Since the invention of high-throughput sequencing, the majority of experiments studying bacterial microbiomes have relied on the PCR amplification of all or part of the gene for the 16S rRNA subunit, which serves as a biomarker for identifying and quantifying the various taxa present in a microbiomic sample. Several computational methods exist for analyzing 16S amplicon based metagenomics, but the most commonly used bioinformatics tools are unable to produce quality genus-level or species-level taxonomic calls and may underestimate the degree to which such calls are possible. In this thesis, I have used 16S sequencing data from mock bacterial communities to evaluate the sensitivity and specificity of several bioinformatics pipelines and genomic reference libraries used for microbiome analyses, with a focus on measuring the accuracy of species-level taxonomic assignments of 16S amplicon reads. With the efficacy of these tools established, I then applied them in the analysis of data from two studies into human microbiomes. I evaluated the metagenomics analysis tools Qiime 2, Mothur, PathoScope 2, and Kraken 2, in conjunction with reference libraries from GreenGenes, Silva, Kraken, and RefSeq, using publicly available mock community data from several sources, comprising 137 samples with varied species richness and evenness, several different amplified regions within the 16S gene, and both DNA spike-ins and cDNA from collections of plated cells. PathoScope 2 and Kraken 2, both tools designed for whole genome metagenomics, outperformed Qiime 2 and Mothur, which are theoretically specialized in 16S analyses. I used PathoScope 2 to analyze longitudinal 16S data from infants in Zambia, exploring the maturation of nasopharyngeal microbiomes in healthy infants, establishing a range of typical healthy taxonomic profiles, and identifying dysbiotic patterns which are associated with the development of severe lower respiratory tract infections in early childhood. I used Qiime 2 to analyze 16S data from human subjects in a controlled dietary intervention study with a focus on dietary carbohydrate quality. I correlated alterations in the gut microbiome with various cardiometabolic risk factors, and identified increases in some butyrate-producing bacteria in response to complex carbohydrates. I also constructed a metatranscriptomics pipeline to analyze paired rRNA-depleted RNAseq data. My evaluation of 16S methods should improve 16S amplicon analyses by advocating for the modernization of computational tools; my analysis of infant nasopharyngeal microbiomes lays groundwork for future predictive models for childhood disease and longitudinal microbiomic studies; my analysis of gut microbes illuminates the mechanisms through which bacteria can mediate cardiovascular health. Taken together, the research I present here represents a significant contribution to 16S metagenomics and its application to epidemiology, clinical nutritional science.

Yes / Background. Bacterial bloodstream infection (bBSI) is one of the leading causes of death in critically ill patients and accurate diagnosis is therefore crucial. We here report a 16S metagenomics approach for diagnosing and understanding bBSI. Methodology/Principal Findings. The proof-of-concept was delivered in 75 children (median age 15 months) with severe febrile illness in Burkina Faso. Standard blood culture and malaria testing were conducted at the time of hospital admission. 16S metagenomics testing was done retrospectively and in duplicate on the blood of all patients. Total DNA was extracted from the blood and the V3–V4 regions of the bacterial 16S rRNA genes were amplified by PCR and deep sequenced on an Illumina MiSeq sequencer. Paired reads were curated, taxonomically labeled, and filtered. Blood culture diagnosed bBSI in 12 patients, but this number increased to 22 patients when combining blood culture and 16S metagenomics results. In addition to superior sensitivity compared to standard blood culture, 16S metagenomics revealed important novel insights into the nature of bBSI. Patients with acute malaria or recovering from malaria had a 7-fold higher risk of presenting polymicrobial bloodstream infections compared to patients with no recent malaria diagnosis (p-value = 0.046). Malaria is known to affect epithelial gut function and may thus facilitate bacterial translocation from the intestinal lumen to the blood. Importantly, patients with such polymicrobial blood infections showed a 9-fold higher risk factor for not surviving their febrile illness (p-value = 0.030). Conclusions/Significance. Our data demonstrate that 16S metagenomics is a powerful approach for the diagnosis and understanding of bBSI. This proof-of-concept study also showed that appropriate control samples are crucial to detect background signals due to environmental contamination. / This work was supported by the Flemish Ministry of Sciences (EWI, SOFI project IDIS). / This paper has been subject to a correction. Please see Correction file above.

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Termites are known to harbor within their gut a diverse assemblage of symbiotic microorganisms. Little work has been done, however, to describe the diversity and function of the bacteria in the economically important eastern subterranean termite, Reticulitermes flavipes. The first object of this study was to characterize the bacterial diversity in the gut of R. flavipes using amplified rDNA restriction analysis (ARDRA) and 16S rRNA gene sequencing. It was determined that ARDRA was an effective technique for characterizing the diversity of the termite gut microbiota. Of the 512 clones analyzed in the ARDRA study, 261 different ARDRA profiles were found. Forty-two 16S rRNA gene sequences were also analyzed, resulting in 33 different ribotypes. Representatives from six major bacterial phyla, Proteobacteria, Spirochaetes, Bacteroidetes, Firmicutes, Actinobacteria, and the newly proposed "Endomicrobia," were discovered. Further analysis indicated that the gut of R. flavipes may harbor as many as 1,318 ribotypes per termite. The second objective was to determine if the gut bacterial diversity could be manipulated by changing the termite's food source. Using ARDRA analysis, I found no evidence that changing the food source affected the termite gut bacterial diversity. In addition, changing the food source did not induce aggression in nestmates fed on different food sources. The third objective was to search for patterns of coevolution between termites and their gut symbiotic bacteria. Using rRNA gene sequences from this study and sequences from public databases (1,450 sequences total), a neighbor-joining tree demonstrated strong evidence for coevolution of termites and their symbiotic bacteria, especially in the phyla Bacteroidetes, Actinobacteria, Spirochaetes, and "Endomicrobia." Many monophyletic clusters were entirely composed of phylotypes specific to Isoptera. / Ph. D.

A superfamília Majoidea contém os caranguejos conhecido popularmente como aranha, encontrados em ambientes marinhos e costeiros, em áreas intermareais rochosas ou de recifes. A imensa diversidade do grupo gerou diferentes propostas de classificação, sendo atualmente aceitas as seguintes famílias: Epialtidae, Inachidae, Inachoididae, Majidae, Mithracidae e Oregoniidae. Epialtidae contém 87 gêneros, dentre eles Libinia com 10 espécies válidas, das quais três ocorrem no Pacífico Oriental (México e Peru) e sete ocorrem no Atlântico Ocidental, desde o Canadá até a Argentina. Em diferentes hipóteses filogenéticas, o gênero posiciona-se com distintos grupos-irmãos (Herbstia, Leucippa, Notolopas, Pisa, Rochinia, Taliepus) que pertencem a subfamílias diferentes, sugerindo o parafiletismo da família, mas sem resolver as relações de parentesco do gênero. No Brasil, embora a posição taxonômica de L. ferreirae e L spinosa não seja duvidosa, podem conviver em simpatria além de possuírem alguns hábitos similares. No entanto, não havia estudos que esclarecessem suas relações de parentesco. Libinia dubia, L. emarginata e L. erinacea coexistem no Golfo do México, em habitat e profundidade similares; apresentaram diferenças morfológicas bastante sutis que justificaram o estudo comparativo das mesmas. Libinia cavirostris foi descrita em 1942, seus caracteres morfológicos a separam das demais espécies do gênero; no entanto não houve mais registros de ocorrência e como consequência ausência de outras informações. Libinia rhomboidea tem distribuição limitada, poucos registros recentes e localidade-tipo duvidosa, o que instigou o exame detalhado de outros espécimes e localidades. Três espécies ocorrem no Pacífico Oriental, L. mexicana, L. setosa e L. peruana, sendo as duas primeiras com distribuição no México e a segunda apenas no Peru, os quais são distinguíveis entre sim, porém não se tem mais registro de L. peruana desde sua descrição em 1983. O presente estudo investigou as relações de parentesco entre as 10 espécies que compõe o gênero Libinia e avaliou a hipótese de monofilia; comparou a morfologia das mesmas e realizou a revisão taxonômica do gênero, levantando caracteres morfológicos informativos de adultos e de jovens de diferentes localidades. As árvores filogenéticas foram construídas a partir de sequências de DNA dos genes 16S e COI alinhadas individualmente e concatenadas, por meio dos métodos de máxima verossimilhança e inferência bayesiana. Todas as dez espécies foram consideradas válidas. As hipóteses filogenéticas suportaram a monofilia de Libinia, indicando pouca proximidade com Stratiolibinia e corroborando a criação do gênero. Gomes, A.F.T. - Tese de Doutorado 2 De forma geral, a morfologia das espécies que ocorrem no Pacífico Oriental é similar e as distinguem das espécies que ocorrem no Atlântico Ocidental. Ainda sim, a hipótese filogenética do gênero não indica clados monofileticos para estes grupos geográficos e ainda evidenciou pouca proximidade entre L. mexicana e L. setosa. Libinia spinosa posicionou-se externamente às demais espécies, L. mexicana é próxima à L. cavirostris, e L. ferreirae tem proximidade filogenética com as espécies que ocorrem no Golfo do México e Caribe. Assim, a hipótese filogenética do gênero Libinia que sugeriu sua monofilia foi confirmada, não apresentando indicativos de clados distintos para as espécies do Pacífico e do Atlântico, e esclareceu as relações internas dentro do gênero / The Majoidea superfamily contains the popularly known spider crabs, found in marine and coastal environments on rocky or reef intertidal areas. Its great diversity resulted on different proposals of classification, thus, combining more recent propositions, there the following families: Epialtidae, Inachidae, Inachoididae, Majidae, Mithracidae e Oregoniidae. Epialtidade consists of 87 genera among them Libinia with 10 valid species, three of them occur in the Eastern Pacific (Mexico and Peru) and seven in the Western Atlantic, from Canada to Argentina. According to distinct phylogenetic hypotheses, this genus can be related to more than one outgroup (Herbstia, Leucippa, Notolopas, Pisa, Rochinia, Taliepus) each belonging to different subfamilies, suggesting that the family is paraphyletic, but without solving the intern relationships. In Brazil, although the taxonomic position of L. ferreirae and L spinosa are not doubtful, they are found in sympatry besides having some similar habits. However, there were no studies that clarified their relationship. Libinia dubia, L. emarginata and L. erinacea occur together in the Gulf of Mexico, or similar habitat and depth; they show subtle morphological differences that justified a comparative study. Libinia cavirostris was described in 1942, its morphological characters differed it from the other species of the genus; however, there were no more recent records, and as a consequence no further information. Libinia rhomboidea has a restricted distribution, few recent records and its type-locality is doubtful, which instigated the detailed examination of other specimens and ocalities. Three species occur in the Eastern Pacific, L. mexicana, L. setosa and L. peruana, the former with distribution in Mexico and the latter only in Peru; they are distinguishable from each other, but L. peruana was not sample since its description in 1983. The main goal of this study was investigating the phylogenetic relationship among the 10 species of Libinia and evaluated the hypothesis of monophyly; compared their morphology and performed the taxonomic revision of the genus, proposing informative morphological characters for adults and juveniles. Phylogenetic trees were obtained from DNA sequences of 16S and COI genes separated and concatenated through the maximum likelihood and Bayesian inference approaches. All species were considered valid. The phylogenetic hypotheses supported the monophyly of Libinia and indicated low proximity with Stratiolibinia, confirming the description of the genus. In general, the morphology of the species that occur in the Eastern Pacific is similar and distinguish them from the ones in the Western Atlantic. Moreover, the phylogenetic hypothesis of the genus does not suggest monophyletic clades for these geographic groups and still suggests low proximity between L. mexicana and L. setosa. Libinia spinosa was positioned externally to the other species, L. mexicana was sister group of L. cavirostris, and L. ferreirae was close related to the species that occur in the Gulf of Mexico and the Caribbean. Finally, the phylogenetic hypothesis of the Libinia genus suggested its monophyly, it did not indicate distinct clades of the Pacific and Atlantic species and clarified the internal relationship among the species of the genus

O gênero Pagurus é um táxon heterogêneo de ermitões, com ampla distribuição mundial, descrito há mais de duzentos anos. A sistemática do grupo é complexa com uma longa história de rearranjos taxonômicos. A classificação conta com a inclusão de numerosas novas espécies e separação de algumas inicialmente contidas no táxon estabelecendo-se novos gêneros. Devido à extensa distribuição das espécies que compõem o táxon, foi necessário restringir o objetivo deste estudo. Assim foi avaliado o status taxonômico das espécies que ocorrem nas costas Pacífica e Atlântica da América do Sul, por meio da combinação de análises morfológicas e moleculares das espécies, utilizando dois marcadores genéticos (16S rDNA e Histona 3). As análises taxonômicas mostraram uma alta variabilidade morfológica nas 22 espécies examinadas. As espécies se encaixam perfeitamente em quatro dos onze grupos preestabelecidos dentro de Pagurus. Além disso, foram fornecidos os caracteres morfológicos que definem um desses grupos. Adicionalmente foi incluída uma chave para ajudar na identificação de todas as espécies. As análises independentes dos dados moleculares mostraram resultados contrastantes. O gene mitocondrial foi mais variável e portanto mais informativo, proporcionando uma hipótese mais clara das relações internas entre os membros de Pagurus. Assim, as topologias moleculares resultantes, concordaram em vários aspectos com o reportado nos dados morfológicos das espécies. De modo que, as semelhanças morfológicas foram refletidas na formação dos nós internos. Assim, as análises do gene 16S e H3 mostraram-se concordante com a morfologia, refletindo-se na formação de alguns dos grupos previamente propostos. Como ponto importante, ressalta-se a separação das espécies que compõe o grupo provenzanoi como um táxon diferenciado dentro de Pagurus. Ao mesmo tempo, as análises com o gene H3 mostraram a espécie Propagurus gaudichaudii inserida dentro de Pagurus, questionando a validade taxonômica de Propagurus. Como só foi incluída uma das cinco espécies do gênero, é claramente necessário a inclusão de outras espécies contidas neste táxon, bem como alguns outros genes uma revisão das espécies contidas neste táxon, junto com análises de outros genes, a fim de resolver definitivamente o status taxonômico de Propagurus. / The genus Pagurus is a heterogeneous taxon of hermit crabs, with worldwide distribution which was described more than two hundred years ago. Systematics of the group is complex and with a long history of taxonomic rearrangements. Thus current classification accounts for inclusion of many new species and splitting-off of some of the original species in order to establish new genera. Because of the extensive distribution of the species that conform this taxon it was necessary to restrict the aim of this study. Thus I evaluated the taxonomic status of the species found in the Pacific and Atlantic coasts of South America using a combination of both morphologic and molecular analyses (16S rDNA and Histona 3). The taxonomic analysis showed high morphological variation among all the 21 examined species. The analyzed species seemed to perfectly fit four out of the eleven morphologically pre-established groups of Pagurus. Furthermore I provide morphological characters that define one of these groups. Additionally, I included a key to aid in the identification of all the target species. Independent analysis of the molecular data showed contrasting results. The mitochondrial gene was the most variable and thus the most informative, providing a clearer hypothesis of the internal relationships among members of Pagurus. Therefore, both 16S and H3 analyses were in general agreement with the morphology. Thus, the resultant molecularly based topologies reflected some of the groups previously proposed. It is important to point out that all the included species belonging to the provenzanoi group were clustered together separated from other clades within Pagurus. At the same time, the analysis with the gen H3 showed Propagurus gaudichaudii clustered within Pagurus, thus questioning the taxonomic validity of Propagurus. As I only included one of the five species of the genus, it is obviously necessary to include other the species contained in this taxon, as well as some other genes in order to definitely solve the taxonomic status of Propagurus.

O Brasil é o maior produtor mundial de cana-de-açúcar, sendo o Estado de São Paulo responsável por mais de 50% do total desta produção. Esta cultura tem um enorme impacto sobre a agricultura brasileira e devido a isto, uma melhor compreensão da composição da comunidade microbiana relacionada a ciclagem do nitrogênio (N) nestes solos é de grande importância para o aprimoramento no cultivo da cana-de-açúcar. No entanto, pouco se sabe sobre a relação entre grupos microbianos e essa cultura. Este trabalho visou determinar variações nas comunidades microbianas que participam das transformações do N nos solos de três áreas utilizadas para a produção de cana-de-açúcar (A, F e J), as quais apresentam uma gama de diferentes condições de manejo e características do solo. Cada área foi analisada em triplicatas, e o DNA extraído do solo foi utilizado para metodologias de sequenciamento de segunda geração (metagenômica e sequenciamento do gene 16S rDNA), PCR quantitativo (qPCR) e polimorfismo dos fragmentos terminais de restrição (T-RFLP). A maioria das sequências derivaram de bactérias (98%; base de dados M5NR); seis etapas do ciclo do nitrogênio foram anotadas pela plataforma MG-RAST (base de dados SEED): amonificação do nitrato e nitrito (ANN); fixação de nitrogênio; desnitrificação; óxido nítrico sintase; redução dissimilatória do nitrito e assimilação de amônia. Este último passo mencionado foi o mais abundante (28%) (genes gltb e gltD) e está diretamente relacionado a multiplicação microbiana nos solos.. O segundo processo mais abundante foi ANN (genes nir e nar), responsável por consumir este substrato durante o ciclo. Proteobacteria, Chloroflexi, Verrucomicrobia e Cyanobacteria estão presentes em todas as etapas do ciclo, representando microrganismos que podem participar das vias de transformação do N e, ademais, foi possível descrever um core microbiano (nível de ordem) representado por Sphingomonadales. Algumas variáveis ambientais, como a aplicação de torta de filtro e a produtividade mostraram uma correlação significativa com a estrutura da comunidade microbiana. Isto também foi encontrado para algumas características do solo como fósforo, magnésio e matéria orgânica. Além disso, identificou-se uma alta abundância de microrganismos carregando genes que codificam enzimas da via de redução do nitrato e nitrito. Portanto, apesar de sua complexidade, o estudo das funções microbianas de nitrogênio em solos cultivados com cana-de-açúcar é inovador por acessar de forma conjunta todas as comunidades envolvidas neste ciclo, caracterizadas por sequenciamento, o que evita os problemas inerentes ao cultivo microbiano, além de permitir inferir sobre a hierarquia das variáveis ambientais que influem sobre esse grupos microbianos. / Brazil is the largest world\'s producer of sugarcane and State of São Paulo accounts for over 50% of this production. This crop has a huge impact on Brazilian agriculture and due to this great importance, a better understanding of the composition of the microbial community related to cycling of nitrogen (N) in these soils is of utmost importance for the improvement in the cultivation of sugarcane. However, little is known about the relationship between microbial groups and this crop. This study aimed to determine changes in microbial communities that participate in the transformation of N in soils derived from three areas used for sugarcane production (named A, F and J), which have a range of different management conditions and soil characteristics. Each area was analyzed in triplicate, and the extracted DNA was used to develop next generation sequencing (shotgun metagenomics and 16S rDNA), quantitative PCR (qPCR) and terminal restriction fragment length polymorphism (T-RFLP). Most of the sequences derived from Bacteria (98%; M5NR database); six stages of nitrogen cycle were annotated by MG-RAST plataform (SEED database): nitrate and nitrite ammonification (NNA); nitrogen fixation; denitrification; nitric oxide synthase; dissimilatory nitrite reductase and ammonia assimilation. This last mentioned step was the most abundant (28%) (gltB and gltD genes) and is directly linked to microbial growth in soil, since the final product of the reaction is glutamate. The second most abundant process was NNA (nir and nar genes), responsible for consuming this substrate during the cycle. Proteobacteria and Chroloflexi are present at all stages of the cycle, representing microorganisms that can participate in the N transformation and, moreover, it was possible to describe a microbial core (at an order level) represented by Sphingomonadales. Some environmental variables, such as the application of filter cake and productivity showed a significant correlation with the structure of the microbial community. This was also found for certain soil characteristics such as phosphorus, magnesium and organic matter. In addition, it was identified a high abundance of microorganisms carrying genes encoding the enzymes for nitrate and nitrite reduction pathway. Therefore, despite its complexity, the study of microbial functions of nitrogen in soils cultivated with sugarcane is innovative by accessing jointly all communities involved in this cycle, characterized by sequencing, which avoids the problems inherent in microbial cultivation and allows to infer about the hierarchy of environmental variables that influence this microbial groups.

Neste trabalho desenvolvemos métodos analíticos e moleculares para a detecção, isolamento e classificação filogenética de Alicyclobacillus spp. a partir de sucos de laranja e frutos ácidos, pelas técnicas: RT-PCR, nested RT-PCR, RAPD, seqüenciamento do 16S rRNA e análise por métodos eletroforéticos. A sensibilidade na detecção dos A. acidoterrestris foi melhorada por meio de reações de nested RT-PCR, utilizando primers internos (amplicon de 191 bp) que foram desenhados a partir do primeiro amplicom de 294 bp. O limite de detecção foi estudado com as reações RT-PCR e nested RT-PCR, sendo capazes de detectar concentrações de 0,1 UFC mL-1 para culturas puras e 2 UFC mL-1 em sucos de laranja artificialmente inoculados. A inibição de esporos de A. acidoterrestris também foi estudada para monitorar a diminuição da viabilidade com tratamento térmico e Sapindus saponaria (200 mg L-1), utilizando RT-PCR e nested RT-PCR. Com o tratamento térmico de 99 oC por 1 h o grau de inibição dos esporos foi de 96,3%. Enquanto que, com a fração purificada de S. saponaria (200 mg L-1) incubada à 45 oC por 2 dias foi de 93,6%, mas com incubação de 99 oC por 1 h foi de 98,7%, na mesma concentração de saponina. Todas as análises de quantificação de produtos de RT-PCR e nested RT-PCR foram analisadas por meio de eletroforese em gel de agarose e eletroforese capilar em microchip no Bioanalyzer 2100 (Agilent), com os kits DNA 500 e DNA 1000 LabChip®, obtendo-se maior sensibilidade nos microchips. A classificação molecular de dezenove cepas, isoladas a partir de diferentes sucos e frutos ácidos, foram estudadas utilizando RAPD-PCR e eletroforese capilar em microchips. Utilizando cinco primers aleatórios nas reações de RAPD, foi possível estudar os polimorfismos analisados nos microchips. Segundo as análises eletroforéticas, as cepas de suco concentrado e diluído de laranja (1, 2, 6) suco concentrado de limão (lim) e suco de laranja in natura (T2, T3), apresentaram similaridades genéticas com a A. acidoterrestris. O estudo de análise filogenética baseada na comparação de seqüências de DNA da região variável do gene 16S rRNA de Alicyclobacillus acidoterrestris, foi utilizado para identificar e agrupar onze cepas isoladas de superfícies e sucos de frutos ácidos. Na árvore filogenética gerada pelo método neighbor joining e bootstrap 1000x, as cepas analisadas mostraram similaridades de 99% entre todas elas, observando-se uma maior similaridade do controle A. acidoterretris (C2) com a cepa isolada de suco concentrado de limão (lim), e uma boa discriminação entre controles das espécies A. acidocaldarius, A. cicloheptanicus, A. sendaiensis e Sulfobacillus acidophilus. / In this work, we developed analytical and molecular methods for detection, isolation and phylogenetic classification of Alicyclobacillus spp. from orange juice and acid fruits using RT-PCR, nested RT-PCR, RAPD and sequencing of 16S rRNA techniques and electrophoretic methods of analysis. The sensitivity on the detection of A. acidoterrestris in orange juice was improved by nested RT-PCR, using internal primers (amplicon of 191 bp) that were designed after sequencing the first amplicon (294 bp). The detection limit was studied with RT-PCR and nested RT-PCR assay, it was able to detect concentrations of 0.1 UFC mL-1 for media culture and 2 UFC mL-1 in inoculated orange juice. The inhibition in spores from A. acidoterrestris was also studied to monitoring the diminution of viability with heat treatment and Sapindus saponaria (200 mg mL-1), using RT-PCR and nested RT-PCR assays. The inhibition by heat treatment at 99 oC for 1 h was 96.3%. However, incubation with S. saponaria at 45 oC for 2 days inhibited 93,6%, however, with incubation of 99 oC for 1 h was 98,7%, in the same concentration of saponin. The quantification of the RT-PCR and nested RT-PCR amplification product were accomplished by capillary electrophoresis in microchips using the Bioanalyzer 2100 in conjunction with the LabChip (TM) DNA 500 and DNA 1000. The molecular classification of nineteen strains isolated from different juice and acidic fruit, were studied using RAPD-PCR and capillary electrophoresis in microchips. Using five random primers in the RAPD assay, it was possible to study the polymorphisms analyzed in microchips. According to electrophoresis analyses, the strains from concentrated and diluted orange juices (1, 2, 6), lemon concentrated juice (lim) and natural orange juice (T2, T3), showed genetic similarities with the A. acidoterrestris. The study of the phylogenetic analyses based on DNA comparison sequences of the variable region of 16S rRNA gene from Alicyclobacillus acidoterrestris, was utilized for the identification and grouping of eleven strains isolated from surface and juice of acid fruits. In the phylogenetic tree produced by neighbor joining and bootstrap 1000, the strains showed similarities of 99% among all strains, showing a high similarity of A. acidoterrestris with a strain isolated from lemon concentrate juice (lim), and a good discrimination between the species A. acidocaldarius, A. cycloheptanicus, A. sendaiensis and Sulfobacillus acidophilus.