Effects of effective microorganisms on the physiological status, intestinal microbiome, and serum metabolites of Eriocheir sinensis / Efectos de microorganismos eficaces sobre el estado fisiológico, el microbioma intestinal y los metabolitos séricos de Eriocheir sinensis

The compound known as effective microorganisms (EMs) is widely used in aquaculture to improve water quality, but how they affect the health of Chinese mitten crab (Eriocheir sinensis) is unclear, especially in terms of intestinal microbiota and serum metabolites. In this study, we fed juvenile crabs with an EM-containing diet to explore the effects of EM on the physiological status, intestinal microbiome, and metabolites of E. sinensis. The activities of alanine aminotransferase and alkaline phosphatase were significantly enhanced by EM, indicating that EM supplementation effectively enhanced the antioxidant capacity of E. sinensis. Proteobacteria, Tenericutes, Firmicutes, Bacteroidetes, and Actinobacteria were the main intestinal microbes in both the control and EM groups. Linear discriminant effect size analysis showed that Fusobacteriaceae, Desulfovibrio, and Morganella were biomarkers in the control group, and Exiguobacterium and Rhodobacteraceae were biomarkers in the EM group. Metabolomics analysis revealed that EM supplementation increased cellular energy sources and decreased protein consumption, and oxidative stress. Together, these results indicate that EM can optimize the intestinal microbiome and serum metabolites, thereby benefiting the health of E. sinensis.(AU)

Composition, diversity and function of gastrointestinal microbiota in wild red-billed choughs (Pyrrhocorax pyrrhocorax)

Hitherto, virtually nothing is known about the microbial communities related to the bird species in the family Corvidae. To fill this gap, the present study was conducted to provide a baseline description of the gut microbiota of wild red-billed choughs (Pyrrhocorax pyrrhocorax). In this study, microbiota from four gastrointestinal locations (oropharynx, gizzard, small intestine, and large intestine) of three wild red-billed choughs were analyzed using the Illumina MiSeq sequencing platform by targeting the V4-V5 regions of the 16S rRNA genes. The gut microbiota of the red-billed choughs were dominated by the phylum Firmicutes (59.56%), followed by Proteobacteria (16.56%), Bacteroidetes (13.86%), and Actinobacteria (7.03%), which were commonly detected in avian gut ecosystems. Genus-level compositions were found to be largely dominated by Lactobacillus (18.21%), Weissella (12.37%), Erysipelatoclostridium (6.94%), Bacteroides (6.63%), Escherichia-Shigella (5.15%), Leuconostoc (4.60%), Proteus (3.33%), Carnobacterium (2.71%), Lactococcus (1.69%), and Enterococcus (1.63%). The overall intestinal microbiota was enriched with functions related to ATP-binding cassette (ABC) transporters, DNA repair and recombination proteins, purine metabolism, ribosome, transcription factors, pyrimidine metabolism, peptidases, and two-component system. In terms of four different gastrointestinal locations, hierarchical clustering analysis and principal coordinate analysis showed that microbial communities of the oropharynx, gizzard, small intestine, and large intestine formed four separated clusters. A total of 825 OTUs and 382 genera were detected in all four gastrointestinal locations, which were considered as the major microbes in the intestines of red-billed choughs. Coexistence of lactic acid bacteria and potential pathogens in the gut environments of red-billed choughs required further investigations

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An altered fecal microbiota profile in patients with non-alcoholic fatty liver disease (NAFLD) associated with obesity

Introduction: increasing evidence suggests a role of intestinal dysbiosis in obesity and non-alcoholic fatty liver disease (NAFLD). The advances in recent years with regard to the role of the gut microbiota raise the potential utility of new therapeutic approaches based on the modification of the microbiome. Objective: the aim of this study was to compare the bacterial communities in obese patients with or without NAFLD to those of healthy controls. Patients and methods: the fecal microbiota composition of 20 healthy adults, 36 obese patients with NAFLD and 17 obese patients without NAFLD was determined by 16S ribosomal RNA sequencing using the Illumina MiSeq system. Results: the results highlighted significant differences in the phylum Firmicutes between patients with and without NAFLD, which was a determining factor of the disease and supported its possible role as a marker of NAFLD. At the genus level, the relative abundance of Blautia, Alkaliphilus, Flavobacterium and Akkermansia was reduced in obese patients, both with or without NAFLD, compared to healthy controls. Furthermore, the number of sequences from the genus Streptococcus was significantly higher in patients with NAFLD in comparison with individuals without the disease, constituting another possible marker. Comparison of bacterial communities at the genus level by a principal coordinate analysis indicated that the bacterial communities of patients with NAFLD were dispersed and did not form a group. Conclusion: in conclusion, these results indicate the role of intestinal dysbiosis in the development of NAFLD associated with obesity. There was a differential microbiota profile between obese patients, with and without NAFLD. Thus, supporting gut microbiota modulation as a therapeutic alternative for the prevention and treatment of NAFLD

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Microbiota y enfermedades gastrointestinales / Microbiota and gastrointestinal diseases

La colonización bacteriana se establece inmediatamente después del nacimiento, por contacto directo con la microbiota materna, y puede modificarse durante la lactancia. Están apareciendo datos indicativos de que modificaciones cuantitativas y cualitativas de la microbiota intestinal son capaces de estimular cambios en la activación del sistema inmune que pueden conducir a la aparición de enfermedades gastrointestinales o extraintestinales. El equilibrio entre la microbiota patógena y beneficiosa durante la niñez y la adolescencia es importante para la salud gastrointestinal, incluyendo la protección frente a patógenos, la inhibición de patógenos, el procesamiento de nutrientes (síntesis de vitamina K), el estímulo de la angiogénesis y la regulación del almacenamiento de la grasa corporal. También los probióticos pueden modular la microbiota intestinal para favorecer la salud del huésped. Este artículo es una revisión sobre la acción moduladora de la microbiota intestinal en la prevención y el tratamiento coadyuvante de las enfermedades gastrointestinales pediátricas

The bacterial colonisation is established immediately after birth, through direct contact with maternal microbiota, and may be influenced during lactation. There is emerging evidence indicating that quantitative and qualitative changes on gut microbiota contribute to alterations in the mucosal activation of the immune system, leading to intra- or extra-intestinal diseases. A balance between pathogenic and beneficial microbiota throughout childhood and adolescence is important to gastrointestinal health, including protection against pathogens, inhibition of pathogens, nutrient processing (synthesis of vitamin K), stimulation of angiogenesis, and regulation of host fat storage. Probiotics can promote an intentional modulation of intestinal microbiota favouring the health of the host. A review is presented on the modulation of intestinal microbiota on prevention, and adjuvant treatment of some paediatric gastrointestinal diseases

Role of colonic microbiota in colorectal carcinogenesis: a systematic review

BACKGROUND AND AIM: The human colonic mucosa is populated by a wide range of microorganisms, usually in a symbiotic relation with the host. Sometimes this balance is lost and a state of dysbiosis arises, exposing the colon to different metabolic and inflammatory stimuli (according to the microbiota's changing profile). Recent findings lead to hypothesize that this unbalance may create a subclinical pro-inflammatory state that increases DNA mutations and, therefore, colorectal carcinogenesis. In this article we aim to systematically review the scientific evidence regarding colonic microbiota and its role in colorectal carcinogenesis. METHODS: Systematic review of PubMed searching results for original articles studying microbiota and colorectal cancer until November 2014. RESULTS: Thirty-one original articles studied the role of colon microbiota in colorectal carcinoma including both human and animal studies. Different and heterogeneous methods were used and different bacteria were considered. Nevertheless, some bacteria are consistently augmented (such as Fusobacteria, Alistipes, Porphyromonadaceae, Coriobacteridae, Staphylococcaceae,Akkermansia spp. and Methanobacteriales), while other are constantly diminished in colorectal cancer (such as Bifidobacterium,Lactobacillus, Ruminococcus, Faecalibacterium spp., Roseburia, and Treponema). Moreover, bacteria metabolites amino acids are increased and butyrate is decreased throughout colonic carcinogenesis. CONCLUSION: Conclusive evidence shows that colorectal carcinogenesis is associated with microbial dysbiosis. This information may be used to create new prophylactic, diagnostic and therapeutic strategies for colorectal cáncer

Functional symbiosis and communication in microbial ecosystems. The case of wood-eating termites and cockroaches

Animal hosts typically have strong specificity for microbial symbionts and their functions. The symbiotic relationships have enhanced the limited metabolic networks of most eukaryotes by contributing several prokaryotic metabolic capabilities, such as methanogenesis, chemolithoautotrophy, nitrogen assimilation, etc. This review will examine the characteristics that determine bacterial «fidelity» to certain groups of animals (e.g., xylophagous insects, such as termites and cockroaches) over generations and throughout evolution. The hindgut bacteria of wood-feeding termites and cockroaches belong to several phyla, including Proteobacteria, especially Deltaproteobacteria, Bacteroidetes, Firmicutes, Actinomycetes, Spirochetes, Verrucomicrobia, and Actinobacteria, as detected by 16S rRNA. Termites effectively feed on many types of lignocelluloses assisted by their gut microbial symbionts. Although the community structures differ between the hosts (termites and cockroaches), with changes in the relative abundances of particular bacterial taxa, the composition of the bacterial community could reflect at least in part the host evolution in that the microbiota may derive from the microbiota of a common ancestor. Therefore, factors other than host phylogeny, such as diet could have had strong influence in shaping the bacterial community structure (AU)

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Disbiosis intestinal en enfermos de Crohn pediátricos / Intestinal dysbiosis in pediatric patients with Crohn's disease

Introducción: La enfermedad de Crohn (EC) pediátrica es un desorden caracterizado por presentar inflamación crónica que puede afectar cualquier segmento del tracto gastrointestinal. La disbiosis intestinal es un factor implicado en la patogénesis multifactorial de esta enfermedad. Diferentes suplementos dietarios se han propuesto como terapia alternativa para inducir o mantener la remisión de la EC. Objetivo: Revisar las evidencias científicas publicadas sobre disbiosis intestinal en pacientes de Crohn pediátricos y la eficacia de la terapia con suplementos dietarios (especialmente probióticos). Material y métodos: Se ha realizado una extensa búsqueda de publicaciones científicas en las principales bases de datos electrónicas especializadas: NCBI, Elsevier, Scielo, Scirus y Science Direct. Resultados y Discusión: Se ha observado en la población pediátrica de EC un aumento de Proteobacteria y una reducción de Firmicutes. Los resultados referentes a los phyla Bacteroidetes y Actinobacteria son divergentes. Referente al uso de suplementos dietarios, el uso de probióticos no ha mostrado ningún impacto positivo en la EC pediátrica. Conclusiones: Los resultados publicados hasta la fecha referentes a la disbiosis intestinal en pacientes pediátricos de Crohn, contribuyen al mejor conocimiento y entendimiento de las modificaciones en la flora bacteriana. Sin embargo, no es posible definir una microbiota asociada o causante de la EC. Además, los resultados publicados hasta la fecha no aportan evidencias sólidas de la eficacia de los probióticos como terapia en dichos pacientes (AU)

Introduction: Paediatric Crohn's disease is a disorder characterised by a chronic inflammation that can affect any part of the gastrointestinal tract. Intestinal dysbiosis is a key factor in the multifactorial pathogenesis of this disease. Different dietary supplements have been proposed as alternative therapy both on induction and on maintaining remission of this disease. Objective: To review current scientific evidence of intestinal dysbiosis in paediatric Crohn's disease patients, as well as efficacy of dietary supplement therapy (especially probiotics). Materials and Methods: Extensive search of scientific publications was performed in specialized electronic databases: NBCI, Elsevier, Scielo, Scirus and Science Direct. Results and discussion: An increase of Proteobacteria and a reduction of Firmicutes were observed in Crohn's disease paediatric patients. However the results referring to phyla Bacteroidetes and Actinobacteria are disperse. Referring the use of dietary supplements, the use of probiotics did not show any positive impact in paediatric Crohn's disease patients. Conclusions: A better knowledge and understanding of the bacterial flora modifications in paediatric Crohn's disease patients is possible with the current published results. However, it is not possible to define the precise microbiota associated or causing this disease. In addition, current results do not bring solid evidence of the efficacy of probiotic therapy in those patients (AU)

Microbial community composition of anoxic marine sediments in the Bay of Cádiz (Spain)

The composition of the microbial community inhabiting the anoxic coastal sediments of the Bay of Cádiz (southern Spain) was investigated using a molecular approach consisting of PCR cloning and denaturing gradient gel electrophoresis (DGGE), based on 16S rRNA sequences. The total cell count was 1-5 × 10⁸ cells/g sediment and, as determined by catalyzed reporter deposition-fluorescent in situ hybridization (CARD-FISH), the proportion of Bacteria to Archaea was about 70:30. The analysis of 16S-rRNA gene sequences revealed a wide spectrum of microorganisms, which could be grouped into 111 operational taxonomic units (OTUs). Many of the OTUs showed high phylogenetic similarity to microorganisms living in marine sediments of diverse geographic origin. The phylogenetic groups that were predominantly detected were Firmicutes, Deltaproteobacteria, and Gammaproteobacteria, accounting for 23, 15, and 14% of the clones, respectively. Diversity in the domain Archaea was significantly lower than in the domain Bacteria. The majority of the archaeal OTUs belonged to the Crenarchaeota phylum. Since most of the sequences could not be identified precisely at the genus/species level, the functional roles of the microorganisms in the ecosystem could not be inferred. However, seven OTUs affiliated with the Delta- and Epsilonproteobacteria were identified down to the genus level, with all of the identified genera known to occur in sulfate-rich marine environments (AU)

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Comparison of the gut microbiota froms oldier and worker castes of the termite Reticulitermes grassei

The bacterial microbiota from the whole gut of soldier and worker castes of the termite Reticulitermes grassei was isolated and studied. In addition, the 16S rDNA bacterial genes from gut DNA were PCR-amplified using Bacteria-selective primers, and the 16S rDNA amplicons subsequently cloned into Escherichia coli. Sequences of the cloned inserts were then used to determine closest relatives by comparison with published sequences and with sequences from our previous work. The clones were found to be affiliated with the phyla Spirochaetes, Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Synergistetes, Verrucomicrobia, and candidate phyla Termite Group 1 (TG1) and Termite Group 2 (TG2). No significant differences were observed with respect to the relative bacterial abundances between soldier and worker phylotypes. The phylotypes obtained in this study were compared with reported sequences from other termites, especially those of phylotypes related to Spirochaetes, Wolbachia (an Alphaproteobacteria), Actinobacteria, and TG1. Many of the clone phylotypes detected in soldiers grouped with those of workers. Moreover, clones CRgS91 (soldiers) and CRgW68 (workers), both affiliated with ‘Endomicrobia’, were the same phylotype. Soldiers and workers also seemed to have similar relative protist abundances. Heterotrophic, poly-β-hydroxyalkanoate-accumulating bacteria were isolated from the gut of soldiers and shown to be affiliated with Actinobacteria and Gammaproteobacteria. We noted that Wolbachia was detected in soldiers but not in workers. Overall, the maintenance by soldiers and workers of comparable axial and radial redox gradients in the gut is consistent with the similarities in the prokaryotes and protists comprising their microbiota (AU)

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Aislamiento de cepas del género Halomonas con interés biotecnológico en Rambla Salada (Murcia) / Isolaton of strains of the genus Halomonas with biotechnologycal interest from Rambla Salada (Murcia)

El género Halomonas es uno de los taxones bacterianos más representativos dentro de las bacterias halófilas moderadas. Se encuentra incluido en el Phyllum Proteobacteria, clase Gamma-Proteobacteria, familia Halomonadaceae1. Son en su mayoría de bacterias halófilas moderadas, con un requerimiento de NaCl para su óptimo crecimiento que oscila entre un 3-15% (p/v). Las especies de esta familia han demostrado ser un grupo de microorganismos extremófilos con un gran potencial biotecnológico, por la producción de solutos compatibles que les confiere capacidad para estabilizar y proteger enzimas así como aplicaciones en tecnología enzimática, en la industria cosmética y dermofarmacia, medicina y agricultura. Estas especies son capaces de producir también compuestos extracelulares como exopolisacáridos y enzimas extracelulares. Los primeros tienen gran interés industrial debido a sus propiedades viscosizantes, estabilizantes, emulgentes y formadoras de geles. Nuestro grupo de investigación a lo largo de estos años ha caracterizado una decena de estos polímeros destacando los de H. eurihalina y H. maura por sus propiedades viscosizantes y emulgentes 2,3 y los de H. stenophila por sus propiedades antitumorales 4. En cuanto a las enzimas extracelulares, tales como lipasas y amilasas, se mantienen estables en un amplio rango de concentraciones salinas y proporcionan así nuevas posibilidades en los procesos biocatalíticos. Otras aplicaciones biotecnológicas son la producción de polihidroxialcanoatos así como la degradación de compuestos tóxicos. Debido al gran interés biotecnológico de las bacterias halófilas moderadas, nuestro grupo de investigación lleva a cabo un estudio de biodiversidad de microorganismos halófilos en Rambla Salada (Murcia) con el fin de aislar nuevas especies de Halomonas productoras de compuestos de aplicación industrial y/o biotecnológica(AU)

Se han realizado cuatro muestreos durante dos años en Rambla Salada (Murcia, España). Las muestras han sido procesadas mediante las técnicas de microbiología clásicas y las bacterias aisladas han sido caracterizadas fenotípica y filogenéticamente. Las cepas pertenecientes al género Halomonas se sembraron en los medios adecuados para estudiar cada una de las funciones biológicas, y se seleccionaron aquellas cepas que dieron una actividad positiva. Se han aislado 164 cepas del género Halomonas, algunas de ellas con actividad lipasa, proteinasa y/odexosirribonucleasa y casi todas son productoras de exopolisacaridos. La presencia de estas cepas conactividad positiva para determinadas funciones biológicas con interés industrial y biotecnológico ponen de manifiesto la necesidad de seguir investigando en este sentido(AU)

The genus Halomonas is one of the most representative taxa amongst the moderately halophilicbacteria. This genus is included into the family Halomonadaceae, class Gamma-Proteobacteria, Phyllum Proteobacteria1. It requires NaCl concentrations 3-15% w/v for optimum growth. Halomonas species have aroused interest amongst biotechnologists because of their ability to accumulate organic compatible solutes which provide stability and protection of enzymes and other molecules and have interest in enzymatic technology, cosmetic, medicine and agriculture. They also produce extracellular compounds, such as exoenzymes and exopolysaccharides (EPS). The extracellular enzymes, such as lipase and amylase, are stable within a wide salt concentration range; this property is important in biocatalytic processes. Other biotechnological applications of the Halomonas species are the production of polyhydroxyalkanoates and the degradation of aromatic compounds. The halophilic EPS are commercially valuable products because of their biotechnology applications as viscosifying, stabilizers and gelling agents. Our research group has characterized to date tenexopolysaccharides-producing halophilic species. Two of them, H. eurihalina and H. maura produce polymers with viscosifying and emulsifying properties 2,3 and H. stenophila synthesizes and EPS with antitumoral properties 4. Isolate new species of the genus Halomonas with industrial and/or medical applications from Rambla Salada (Murcia, Spain)(AU)

Samples of saline soils, sediments and waters were taken periodically from Rambla Salada (Murcia, Spain) along two years. The samples were processed by classical methods and the isolated strains were identified by mean of phenotypic and phylogenetic techniques. The species belonging to the genus Halomonas were analyzed in order to find compounds of biotechnological interest. We have isolated 164 strains of the genus Halomonas. Some of them have lipases protease and/ordeoxyribonuclease activities and most of them are exopolysaccharide-producing bacteria. The results presented in this work show that extreme environments, such as Rambla Salada, constitute anunexplorable resource of discovering new bacteria and biomolecules(AU)

Culturable aerobic bacteria from the upstream region of a karst water rivulet

The composition of 681 aerobic and heterotrophic strains that were isolated on two different media was assessed at four sampling points along a approximately 300 m stretch of a karst water rivulet. Based on partial sequence analysis of 16S rRNA genes, members of 35 genera were identified; however, only a few species dominated as their representatives were repeatedly isolated at different sampling sites. Determination of the phylum affiliation showed that the isolates included members of Bacteriodetes (especially the genus Flavobacterium) and Proteobacteria (mainly Pseudomonas and Stenotrophomonas). MALDI-TOF analysis and/or similarities of partial sequences of flavobacterial strains resulted in the generation of almost complete 16S rRNA gene sequences for 100 isolates, about 60 of which may represent novel phylospecies. The number as well as the intra-phylum distribution of the isolates changed with distance from the discharge site. While phylogenetically restricted at the spring, diversity increased at downstream sampling sites (AU)

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Microbial community composition in petroleum-contaminated and uncontaminated soil from Francisco de Orellana, in the northern Ecuadorian Amazon

The microbial compositions of two soils from the northern Ecuadorian Amazon (Francisco de Orellana province), one contaminated with petroleum and the other uncontaminated, were compared. Classical culture and molecular techniques were used to analyze microbial diversity. The cultivable Bacteria from contaminated soil belonged to betaproteobacteria (16.6%), gammaproteobacteria (66.6%), and Firmicutes (16,6%), whereas in uncontaminated soil, cultivable Bacteria were identified as gammaproteobacteria (80%) and Firmicutes (20%). Analysis of the 16S rRNA showed that in the contaminated soil proteobacterial populations (alpha-, beta- and deltaproteobacteria) were more abundant than acidobacterial populations. The Shannon index (H cent ) was used to estimate diversity in the contaminated and uncontaminated soil. Diversity was higher in the uncontaminated (H cent = 2.16) than in the contaminated (H cent = 1.72) soil sample. Further studies are needed to determine whether the differences between contaminated and non-contaminated soil samples were due to spontaneous bioremediation microbial activity (AU)

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Polygenic analysis of ammonia-oxidizing bacteria using 16S rDNA, amoA, and amoB genes / Análisis poligénico de cepas de bacterias oxidadoras de amoníaco por medio de los genes 16S rDNA, amoA y amoB

Finding a unique molecular marker capable of quickly providing rigorous and useful phylogenetic information would facilitate assessing the diversity of ammonia-oxidizing bacteria in environmental samples. Since only one of several available markers can be used at a time in these kinds of studies, the 16S rDNA, amoA and amoB genes were evaluated individually and then compared in order to identify the one that best fits the information provided by the composite dataset. Distance-based neighbor-joining and maximum parsimony trees generated using the sequences of the three mentioned genes were analyzed with respect to the combined polygenic trees. Maximum parsimony trees were found to be more accurate than distance-based ones, and the polygenic topology was shown to best fit the information contained in the sequences. However, the taxonomic and phylogenetic information provided by the three markers separately was also valid. Therefore, either of the functional markers (amoA or amoB) can be used to trace ammonia oxidizers in environmental studies in which only one gene can be targeted (AU)

Encontrar un marcador molecular único capaz de proporcionar rápidamente información filogenética rigurosa y útil facilitaría evaluación de la diversidad de las bacterias oxidadoras de amoníaco en muestras ambientales. En esta clase de estudios no se puede utilizar simultáneamente más que uno de los marcadores disponibles. Los genes 16S rDNA, amoA y amoB se evaluaron individualmente para identificar el que se ajusta mejor a la información proporcionada por el conjunto de datos de los tres genes. Se compararon los árboles de Neighbor-Joining, basados en las distancias, y los árboles de máxima parsimonia basados en las secuencias conocidas de los tres genes mencionados, y se analizaron en relación con los árboles poligénicos construidos con la información combinada proporcionada por los tres genes. Los árboles de máxima parsimonia resultaron más fieles que los basados en las distancias, y la topología poligénica era la que mejor se ajustaba a la información contenida en las secuencias. Sin embargo, la información taxonómica y filogenética proporcionada por los tres marcadores por separado también resultó válida. Por tanto, cualquiera de los dos marcadores funcionales (amoA o amoB) se puede utilizar para detectar los oxidantes del amoníaco en estudios ambientales en los que solamente puede usarse un gen (AU)

The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins

The presence of shared conserved inserts and deletions (indels or signature sequences) in proteins provides a powerful means for understanding the evolutionary relationships among the Bacteria. Using such indels, all of the main groups within the Bacteria can be defined in clear molecular terms and it has become possible to deduce that they branched from a common ancestor in the following order: Low G + C gram-positive --> High G+C gram-positive --> Deinococcus Thermus --> Cyanobacteria --> Spirochetes --> Aquifex-Chlamydia-Cytophaga --> Proteobacteria-1 (epsilon, delta) --> Proteobacteria-2 (alpha) --> Proteobacteria-3 (beta) --> Proteobacteria -4 (gamma). The usefulness of this approach for understanding bacterial phylogeny was examined here using sequence data from various completed bacterial genomes. By using 12 indels in highly conserved and widely represented proteins, the species from all 41 completed bacterial genomes were assigned to different groups; and the observed distribution of these indels in different species was then compared with that predicted by the signature sequence model. The presence or absence of these indels in various proteins in different bacteria followed the pattern exactly as predicted: and, in more than 450 observations, no exceptions or contradictions in the placement of indels were observed. These results provide strong evidence that lateral gene transfer events have not affected the genes containing these indels to any significant extent. The phylogenetic placement of bacteria into different groups based on signature sequences also showed an excellent correlation with the 16 S rRNA with 39 of the 41 species assigned to the same group by both methods. These results strongly vindicate the usefulness of the signature sequence approach to understanding phylogeny within the Bacteria and show that it provides a reliable and internally consistent means for the placement of bacterial species into different groups and for determining the relative branching order of the groups (AU)

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Intracellular bacteria in ciliates

Ciliates are frequently colonized by other micro-organisms. The large size of ciliate cells offers habitats for hundreds to thousands of bacteria in different compartments, such as cytoplasm, nuclei and even perinuclear spaces. Size, phagocytic feeding habit and other features appear to be favorable pre-adaptations of ciliates for symbiosis with bacteria. Certain intracellular bacteria are permanent symbionts that are not infectious, whereas others are highly infectious. Both types show specific adaptations. With their wide spectrum of phylogenetic positions, intracellular bacteria in ciliates show relationships to different taxa of free-living bacteria and even archaea. Certain symbionts may be deleterious for their host ciliates, whereas others may provide a selective advantage under appropriate conditions or even be essential for the host cells. Depending on the nature of a symbiont, its prevalence in a host population may be low or high. Symbionts that express a killer toxin affecting non-infected ciliates achieve high infection rates in a host population, whereas certain infectious bacteria may only show a low prevalence (AU)

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