram ser corrosivos, após a imersão por 1 hora, tanto por pesagem quanto por MEV. Foi observado que o PAA foi o agente mais eficaz para ser utilizado como desinfetante de instrumentos, durante o período transoperatório do tratamento endodôntico.

Eficácia de um protocolo de higiene bucal com utilização de solução de clorexidina a 0,12% na prevenção de pneumonias associadas à ventilação mecânica (PAVM) e os efeitos sobre a microbiota da mucosa bucal de pacientes internados em unidades de terapia intensiva

A presente investigação teve como objetivo avaliar a prática de cirurgiões dentistas em uma unidade de terapia intensiva (UTI) de um hospital militar, o estabelecimento de um protocolo de higiene oral e os seus efeitos sobre a redução de pneumonias associadas à ventilação mecânica (PAVM). As percepções da equipe da UTI sobre as atividades dos cirurgiões dentistas também foram avaliadas por meio de um questionário. O perfil de colonização microbiana da mucosa oral antes e depois do estabelecimento das medidas de higiene oral também foi avaliado tanto por diluição e plaqueamento em meios de cultura microbiológicos seletivos e enriquecidos e através da amplificação pelo método de PCR e eletroforese em gel desnaturante em gradiente (DGGE), subsequente ao sequenciamento dos amplicons. A carga microbiana foi avaliada após a contagem de placas de agar e através da amplificação por PCR em tempo real (qPCR) do gene rrs nas amostras. O protocolo de higiene oral, realizado pelos cirurgiões dentistas, foi capaz de reduzir a incidência de PAVM (p <0,05). O questionário revelou que a modificação da halitose foi percebida por 93,33% dos participantes. A redução da ocorrência das úlceras orais e dos lábios durante a internação dos pacientes foi observada por 80% da equipe da UTI. Foi observada a redução da produção das secreções nasais e bucais por 70% da equipe dos profissionais da UTI. Para 86,66% dos participantes a assistência aos pacientes tornou-se mais agradável após a instituição dos cuidados bucais. O protocolo, realizado com a utilização de solução 0,12% de clorexidina, não foi capaz de evitar a colonização da mucosa oral por patógenos microbianos usualmente encontrados no ambiente hospitalar tais como os bastonetes Gram-negativos entéricos e não fermentadores, nem foi capaz de eliminá-los quando tais micro-organismos já se encontravam presentes antes dos procedimentos de higiene bucal. Alguns Bastonetes Gram-positivos (Lactobacillus sp e corinebactérias) e Staphylococcus epidermidis permaneceram após a realização dos procedimentos. O protocolo de higiene oral permitiu a redução da carga microbiana na mucosa oral de 50% dos pacientes considerando-se o método de contagem microbiana e para 35% dos pacientes pela avaliação dos números de cópias de genes rrs através de qPCR. Em conclusão, o protocolo de higiene oral desenvolvido pelos cirurgiões dentistas foi capaz de reduzir a incidência de PAV na UTI, embora não tenha sido capaz de prevenir a colonização da mucosa oral por supostos patógenos microbianos. O protocolo de higiene oral com a participação ativa dos cirurgiões dentistas foi bem aceito pelos profissionais da UTI e foi capaz de melhorar a qualidade da assistência aos pacientes críticos.

Ensiled product from fish by microbial fermentation

Fish ensilage for animal feed stuff was prepared from Jew fish (Pseudosciaena spp.) and Silver bellies (Leiognathus spp.) by fermentation with pure culture of Lactobacillus piantarum NCIB 6105. The precooked ensiled product gave better product of fish silage (high content of lactic acid, about 5%). Protein Nitrogen content ranged between 1.76 to 1.94%. During storage for one year, the Protein Nitrogen loss was not significant. The material can be used as a supplemental animal ration.

Inhibition of seafood-borne bacteria in cooked mackerel (Rastrelliger kanagurta) fish meat by lactic acid bacteria

Antagonistic activity of lactic acid bacteria (LAB) namely Streptococcus faecalis, Pediococcus cerevisiae and Lactobacillus casei was tested against seafood-borne bacteria such as Staphylococcus aureus, Bacillus cereus, Escherichia coli, Clostridium perfringens and Listeria monocytogenes. Three lactic acid bacteria such as Streptococcus faecalis, Lactobacillus casei and Pediococcus cerevisiae were coated on cooked mackerel meat, individually and in combination against fish-borne bacteria. S. faecalis inhibited C. perfringens in individual coat by 3.7 log units as compared to control, whereas L. casei did not inhibit C. perfringens. P. cerevisiae inhibited S. aureus by 5 log units. L. casei, inhibited L. monocytogenes by 3.3 log units on the third day of storage as compared to control. On the other hand, S. aureus and B. cereus were inhibited on the third and second day by 4.9 log and 5.2 log units respectively. B. cereus, S. aureus, L. monocytogenes were the most sensitive to all three LAB. C. perfringens was the least inhibited among all the seafood-borne bacteria tried. Multiple LAB or LAB strains in combination showed much earlier inhibitory activity on seafood-borne bacteria than single LAB coat.

Comparative effect of Pediococcus acidilactici and Lactococcus lactis on growth performance, survival and enzyme activity of western white leg shrimp (Litopenaeus vannamei)

This study was done in Shahid Kiani Marine Aquaculture Development Center, Choebde, Abadan in order to evaluate the effects of Pediiococcus acidilactici, Lactococcus lactis and vitamin C on growth performance, survival, enzymatic activities and immune responses of L. vannamei during three months. Treatments were included control group, Pediiococcus and Lactococcus treatments which fed with diet containing 1×10P9P cfu gP_1P bacteria and vitamin C. At the end of the experiment, the growth factors, immune parameters, digestive enzymes, intestinal, histology of intestine, carcasses and microbial flora (bacterial total count and lactic acid count) were evaluated. The results indicated that administration of lactobacillus had significant effects on the growth factors as the highest weight, increase specific growth rate, relative growth rate, feed conversion ratio and protein efficiency in the shrimps received pediococcus and then Lactococcus (P<0.05). The best immune function was also observed in the shrimps fed by probiotics, so that proteins and hemoglobin̛ hemolymph, phenoloxidase activity and challenged with V. parahaemolyticus showed a statistical difference comparing to the control group and the group received vitamin C (P<0.05). Some digestive enzymes, in pediococcus treatment showed a significant increase when compared to other treatments (P<0.05). Significant changes in bacterial intestinal flora were observed in probiotic groups compared with control and vitamin C groups (P < 0.05). Histological results showed the positive effects of probiotics in the gut (P < 0.05). While these supplements cannot caused to significant impacts on the shrimp carcass composition (P ˃ 0.05). As a result pediococcus group had the best performance among treatments.

Application of combined effect of sodium acetate and nisin on reduction of contamination by Listeria monocytogenes in vacuum packaged grass carp (Ctenopharyngodon idella) fillets kept at 4°C

In this study microbiological , chemical quality and fatty acid composition of grass carp (Ctenopharyngodon idella) fillets treated by dipping in sodium acetate (%1 and %3), nisin (% 0.1 and % 0.2) and combination of sodium acetate and nisin was evaluated during 16 days of refrigerated of 4°C Antilisterial effect of nisin was enhanced with the increased concentration of sodium acetate. At day 12 post storage, Listeria monocytogenese count was higher in the control group than the recommended value, however in sodium acetate and nisin treated samples, the count was lower (5.17-5.91 log cfu/g). With increasing the concentrations of sodium acetate, mesophilic counts were lower. Regarding nisin, better results was obtained by applying %0.1 nisin. Greater inhibition of mesophile bacteria was observed when combination treatment was used. The number of lactobacillus was lower when higher concentrations of sodium acetate and nisin were used. Total Volatile Nitrogen values at the end of the experiment were lower in the samples treated with both nisin and sodium acetate and the better results were obtained in combination treatments. Peroxide (PV) at the end of the experiment was 1.9 meq/kg in control, and the lowest values were observed for the treatments 3(%0 sodium acetate +% 0.2 nisin) and 9(%3 sodium acetate +% 0.2 nisin) between 1.08 and 1.62 meq/kg without significant difference. Thiobarbituric acid (TBA) levels at the end of experiment have been shown to be 0.46 mg malonaldehyde per kg in the control. On the other hand treatments 9 had the TBA values of 0.19 mg malonaldehyde per kg which was significantly lower than that of control. Polyunsaturated fatty acids increased by increasing the sodium acetate doses and instead saturated fatty acids and n-6/n-3 ratio decreased. The ratio of UFA/SFA and also C22:6/C16:0 increased when a higher concentration of sodium acetate has been used. The best result obtained by using 3% of sodium acetate but no such relation with nisin was observed.

Study on effects of extracted probiotics from microbial flora of digestive system on growth indices in beluga (Huso huso) and Persian sturgeon (Acipenser persicus)

Isolation of Lactic Acid Bacteria (LAB) was carried out from gastro intestinal tract of beluga and Persian sturgeon at international sturgeon research institute and PCR has been used for bacteria Identification. Two species of LAB including Enterococcus seriolicida and Leuconostoc mesenteroides were isolated from Gastrointestinal tract (GI) of persian sturgeon in this study and the counts of Leu. mesenteroides (4.63×102 CFU/gr of GI) was significantly higher than other species. Lactobacillus curvatus, Lactococcus raffinolactis, Lactococcus lactis and Streptococcus sp. were also isolated from GI of beluga and maximum counts was belonged to Lb. curvatus (4.63×102 CFU/gr of GI) in this species. Dominant species were lyophilized and adding to the water since start of mix feeding of sturgeon with different counts including 2×109, 5×109 and 9×109 CFU/gr of live food, 4 times a day. The results revealed that the maximum and minimum growth rate and protease, amylase, and lipase activity in beluga was gained by using of Lb. curvatus with total viable count of 9×10 9 CFU/gr of live food and Leu. mesenteroides with total viable count of 9×109 CFU/gr of live food. According to the results of this study, the maximum and minimum growth rate and protease, amylase, and lipase activity in Persian sturgeon was gained by using of Leu. mesenteroides with total viable count of 2×10 9 CFU/gr of live food and Lb. curvatus with total viable count of 9×109 CFU/gr of live food. Histological study showed that gastrointestinal development was same during larva rearing in control and other treatments but the size of liver was bigger in treatments that received nonspecific LAB in both species. According to the results, positive effects of using dominant specific LAB bacteria for larviculture of sturgeon has been proved in this study.

四种药用植物的化学成分及芍药苷的微生物转化研究

本学位论文共有5章。第一章报道白芍的化学成分及芍药苷的微生物转化研究成果；第二章报道天山雪莲的化学成分研究；第三章报道两面针的化学成分研究；第四章报道通关藤的化学成分研究成果；第五章概述了花椒属植物中最近十年报道的新化合物及药理研究情况。 在第1章的第一部分报道了白芍（Paeonia lactiflora Pall.）的化学成分。我们采用正、反相硅胶柱层析等各种分离方法，从白芍的干燥根中共分离出14个化合物，其中1个为新化合物，其结构通过波谱分析证实为没食子酰白芍苷，另外还有2个为首次从该植物中分离得到。第二部分报道了芍药苷的微生物转化生产芍药苷代谢素-I的研究，从15株厌氧菌中筛选出10株有转化活性的菌株，其中短乳杆菌Lactobacillus brevis AS1.12的转化活性最好，对其转化条件进行了初步的筛选，确定了相对合理的转化工艺。 在第2章报道了天山雪莲（Saussurea involucrate Kar.et Kir.）全草乙醇提取物化学成分的分离纯化和结构鉴定。通过正、反相硅胶柱层析等分离纯化和MS、NMR等波谱解析，共分离鉴定了28个化合物，结构类型分属于黄酮、倍半萜和木脂素等，其中2个新倍半萜化合物的结构分别表征为6α-羟基云木香酸6-β-D-吡喃葡萄糖苷和11βH-11,13-二氢去氢云木香内酯8α-O-(6′-乙酰)-β-D-吡喃葡萄糖苷。 第3章报道了两面针（Zanthoxylum nitidum （Roxb.）DC.）干燥根的乙醇提取物化学成分的分离纯化和结构鉴定。通过正、反相硅胶柱层析等分离纯化和MS、NMR等波谱解析以及X-射线单晶衍射，共分离鉴定了16个生物碱，结构类型分属于苯并啡啶类、喹啉类和阿朴啡类等，其中2个新苯并啡啶类生物碱的结构分别表征为二聚双氢两面针碱和丙酮基双氢崖定椒碱。 第4章报道了通关藤（Marsdenia tenacissima (Roxb.) Wight et Arn.）水提取物化学成分的分离纯化和结构鉴定。通过正、反相硅胶柱层析等分离纯化和MS、NMR等波谱解析以及X-射线单晶衍射，共分离鉴定了14个化合物，结构类型均属于C21多羟基甾醇，其中4个新化合物tenacigenoside A, tenacigenoside B, tenacigenoside C和tenacigenoside D的结构分别表征为3-O-6-deoxy-3-O-methyl-β-D-allopyranosyl-(1→4)-β-D-oleandropyranosyl-17β-tenacigenin B (62), 3-O-2,6- dideoxy-4-O-methyl-D-lyxo-hexopyranosly-11α-O- methylbutyryl-12β-O-acetyl-tenacigenin B (63), 3-O-6-deoxy-3-O-methyl-β-D- allopyranosyl-(1→4)-β-D-oleandropyranosyl-11α-O-tigloyl-tenacigenin C (64)和3-O-6-deoxy-3-O-methyl-β-D-allopyranosyl-(1→4)-β-D-oleandropyranosyl-11α-O-2- methylbutyryl-tenacigenin C (65)。 第5章概述了花椒属植物的化学成分及药理活性研究进展。 This dissertation consists of 5 chapters. The first chapter elaborate the phytochemical investigation of Paeonia lactiflora Pall., and microbial transformation of paeoniforin. The second, third and four chapters elaborate the phytochemical investigation of Saussurea involucrate Kar.et Kir., Zanthoxylum nitidum (Roxb.) DC. and Marsdenia tenacissima (Roxb.) Wight et Arn., respectively. Chapter 5 is a review on chemical constituents and bioactivities of Zanthoxylum species. The part one of chapter 1 focus on the isolation and identification of chemical constituents from P. lactiflora. Fourteen compounds were isolated from the roots of P. lactiflora by repeat column chromatography over normal and reversed phase silica gel. Among them, one is a new compound and the structure was suggested as galloyl-albiflorin by spectral evidence. In addition, two compounds were firstly reported in this plant. The part 2 is about microbial transformation of paeoniforin. Chapters 2, 3 and 4 were isolations and identifications of chemical constituents from S. involucrate, Z. nitidum and M. tenacissima, respectively. From the aerial parts of S. involucrate, 28 compounds including 7 flavonoids and 13 sesquiterpenoids were isolated and identified. Among them, 2 new compounds were characterized as 6α-hydroxycostic acid 6-β-D-glucoside and 11βH-11,13-dihydrodehydro- costuslactone 8α-O-(6'-acetyl)-β-D-glucoside, respectively, by means of spectroscopic analysis. Otherwise, 11 ones were firstly reported from this plant. The third chapter is about the phytochemical investigation of Z. nitidum. Sixteen compounds were isolated and identified. Among them, 2 new benzophenanthridine alkaloids were characterized as 8-acetonyldihydrofagaridine and 1,3-bis(8-dihydronitidinyl)-acetone by spectroscopic analysis. The fourth chapter is about the phytochemical investigation of M. tenacissima. Fourteen compounds were isolated and identified. Among them, 4 new compounds, tenacigenosides A~D, were characterized as 3-O-6-deoxy-3-O-methyl-β-D-allopyranosyl-(1→4)-β-D-oleandropyranosyl-17β- tenacigenin B, 3-O-2,6-dideoxy-4-O-methyl-D-lyxo-hexopyranosly-11α-O-methyl butyryl-12β-O-acetyl-tenacigenin B, 3-O-6-deoxy-3-O-methyl-β-D-allopyranosyl- (1→4)-β-D-oleandropyranosyl-11α-O-tigloyl-tenacigenin C, and 3-O-6-deoxy-3-O- methyl-β-D-allopyranosyl-(1→4)-β-D-oleandropyranosyl-11α-O-2-methylbutyryl- tenacigenin C. Chapter 5 is a review on recent progress in bioactive constituents from plants of Zanthoxylum species.

泸州老窖古酿酒作坊空气微生物分布特征研究

本文主要研究了泸州老窖古酿酒作坊内外环境空气真菌和空气细菌的群落结构和分布特征。结果如下： 作坊内外环境空气微生物浓度差别显著，并随季节变换而变化，春、夏季微生物浓度较高，秋、冬季较低，空气真菌在夏季达到最高，细菌在春季最高。 古作坊内外环境检测到的真菌均为16 属，但优势菌属不同，作坊外的优势菌属为青霉属(Penicillium)、曲霉属(Aspergillus)、无孢菌(non-sporing)、枝孢霉属(Cladosporium)和链格孢属(Alternaria)；而作坊内优势菌属为曲霉属、青霉属、酵母菌(Yeast)、无孢菌，作坊内还含有较高浓度的根霉属（Rhizopus）、毛霉属（Mucor）、短梗霉属（Aureobasidiu），枝孢霉属和链格孢属等，曲霉属、酵母菌、根霉属、毛霉属为古酿酒作坊重要的酿酒真菌，青霉属、链格孢属为酿酒不利菌群。对古作坊内曲霉属进行了初步鉴定，主要是小冠曲霉（A.cristatellus）、米曲霉（A.oryzae）、黑曲霉（A.niger）和白曲霉（A.cadidus）。 空气细菌10 属21 种，作坊内外环境的优势菌属均为芽孢杆菌属（Bacillus）、微球菌属(Micrococcus)、葡萄球菌属(Staphylococcus)、假单胞菌属(Pseudomonad)，其中芽孢杆菌属在作坊内占有绝对的优势，浓度比在40℅以上，是古酿酒作坊重要的酿酒细菌，另外还检测到较高浓度的乳酸杆菌（lactobucillus），这类菌容易使酒味发涩发苦，为酿酒不利菌。 作坊内外环境空气微生物表现出明显的交流现象。作坊内，青霉属、枝孢霉属、链格孢属、葡萄球菌属等杂菌占有一定比例；而在作坊外,芽孢杆菌属、曲霉属、根霉属(Rhizopus)、酵母菌等处于相对较高水平，绿化环境较好的营沟头作坊内的短梗霉属，枝孢霉属和链格孢属等杂菌含量低于什字头和新街子作坊。 The community structure and distribution characteristic of airborne microbes was investigated in ancient brewage workshops of luzhoulaojiao. The results are as follows: The concentration of airborne microbes was different in interior and exterior environment of ancient workshops, and also varied by seasons. microbial concentration was higher in spring and summer, and lower in fall and winner. The highest levels of airborne bacteria was in spring, but the fungal’s in summer. The identified genus of fungi were 16 in interior and exterior environment of the ancient workshops. But the dominant genus were different , The advantage genus in the interior were Aspergillus, Yeasts, Penicillum and Nonsporing and in the exterior were Penicillum, Nonsporing, Cladosporium, Aspergillus and Aureobasidiu. Rhizopus ,mucor, Aureobasidiu, Cladosporium, Alternaria and all also were at a higher level. Among these, Aspergillus, Yeasts, Rhizopus ,mucor are important vintage flora . Penicillum, Alternaria do harm to vintage. Aspergillus of ancient workshops was identified , the preponderant aspergillus species were A.cristatellus, A.oryzae, A.niger and A.cadidus in ancient brewage workshops. 10 genus 21 species bacteria were identified, the advantage genuses among the interior and exterior of the three workshops were bacillus, microccus, Staphylococcus Pseudomonas. Bacillus, which account for beyond 40℅ of the total bacteria concentration in all sampling pots, was the most dominant genus. Lactobacillus was identified at a high level in ancient workshops, it makes spirit taste bitter and astringent. So it is not a kind of good bacterium for vintage. The fungus in the interior and exterior atmosphere characterized intercommunion phenomenon. Obviously, the concentration of profitless fungus such as Penicillum, Cladosporium, Alternaria appeared in the interior, and the fungus such as Bacillus, Aspergillus, Rhizopus and Yeasts in the exterior were at a relatively high level. the harmfull fungus in yinggoutou workshops such as Aureobasidiu, Cladosporium, Alternaria and all were lower than shenzitou and xinjiezi workshops.

Enrichment of the hydrogen-producing microbial community from marine intertidal sludge by different pretreatment methods

To determine the effects of pretreatment on hydrogen production and the hydrogen-producing microbial community, we treated the sludge from the intertidal zone of a bathing beach in Tianjin with four different pretreatment methods, including acid treatment, heat-shock, base treatment as well as freezing and thawing. The results showed that acid pretreatment significantly promoted the hydrogen production by sludge and provided the highest efficiency of hydrogen production among the four methods. The efficiency of the hydrogen production of the acid-pretreated sludge was 0.86 +/- 0.07 mol H-2/mol glucose (mean +/- S.E.), whereas that of the sludge treated with heat-shock, freezing and thawing, base method and control was 0.41 +/- 0.03 mol H-2/mol glucose, 0.17 +/- 0.01 mol H-2/mol glucose, 0.11 +/- 0.01 mol H-2/mol glucose and 0.20 +/- 0.04 mol H-2/mol glucose, respectively. The result of denaturing gradient gel electrophoresis (DGGE) showed that pretreatment methods altered the composition of the microbial community that accounts for hydrogen production. Acid and heat pretreatments were favorable to enrich the dominant hydrogen-producing bacterium, i.e. Clostridium sp., Enterococcus sp. and Bacillus sp., However, besides hydrogen-producing bacteria, much non-hydrogen-producing Lactobacillus sp. was also found in the sludge pretreated with base, freezing and thawing methods. Therefore, based on our results, we concluded that, among the four pretreatment methods using acid, heat-shock, base or freezing and thawing, acid pretreatment was the most effective method for promoting hydrogen production of microbial community. (C) 2009 Professor T. Nejat Veziroglu. Published by Elsevier Ltd. All rights reserved.

Genome-scale analyses of health-promoting bacteria: probiogenomics

The human body is colonized by an enormous population of bacteria (microbiota) that provides the host with coding capacity and metabolic activities. Among the human gut microbiota are health-promoting indigenous species (probiotic bacteria) that are commonly consumed as live dietary supplements. Recent genomics-based studies (probiogenomics) are starting to provide insights into how probiotic bacteria sense and adapt to the gastrointestinal tract environment. In this Review, we discuss the application of probiogenomics in the elucidation of the molecular basis of probiosis using the well-recognized model probiotic bacteria genera Bifidobacterium and Lactobacillus as examples.

Functional genomics of motile commensal intestinal bacteria

Flagella confer upon bacteria the ability to move and are therefore organelles of significant bacteriological importance. The innate immune system has evolved to recognise flagellin, (the major protein component of the bacterial flagellar filament). Flagellate microbes can potentially stimulate the immune systems of mammals, and thus have significant immunomodulatory potential. The flagellum-biogenesis genotype and phenotype of Lactobacillus ruminis, an autochthonous intestinal commensal, was studied. The flagellum-biogenesis genotypes of motile enteric Eubacterium and Roseburia species were also investigated. Flagellin proteins were recovered from these commensal species, their amino-termini were sequenced and the proteins were found to be pro-inflammatory, as assessed by measurement of interleukin-8 (IL-8) secretion from human intestinal epithelial cell lines. For L. ruminis, this IL-8 secretion required signalling through Toll Like Receptor 5. A model for the regulation of flagellum-biogenesis in L. ruminis was inferred from transcriptomics data and bioinformatics analyses. Motility gene expression in this species may be under the control of a novel regulator, LRC_15730. Potential promoters for genes encoding flagellin proteins in the Eubacterium and Roseburia genomes analysed were inferred in silico. Relative abundances of the target Eubacterium and Roseburia species in the intestinal microbiota of 25 elderly individuals were determined. These species were found to be variably abundant in these individuals. Motility genes from these species were variably detected in the shotgun metagenome databases generated by the ELDERMET project. This suggested that a greater depth of sequencing, or improved evenness of sequencing, would be required to capture the full diversity of microbial functions for specific target or low abundance species in microbial communities by metagenomics. In summary, this thesis used a functional genomics approach to describe flagellum-mediated motility in selected Gram-positive commensal bacteria. The regulation of flagellum biosynthesis in these species, and the consequences of flagella expression from a host-interaction perspective were also considered.

Evaluation of microbial adjuncts and their effect on the ripening of cheddar cheese

A bacteriocin-producing strain of Lactobacillus paracasei DPC 4715 was used as an adjunct culture in Cheddar cheese in order to control the growth of “wild” nonstarter lactic acid bacteria. No suppression of growth of the indicator strain was observed in the experimental cheese. The bacteriocin produced by Lactobacillus paracasei DPC 4715 was sensitive to chymosin and cathepsin D and it may have been cleaved by the rennet used for the cheese manufactured or by indigenous milk proteases. A series of studies were performed using various microbial adjuncts to influence cheese ripening. Microbacterium casei DPC 5281, Corynebacterium casei DPC 5293 and Corynebacterium variabile DPC 5305 were added to the cheesemilk at level of 109 cfu/ml resulting in a final concentration of 108 cfu/g in Cheddar cheese. The strains significantly increased the level of pH 4.6-soluble nitrogen, total free amino acids after 60 and 180 d of ripening and some individual free amino acids after 180 d. Yarrowia lipolytica DPC 6266, Yarrowia lipolytica DPC 6268 and Candida intermedia DPC 6271 were used to accelerate the ripening of Cheddar cheese. Strains were grown in YG broth to a final concentration of 107 cfu/ml, microfluidized, freeze-dried and added to the curd during salting at level of 2% w/w. The yeasts positively affected the primary, secondary proteolysis and lipolysis of cheeses and had aminopeptidase, dipeptidase, esterase and 5’ phosphodiestere activities that contributed to accelerate the ripening and improve the flavor of cheese. Hafia alvei was added to Cheddar cheesemilk at levels of 107 cfu/ml and 108 cfu/ml and its contribution during ripening was evaluated. The strain significantly increased the level of pH 4.6-soluble nitrogen, total free amino-acids, and some individual free amino-acids of Cheddar cheese, whereas no differences in the urea-polyacrylamide gel electrophoresis (urea-PAGE) electrophoretograms of the cheeses were detected. Hafia alvei also significantly increased the level of some biogenic amines. A low-fat Cheddar cheese was made with Bifidobacterium animalis subsp. lactis, strain BB-12® at level of 108 cfu/ml, as a probiotic adjunct culture and Hi-Maize® 260 (resistant high amylose maize starch) at level of 2% and 4% w/v, as a prebiotic fiber which also played the role of fat replacer. Bifidobacterium BB-12 decreased by 1 log cycle after 60 d of ripening and remained steady at level of ~107 cfu/g during ripening. The Young’s modulus also increased proportionally with increasing levels of Hi-maize. Hencky strain at fracture decreased over ripening and increased with increasing in fat replacer. A cheese based medium (CBM) was developed with the purpose of mimicking the cheese environment at an early ripening stage. The strains grown in CBM showed aminopeptidase activity against Gly-, Arg-, Pro- and Phe-p-nitroanalide, whereas, when grown in MRS they were active against all the substrates tested. Both Lb. danicus strains grown in MRS and in CBM had aminotransferase activity towards aromatic amino acids (Phe and Trp) and also branched-chain amino acids (Leu and Val). Esterase activity was expressed against p-nitrophenyl-acetate (C2), pnitrophenyl- butyrate (C4) and p-nitrophenyl-palmitate (C16) and was significantly higher in CBM than in MRS.

Characterisation of the microbiota of traditional fermented beverages and screening these and other populations for novel antimicrobial producers and gene clusters

To screen for novel ribosomally synthesised antimicrobials, in-silico genome mining was performed on all publically available fully sequenced bacterial genomes. 49 novel type 1 lantibiotic clusters were identified from a number of species, genera and phyla not usually associated with lantibiotic production, and indicates high prevalence. A crucial step towards the commercialisation of fermented beverages is the characterisation of the microbial content. To achieve this goal, we applied next-generation sequencing techniques to analyse the bacterial and yeast populations of the organic, symbiotically-fermented beverages kefir, water kefir and kombucha. A number of minor components were revealed, many of which had not previously been associated with these beverages. The dominant microorganism in each of the water kefir grains and fermentates was Zymomonas, an ethanol-producing bacterium that had not previously been detected on such a scale. These studies represent the most accurate description of these populations to date, and should aid in future starter design and in determining which species are responsible for specific attributes of the beverages. Finally, high-throughput robotics was applied to screen for the presence of antimicrobial producers associated with these beverages. This revealed a low frequency of bacteriocin production amongst the bacterial isolates, with only lactococcins A, B and LcnN of lactococcin M being identified. However, a proteinaceous antimicrobial produced by the yeast Dekkera bruxellensis, isolated from kombucha, was found to be active against Lactobacillus bulgaricus. This peptide was patially purified.

Assessment of the immunomodulatory effects of raw/farm milk and probiotic bacteria

The overall aims of this study were to investigate the differences between raw/farm milk and pasteurised milk with respect to potential immune modifying effects following consumption and investigate the bacterial composition of raw milk compared to pasteurised milk. Furthermore, in this thesis, panels of potential probiotic bacteria from the Bifidobacterium and Lactobacillus genera were investigated. The overall bacterial composition of raw milk was compared with pasteurised milk using samples obtained from commercial milk producers around Ireland using next generation sequencing technology (454 pyrosequencing). Here the presence of previously unrecognised and diverse bacterial populations in unpasteurised cow’s milk was identified. Futhermore the bacterial content of pasteurised milk was found to be more diverse than previously thought. The global response of the adenocarcinoma cell line HT-29 to raw milk and pasteurised milk exposures were also characterised using whole genome microarray technology. Over one thousand differentially expressed genes were identified which were found to be involved in a plethora of cellular functions. Interestingly a reduction in immune related activity (e.g. Major histocompatability complex class II signalling and T and B cell proliferation) was identified in cells exposed to pasteurised milk compared with raw milk exposures. Further studies comparing human cell response to raw versus pasteurised milk was performed using peripheral blood mononuclear cells (PBMC) from healthy donors. A reduction in CD14 was identified following raw milk exposures compared with pasteurised milk and the pattern of cytokine production may indicate that gram positive bacteria in the raw milk were contributing to the differences in the cellular response to raw versus pasteurised milk. Panels of potentially probiotic bacteria (comprising of lactobacilli and bifidobacteria) were further assessed for immunomodulatory capabilities using cell culture based models. Gene expression and cytokine production were used to evaluate stimulated and unstimulated (LPS) cellular responses as well as interaction mechanisms