Background: Human breast milk is a primary source of bacteria for the infant gut. This study aims to develop bacterial DNA extraction methods to determine whether a relationship exists between breast milk and infant gut microbiota with respect to obesogenic bacteria. Study design: Total of 16 breast milk and respective infants fecal samples were collected to analyze. Methods: Fecal and breast milk bacterial DNA were analyzed to identify the strains up to genus level. Results: Fermicutes was high in breast milk from overweight women and their infant’s gut microbiota but Bacteroidetes increased only in infants’ gut microbiota of overweight women. However, there were no significant relationships between normal-weight and overweight women’ breast milk and between their respective infants’ gut microbiota. Conclusion: This pilot study has shown means that obesogenic bacteria may be introduced into infant gut through the breast milk. However, we were impossible to answer whole concept statistically. / October 2015

Le microbiote intestinal humain a été fortement corrélé avec la santé humaine et les maladies et a montré un potentiel dans les développements thérapeutiques. La métagénomique a déjà montré qu'elle était capable de générer beaucoup de données, dont certaines sont dénuées de sens et constituaient la "matière noire". Alors culturomics a été développée pour compléter la métagénomique en ciblant des espèces bactériennes précédemment non cultivées. En utilisant la culturomics, nous avons décrit le microbiote intestinal humain des Pygmées et réussi à isoler un nombre significatif d'espèces bactériennes parmi lesquelles 38 étaient de nouvelles espèces. En comparant les résultats métagénomiques aux données culturomics, on constate que seulement 26% des espèces isolées ont été récupérées par métagénomique et que jusqu'à 59% des Operational taxonomic units détectées correspondaient à de nouvelles espèces bactériennes isolées par culturomique dans cette étude ou dans les précédentes. / The human gut microbiota has been correlated in general health and diseases. Thus its description became mandatory to better understand its role and therapeutic potential. However, metagenomics has previously showed to be able to generate a lot of data, of which some are meaningless and constituted the “Dark matter”. Thus, culturomics was developed to complement metagenomics by targeting previously uncultured bacterial species. Using culturomics, we described the human gut microbiota of Pygmy people and succeeded in isolating a significant number of bacterial species out of which 38 were new species. Comparing metagenomics results to culturomics data, we see that only 26% of the isolated species were recovered by metagenomics and that up to 59% of the Operational taxonomic units detected corresponded to new bacterial species isolated by culturomics either in this study or in previous ones.

SOUSA, R. B. R. A. Avaliação da microbiota de dentes decíduos necrosados utilizando a reação da polimerase em cadeia. 2014. 71 f. Tese (Doutorado em Odontologia) - Faculdade de Farmácia, Odontologia e Enfermagem, Universidade Federal Do Ceará, Fortaleza, 2014. / Submitted by PPGO UFC (ufcppgo@gmail.com) on 2017-10-30T12:56:37Z No. of bitstreams: 1 2014_tese_rbrasousa.pdf: 1491594 bytes, checksum: f79f355313155d91e89d5fc5556db7a9 (MD5) / Approved for entry into archive by Maria Carvalho (lolitaprado@ufc.br) on 2017-10-30T15:12:25Z (GMT) No. of bitstreams: 1 2014_tese_rbrasousa.pdf: 1491594 bytes, checksum: f79f355313155d91e89d5fc5556db7a9 (MD5) / Made available in DSpace on 2017-10-30T15:12:25Z (GMT). No. of bitstreams: 1 2014_tese_rbrasousa.pdf: 1491594 bytes, checksum: f79f355313155d91e89d5fc5556db7a9 (MD5) Previous issue date: 2014-01-30 / This study aims to evaluate the microbiota of necrotic primary teeth through the technique of polymerase chain reaction (PCR), whereas primary endodontic infections, comparing the microbiota of necrotic caries and dental trauma. This study also evaluated the bacterial viability in three transport medias (Reduced to Fluid Transport , Tris - EDTA and Viability Medium Göteborg anaerobically III), simulating the conditions of carriage of the endodontic microbiota from the clinic to the laboratory, considering the time elapsed between the collection and processing. This clinical study involved 43 children from two to nine years of age, who sought care at the Pediatric Dentistry Clinic of Federal University of Ceará. They might present necrosis in primary teeth. Healthy patients formed a sample with 47 necrotic channels. Were included teeth with at least two-thirds of root and able to be restored. Patients who were making use of antibiotic therapy or those who did the last three months before the start of the study, and those with inappropriate behavior for the research were excluded. For microbiological collection after infiltration anesthesia and absolute isolation, disinfection of the operative field to open the coronary cavity was performed. The collection was made from the introduction of three absorbent paper cones in the wider channel for one minute each. The storage and transport of these listed microorganisms were performed using the VMGA III selected from a laboratory experiment. In this experiment we evaluated the feasibility of a strain of Porphiromonas gingivalis , stored in fluid Reduced to transport (RTF), TE and Viability Medium Göteborg anaerobically, VMGA III. In a laboratory under anaerobic conditions, were inoculated in eppendorffs® for periods of one hour, two and four hours. Then inoculated in Petri dishes in these different times, with Fastidious Anaerobe Agar (FAA) enriched. Last 72 hours counting of bacterial colonies was performed. This evaluation showed that the VMGAIII was the means of transportation that allowed an upper storage to four hours of processing Porphiromonas gingivalis in culture when compared with the RTF and the TE. Thus, microbiological samples were introduced in eppendorffs® with VMGA III for further processing of the samples. DNA of bacterial samples for subsequent implementation of the technique of polymerase chain reaction (PCR) followed by eletrofores, through which was extracted identified the presence of the following bacteria: Fusobacterium nucleatum, Parvimona microns, Porphyromonas endodontalis, Porphyromonas gingivalis, Dislister pneumonsites, alocis Filifactor, Treponema denticola, Tannerella forsythia, Enterococcus faecalis, Streptococcus mitis, Streptococcus mutans, Streptococcus sanguis, Prevotela nigrescens, Actinomyces naeslundi and Enterococcus faecalis. Then identify a microbial organisms comprising predominantly anaerobic Gram negative for the test. The most common were: Prevotella nigrescens (17.92%), Parvimona micra (16.24%) and Actinomyces naeslundi (12.88 %). The less frequent were Filifactor alocis (1.12 %), Streptococcus mitis (1.12%), Enterococcus faecalis (0.56 %) and Streptococcus mutans (0.56 %). Whereas the cause of pulp necrosis, caries was associated with Parvimona micra (p = 0.036), and trauma, Streptococcus mitis (0.022). Thus it is concluded from clinical samples of necrotic primary teeth, the methodology involved in the bacterial collection and storage process as the means of transport, can influence our findings. The sample had a higher frequency of the Gram negative anaerobic bacteria test. The cause of necrosis may influence the establishment of the microbiota, where the decay is associated with positive and negative anaerobic bacteria to the Gram test, as Parvimona micra and Treponema denticola, and were associated with the trauma and positive facultative bacteria to the Gram test such as forsythia Tanarella, Streptococcus mitis and Streptococcus sanguis. / Este estudo tem por objetivo avaliar a microbiota de dentes decíduos necrosados através da técnica da Reação em cadeia da polimerase (PCR), considerando as infecções endodônticas primárias de dentes decíduos, comparando a microbiota dos necrosados por cárie e traumatismos dentários. Este trabalho também avaliou a viabilidade bacteriana em três meios de transporte (Fluido Reduzido para Transporte, Tris- EDTA e Viability Medium Göteborg Anaerobically III), simulando as condições de transporte da microbiota endodôntica da clínica ao laboratório, considerando o tempo decorrido entre a coleta e o processamento. Participaram deste estudo clínico 43 crianças, de dois a nove anos de idade, que buscaram atendimento na Clínica de Odontopediatria da Universidade Federal do Ceará por apresentarem necrose em dentes decíduos. Foram incluídos 47 canais necrosados de pacientes normossistênicos com no mínimo de dois terços de raíz, possíveis de serem restaurados. Foram excluídos pacientes que estavam fazendo uso de antibiótico terapia ou aqueles que o fizeram nos últimos três meses, previamente ao início da pesquisa, e os que apresentavam comportamento inadequado para a realização da pesquisa. Para a coleta microbiológica, após a anestesia infiltrativa e isolamento absoluto, foi realizada a desinfecção do campo operatório para abertura da cavidade coronária. A coleta foi feita a partir da introdução de três cones de papel absorvente no canal mais amplo, por um minuto cada um. O armazenamento e transporte, destes microrganismos coletados, foram realizados utilizando o VMGA III, selecionado a partir de um experimento laboratorial. Neste experimento avaliou-se a viabilidade de uma cepa de Porphiromonas gingivalis, armazenadas em Flúido Reduzido para transporte (RTF), TE e Viability Medium Göteborg Anaerobically, VMGA III. Em um laboratório, sob condições de anaerobiose, foram inoculados em eppendorffs® por períodos de uma hora, duas e quatro horas. Em seguida, inoculadas em placas de Petri nestes diferentes tempos, com Fastidious Anaerobe Agar (FAA), enriquecidas. Passada 72 horas foi realizada a contagem das colônias bacterianas. Esta avaliação demonstrou que o VMGAIII foi o meio de transporte que permitiu um armazenamento superior a quatro horas, das Porphiromonas gingivalis para processamento em cultura, quando comparado com o RTF e o TE. Assim, as coletas microbiológicas foram introduzidas em eppendorffs® com VMGA III para posterior processamento das amostras. Das amostras foram extraídos o DNA bacteriano para posterior realização da técnica da reação em cadeia da polimerase (PCR) seguida da eletrofores, através da qual se identificaram a presença das seguintes bactérias: Fusobacterium nucleatum, Parvimona micra, Porphyromonas endodontalis, Porphyromonas gingivalis, Dislister pneumonsites, Filifactor alocis, Treponema denticola, Tanerella forsythia, Enterococcus faecalis, Streptococcus mitis, Streptococcus mutans, Streptococcus sanguis, Prevotela nigrescens, Actinomyces naeslundi e o Enterococcus faecalis. Foi então identificada uma microbiota composta de microrganismos, predominantemente, anaeróbios negativos ao teste de Gram. Os mais frequentes foram: Prevotella nigrescens (17,92%), Parvimona micra (16,24%) e Actinomyces naeslundi (12,88%). O menos frequentes foram: Filifactor alocis (1,12%), Streptococcus mitis (1,12%), Enterococcus faecalis (0,56%) e Streptococcus mutans (0,56%). Considerando a causa da necrose pulpar, a cárie associou-se à Parvimona micra (p=0,036) e, ao trauma, o Streptococcus mitis (0,022). Desta forma conclui-se, a partir de coletas clínicas de dentes decíduos necrosados, que a metodologia envolvida no processo de coleta e armazenamento bacteriano, como o meio de transporte, pode influenciar em nossos achados. A amostra teve uma maior frequência de bactérias 9 anaeróbias, negativas ao teste de Gram. A causa da necrose pode influenciar na constituição da microbiota, onde a cárie associa-se a bactérias anaeróbias positivas e negativas ao teste de Gram, como Parvimona micra e Treponema denticola, e associam-se ao trauma as bactérias facultativas e positivas ao teste de Gram, como a Tanarella forsythia, Streptococcus sanguis e Streptococcus mitis.

It seemed desirable to investigate more fully the effect of hexadecanol on the microbial population of a reservoir. It was the purpose of this investigation to determine the effect of hexadecanol on the micro-biota of Lake Hefner, to ascertain which organisms were stimulated by hexadecanol both in the laboratory and the reservoir, and to investigate the degradation of hexadecanol by microorganisms selected from Lake Hefner.

Depression and anxiety are etiologically heterogeneous disorders and their pathophysiology remains largely unknown. Gut microbiota has been shown to modulate brain function, behavior, and immune responses, and it has also been proposed to play a role in the pathophysiology of depression and anxiety. Our study aimed to investigate whether microbiota from patients with Generalized Anxiety Disorder (GAD) can induce anxiety and depressive-like behaviour in germ-free mice and whether this is accompanied by changes in immune markers and brain activity. Germ-free NIH Swiss mice (n=27) were colonized with microbiota from either a GAD patient (n=13) with severe anxiety and comorbid depression or an age and sex-matched healthy control (HC) (n=14). Six mice from each group were treated with infliximab for three weeks (5mg/kg/week) starting at week 1 post-colonization. Microbiota profiles were assessed via 16S rRNA based Illumina. Three weeks post-colonization, all mice underwent six standard psychometric tests, including the open field, digging, marble-burying, and tail-suspension test. Cecal -defensin-3 and serum kynurenine/tryptophan were measured via ELISA. BDNF expression was assessed by immunofluorescence, and gene expression by using Nanostring gene assay. Fecal -defensin levels were higher in GAD patients than in healthy controls. Similarly, -defensin levels were higher in GAD-colonized mice than in HC-colonized mice. GAD and HC-colonized mice had a unique and distinct microbiota, similar to that of their respective human donors. GAD-colonized mice exhibited anxiety and depressive-like behavior compared to HC- colonized mice, as assessed by the open field, digging, marble burying and tail suspension tests. BDNF expression was decreased in the hippocampus but increased in the amygdala of GAD-colonized mice. GAD-colonized mice also had a greater kynurenine/tryptophan ratio than HC-colonized mice. GAD and HC infliximab-treated mice showed no differences in behavior, central BDNF expression or kynurenine/tryptophan levels. Our results suggest that GAD microbiota has the ability to induce anxiety and depressive-like behavior and alter brain BDNF expression in a murine host. These changes are accompanied by the activation of the innate immune system and seem to be TNF- dependent. / Thesis / Master of Science (MSc)

Currently, the leading route of new HIV-1 infection is via heterosexual transmission, in which women are disproportionately burdened. One key factor associated with a fourfold increased risk of HIV-1 acquisition is a dysbiotic vaginal microbiota (VMB). A dysbiotic VMB is characterized by a diverse mix of anaerobic species without any appreciable amounts of beneficial Lactobacillus species. Our understanding of the species-specific manner by which vaginal bacteria interact with one another and with the host to induce susceptibility remains incompletely understood. With this, this study was designed to elucidate the interactions between common vaginal bacteria and host vaginal epithelial cells. The phenotypic and metabolic characteristics of these bacteria were also examined to provide a deeper understanding about the conditions in which each species may be able to survive and thrive. Common vaginal bacteria analyzed included dysbiosis associated species Gardnerella vaginalis and Prevotella bivia, as well as Lactobacillus species L. crispatus and L. iners. The presence of P. bivia, G. vaginalis and L. iners cocultured with vaginal epithelial cells in vitro resulted in reduced viability of vaginal epithelial cells, reduced barrier integrity and the production of pro-inflammatory cytokines. Conversely, the presence of L. crispatus did not, and was able to negate these adverse effects when placed in a dual species coculture with either of the other species. Additionally, we found that L. crispatus was the only one of these four species to produce hydrogen peroxide, and its supernatant was capable of inhibiting the growth of G. vaginalis and P. bivia. While we found that all four vaginal species could use glycogen for their growth, L. crispatus was able to use the widest range of carbohydrates tested. This translated to L. crispatus significantly outcompeting the other three bacterial species when cocultured in bacterial broth media with various carbohydrates tested. Our data provides insight into the species-specific nature by which common vaginal bacteria may interact with vaginal epithelial cells to increase host susceptibility to infection through cytotoxicity, decreased barrier function, and inflammation. We importantly observed the ability of L. crispatus to largely mitigate these effects and our phenotypic characterization place L. crispatus as the species most adept to provide protection in the FRT. Together, this work contributes to a better understanding of the interactions that govern the dynamics of the VMB and can be built upon to develop more rationale therapeutic or prophylactic interventions to improve the reproductive health of many vulnerable women. / Thesis / Master of Science (MSc)

La prevalencia de la obesidad es cada vez mayor y especialmente en niños y adolescentes. En el desarrollo de la obesidad interviene la dieta, factores genéticos, endócrinos, psicológicos y ambientales. El primer objetivo específico fue determinar la influencia de una intervención para el tratamiento de la obesidad sobre la microbiota intestinal de adolescentes obesos y con sobrepeso. Mediante las técnicas de la reacción en cadena de la polimerasa a tiempo real (q-PCR) y de hibridación con fluorescencia in situ (FISH) se cuantificaron los principales grupos bacterianos del tracto intestinal. Los adolescentes que experimentaron mayor perdida de peso, presentaron mayor cantidad de bacterias de los grupos Bacteroides fragilis, Clostridium leptum, Bifidobacterium catenulatum, Lactobacillus, y menor de los grupos y especies de Bifidobacterium, Lactobacillus, Clostridium coccoides, B. breve y B.bifidum, antes y después de la intervención con respecto al grupo de menor pérdida de peso. El segundo objetivo fue evaluar la microbiota intestinal de mujeres embarazadas con sobrepeso debido a que su microbiota influye en la microbiota del hijo. Con el análisis de la microbiota por qPCR y de parámetros bioquímicos se obtuvo que las mujeres con sobrepeso presentaron menor cantidad de Bifidobacterias y Bacteroides, y mayor cantidad de Staphylococcus, Enterobacterias y E.coli. que en el grupo normopeso. El número de Staphylococcus presentó una correlación positiva con el colesterol total, Bacteroides positiva con el colesterol HDL y con el ácido fólico, y negativa con los triglicéridos, el número de Bifidobacteriums presentó una correlación positiva con el ácido fólico, y los de Enterobacteriaceae y E.coli presentaron una correlación positiva con ferritina y negativa con transferrina. Por todo ello se puede decir, que la microbiota intestinal esta relacionada con el peso corporal, con la ganancia de peso y los parámetros metabólicos durante el embarazo, lo cual puede ser / Santacruz López, YA. (2012). Influencia de la microbiota intestinal en la obesidad [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/16927

Until recently it was assumed that the healthy mammalian lung did not harbour a microbiota, unlike other body sites. However, through the use of sequencing based technologies this has been shown to not be the case. Low biomass communities of microbes can be identified in the healthy lung and the lung microbiota in various diseases states has been shown to differ form these 'healthy' communities. The sheep respiratory microbiota is of interest from both an animal health perspective and due to the potential use of the sheep as a large animal model for studying the lung microbiota. In this thesis I seek to characterise the composition and variability of the sheep lung microbiota; the differences between the sheep upper and lower respiratory tract bacterial communities and to assess whether exhaled breath condensate collection can be used as a non-invasive lung microbiota sampling method. To study the bacterial communities present in samples I have used 16S rRNA gene sequencing and analysis. In Chapter 3 I examine the inter-individual and spatial variability present within the sheep lung microbiota. Protected specimen brushings were collected from three lung segments in six animals at three time-points. In a separate sheep a greater number of brushings was taken (n=16) in order to examine the amount of variability over a smaller spatial scale. I find that there can be large differences between the bacterial communities isolated from different locations within the lung, even over short distances. Samples also cluster by the sheep from which they were taken, indicating a host specific influence on the lung microbiota. In Chapter 4 I compare whole lung washes and oropharyngeal swabs from 40 lambs in order to examine the differences between the upper and lower respiratory tract microbiotas. I find that oropharyngeal swabs separate into rumen-like or upper respiratory tract-like bacterial communities. Despite the fact that in humans the upper and lower respiratory microbiotas have been shown to have similar compositions, the sheep lung microbiota samples in this study do not resemble either oropharyngeal samples or reagent only controls. In my first two results chapters, lung sampling methods were used which involved either anaesthesia combined with a bronchoscopic procedure (Chapter 3) or samples being taken from dead animals (Chapter 4). In Chapter 5 I assess whether there is a less invasive way of taking lung microbiota samples from a living individual, both to minimise the procedural stress on animals used as models and to increase the pool of potential volunteers for human lung microbiota studies. I compared samples taken via protected specimen brushings to samples taken via exhaled breath condensate collection, a less invasive sampling technique. I find that condensate samples contain less bacterial DNA and different bacteria than brushing samples, indicating that it is unlikely they could be used as a replacement for invasive sampling methods. In my final results chapter I compare the results across Chapters 3, 4 and 5 to identify bacteria which occur consistently in the sheep lung and could therefore potentially be described as core lung microbiota members. In conclusion, while I have found that there are large differences between the sheep lung microbiota and that which has previously been described in humans, the sheep can still be of use as a model in studies where these differences would not have a significant impact, such as in Chapter 5 of this thesis. I have identified several bacterial members of the core sheep lung microbiota which in future it would be interesting to better characterise and to assess whether they play a role in sheep health.

Orientador: Luis Guillermo Bahamondes / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciencias Medicas / Made available in DSpace on 2018-08-13T11:58:54Z (GMT). No. of bitstreams: 1 Brolazo_ElianeMelo_D.pdf: 580434 bytes, checksum: 24b8356368950df00b8a139f02ad0fef (MD5) Previous issue date: 2009 / Resumo: A microflora vaginal de mulheres saudáveis em idade reprodutiva é composta por uma variedade de bactérias aeróbias e anaeróbias, mas as espécies dominantes são os lactobacilos (bacilos de Döderlein), que exercem significante influência sobre a microbiota local. Além de restringir o crescimento de patógenos competindo pelo espaço e nutrientes, os lactobacilos produzem substâncias antimicrobianas como ácidos orgânicos, peróxido de hidrogênio (H2O2) e bacteriocinas. Esta atividade antagonista é importante na proteção contra várias infecções, principalmente a vaginose bacteriana (VB). Objetivos: Identificar as espécies de lactobacilos isolados do conteúdo vaginal de mulheres saudáveis e assintomáticas e determinar as espécies mais prevalentes e caracterizá-las quanto à produção de ácido láctico, peróxido de hidrogênio (H2O2) e sua capacidade de adesão às células do epitélio vaginal. Métodos: Foram isoladas 83 linhagens de lactobacilos de amostras de conteúdo vaginal de 135 mulheres, sem queixa de corrimento e com diagnóstico laboratorial negativo para infecções vaginais, acompanhadas no ambulatório de Planejamento Familiar da Faculdade de Ciências Médicas - UNICAMP. As linhagens isoladas foram identificadas por PCR multiplex e, quando necessário, submetidas ao sequenciamento do gene RNAr 16S. Foram então avaliadas quanto à produção de ácido láctico, de H2O2, bacteriocinas e a capacidade de adesão às células epiteliais. Resultados: A espécie predominante foi L. crispatus presente em 30,1% das mulheres, seguida de L. jensenii (26,5%), L. gasseri (22,9%) e L. vaginalis (8,4%). As outras espécies isoladas foram L. delbrueckii, L fermentum, L reuteri e L rhamnosus, com duas linhagens cada uma, e L. mucosae e L. salivarius com uma cepa cada. Das 83 linhagens de lactobacilos analisadas, apenas 20 não apresentaram produção de H2O2 detectável pela técnica de cultivo em agar MRS com TMB. Foram selecionadas 37 linhagens para teste de adesão às células epiteliais. Destas, 12 tiveram adesão entre 50% e 69% e 10 igual ou maior a 70%. As linhagens restantes apresentaram pouca capacidade de aderir às células epiteliais. Nenhuma das linhagens testadas produziu bacteriocinas. Conclusões: As espécies de lactobacilos mais prevalentes em mulheres sem vulvovaginites, isoladas em meio de cultura seletivo e identificadas por métodos moleculares, foram L. crispatus, L. jensenii e L. gasseri. Dentre as linhagens analisadas, além de mais frequentes, estas também foram as que atingiram menores valores de pH em meio de cultura e apresentaram melhor produção de H2O2 / Abstract: The vaginal microflora of healthy women is composed of a large variety of aerobic and anaerobic bacteria. The dominant species is a group of lactobacilli (Doderlein's bacillus), which has a significant effect on vaginal microbiota, curtailing the growth of pathogens competing for space and nutrients. The lactobacilli specie produces various antimicrobial substances that include organic acids, hydrogen peroxide (H202) and bacteriocins. Objectives: Identify the prevalence of the different species of lactobacilli isolated from the vagina of healthy asymptomatic women, determine the most prevalent species and characterize them regarding the production of lactic acid, hydrogen peroxide (H2O2) and their capacity to adhere to vaginal epithelial cells. Methods: Eightythree strains of lactobacilli were isolated from the vagina of 135 women, with no complaints of vaginal discharge and negative laboratory diagnosis for vaginal infection, who were being followed up at the Family Planning clinic of the Medical school, Unicamp. The isolates were identified using multiplex polymerase chain reaction (PCR) and, when necessary, 16S rRNA gene sequencing. They were then evaluated with regards to the production of lactic acid, H2O2, bacteriocins, and their capacity to adhere to epithelial cells. Results: The predominant species found were L. crispatus (in 30.1% of the women), followed by L. jensenii (26.5%), L. gasseri (22.9%) and L. vaginalis (8.4%). The other species isolated were L. delbrueckii, L fermentum, L reuteri and L rhamnosus (two strains) and L. mucosae and L. salivarius (one strain). Only 20 out of 83 lactobacilli analyzed using the plate technique (in MRS agar with TMB) were found to be non-producers of H2O2. Thirty-seven lineages were selected and tested for their capacity to adhere to epithelial cells. Of these, 12 had an adhesion between 50% and 69% and 10 equal or superior to 70%. The remainder had little capacity to adhere to epithelial cells. None of the strains tested produced bacteriocins. Conclusions: L. crispatus, L. jensenii and L. gasseri were the most prevalent species isolated in selective culture media and identified through molecular techniques. Besides their frequencies, they also presented best H2O2 production and lowest pH in culture media / Doutorado / Ciencias Biomedicas / Doutor em Tocoginecologia

The collection of microbes that inhabits the human gastrointestinal tract is known as intestinal microbiota, and an enormous body of work has shown that their activities contribute to health and disease. Ulcerative colitis (UC), which is a type of inflammatory bowel disease, is considered to arise due to a disruption in the balance between the immune system and microbiota. However, there is little consensus on the mechanism of action and microbes involved in the disease manifestation. In this work, I applied culture-enriched metagenomics (CEMG) to characterize the dynamics of gut microbiota in healthy individuals and UC patients. I showed that CEMG provides a higher resolution to study these microbial communities, and we used this approach to understand microbial colonization after fecal microbiota transplantation (FMT) therapy in UC patient. I showed that sequencing approaches alone did not reveal consistent engraftment across FMT responders. Using CEMG and a collection of bacterial whole-genome sequences, I showed patient-specific microbial strain transfer and a signature of commonly engrafted genes only in patients who responded to FMT. In this work, I also investigated the dynamics of a highly abundant bacteriophage, crAssphage, in an FMT donor and implemented a new method to detect bacteriophage engraftment post-FMT using SNP analysis. Finally, it has been suggested that antibiotic treatment before FMT may increase the efficacy of FMT. However, in this work, I show that while antibiotics alter the microbiome, there was no difference in the composition of the microbiome of antibiotic vs placebo group post-FMT. This is consistent with the randomized controlled trial results that shows pretreatment with antibiotics does not improve FMT outcome. Together, this work demonstrate the importance of in-depth microbiome analysis applied to culture-dependent and -independent sequencing to characterize microbial changes post-FMT. / Dissertation / Doctor of Philosophy (PhD) / Many bacteria reside in the human gut, and they are essential in our health and in disease. It is evident that these bacteria are associated with inflammatory bowel disease, but we do not yet know how and what bacteria are involved in this disease. In this work, I describe a method to study these bacteria from stool that relies on growing them and investigating their DNA. I showed that our approach helped us recover a greater diversity of these bacteria and their genetic content in healthy individuals and patients with inflammatory bowel disease compared to methods that use only DNA based approaches. Using this method, we could better understand why some patients responded to a treatment consisting of transferring stool content from healthy donor to patient. I also investigated a group of viruses that infect bacteria and implemented a new computational method based on DNA sequencing to test whether these viruses transfer to the patient after receiving the fecal therapy. We also found that antibiotic treatment before fecal therapy in patients with inflammatory bowel disease does not improve the patient’s recovery.