Whole-genome analysis of Mannheimia haemolytica serotype A2 to identify potential vaccine candidates against acute pneumonia in alpacas

El objetivo del presente trabajo fue identificar antígenos inmunoprotectivos en la secuencia genómica de Mannheimia haemolytica serotipo A2 Ovino, aislado de ovino y disponible en las bases de datos, que puedan ser utilizados como potenciales candidatos vacunales contra la neumonía en alpacas. Para ello, se empleó la secuencia completa del genoma de este microorganismo disponible en las bases de datos y mediante el uso de herramientas bioinformáticas se procedió a la búsqueda e identificación de genes candidatos, la anotación funcional, la predicción de la localización subcelular y la identificación de motivos de secuencias, incluyendo dominios transmembrana, peptidos señal de secreción y lipoproteínas. Los factores de virulencia fueron identificados en la base de datos de factores de virulencia (VFDB) y en la base de datos microbiana de virulencia (MvirDB). Los criterios de selección incluyeron proteínas conservadas, secretadas y asociadas a superficie con hélices transmembrana d»1. Se realizó la búsqueda de homología de genes con la base de datos de antígenos protectivos (Protegen), permitiendo la identificación de 23 antígenos potencialmente inmunoprotectivos, conservados entre los serotipos virulentos de M. haemolytica y otros patógenos de la familia Pasteurellaceae. Los genes identificados están relacionados con la patogénesis, virulencia y evasión del sistema immune del hospedero y podrían ser grandes candidatos a ser evaluados como potenciales vacunas contra la pasteurelosis neumónica.The aim of this study was to identify immunoprotective antigens in the genomic sequence of Mannheimia haemolytica serotype A2 isolated from sheep and available in databases that can be used as potential vaccine candidates against pneumonia in alpacas. To do this, the complete genome sequence of this organism available in databases was used and by using bioinformatics tools was proceeded to search for and identification of candidate genes, functional annotation, predicting the subcellular localization and identification of sequence motifs including transmembrane domains, secretion signal peptides and lipoproteins. Virulence factors were identified in the database of virulence factors (VFDB) and the microbial database of virulence factors (MvirDB). Selection criteria included conserved proteins, secreted and associated surface with transmembrane helices <1. Homology search of genes was performed with the database of protective antigens (Protegen), allowing the identification of 23 potentially immunoprotective antigens conserved between virulent M. haemolytica serotypes and other pathogens of the family Pasteurellaceae. The genes identified are related to the pathogenesis, virulence and immune system evasion of the host and they could be great candidates to be evaluated as potential vaccines against pneumonic pasteurellosis

DNA extraction methods from vicuña fecal samples (Vicugna vicugna mensalis)

Actualmente es posible determinar el estatus de especies silvestres mediante el análisis de ADN extraído de muestras no invasivas como las heces. Aunque dichos análisis suelen ser dificultosos debido principalmente a la composición y conservación de las heces, se ha demostrado en muchas especies que con el desarrollo de métodos adecuados de extracción es posible maximizar la fiabilidad y eficacia de este procedimiento. Por tanto, el objetivo del presente estudio fue optimizar un método de extracción de ADN de heces de vicuña Vicugna vicugna mensalis, especie clasificada como casi amenazada en el Perú, con la finalidad de obtener ADN de suficiente calidad para análisis moleculares. Se recolectaron 51 muestras de heces durante los meses de agosto y septiembre de 2008 en dos comunidades vicuñeras ubicadas a más de 4600 msnm en los departamentos de Junín y Moquegua. Luego de observar la defecación, las muestras fueron recolectadas en forma inmediata, conservadas en etanol y transportadas al laboratorio para la extracción del ADN. El kit comercial QIAamp® DNA Stool Mini Kit (QIAGEN) fue modificado para incluir un vigoroso y extenso proceso de agitación y los resultados fueron comparados con dos protocolos comúnmente utilizados: fenol/cloroformo/alcohol isoamílico y el mismo kit QIAGEN. La cantidad del ADN extraído fue observado en electroforesis horizontal en geles de agarosa, y la calidad evaluada mediante la amplificación y visualización de los tamaños esperados de los microsatélites YWLL46 y LCA19. Aunque se logró extraer ADN con los tres métodos, solamente el método modificado permitió obtener ADN de suficiente calidad para ser utilizado en pruebas moleculares.At present, the use of DNA extracted from non-invasive samples, especially feces, is common practice in the discipline of conservation genetics. Even though DNA analysis is often difficult mainly due to the composition and preservation of feces has been shown in many species with the development of suitable extraction methods is possible to maximize the reliability and effectiveness of such procedures. The objective of this study has been optimization of a protocol for the extraction of DNA from vicuña feces (Vicugna vicugna mensalis), species classified as Near Threatened in Peru, in order to obtain DNA of sufficient quality for molecular analysis. A total of 51 samples were taken from vicuña dung piles in two communities located 4600 meters above sea level in the dry Puna ecosystems of the regions of Junin and Moquegua between August and September 2008. After observing defecation, samples were collected immediately, preserved in ethanol and transported to the laboratory for DNA extraction. Modification of the protocol of the QIAamp ® DNA Stool Mini Kit (QIAGEN) to include an extended period of vigorous shaking was found to producer higher quality DNA than was obtained using both the kit protocol and PCI (Phenol/chloroform/isoamyl alcohol). The amount of extracted DNA was visualized using horizontal agarose gel electrophoresis, and the quality was tested analyzing microsatellite markers LCA 19 and YWLL 46 on polyacrylamide gels. Although DNA was obtained by all three methods, only the modified protocol produced DNA of sufficient quality for use in molecular analyses

AVANCES EN EL ESTUDIO DE LA PATOGÉNESIS Y PREVENCIÓN DE LA ENTEROTOXEMIA DE LAS ALPACAS.

The results of our recent research work on enterotoxemia in Peruvian alpacas are presented. Microbiological and molecular analyses found that the majority of the isolates corresponded to Clostridium perfringens and contained the cpa coding gene for α toxin (A genotype) while 0.4% contained both the cpa and cpb genes of the α and β toxins (C genotype). A parallel study revealed that 8.5% of the genotype A isolates also had cpb2, but the cpe (enterotoxin) gene was absent in all cases. These results highly suggest that the exotoxins secreted by C. perfringens are the virulent factors in enterotoxemia, rather than the endogenous enterotoxin. Additionally, an histopathological study of intestinal samples from fatal cases showed that 30.6% had abundant immature structures of Eimeria macusaniensis affecting deep mucosa and cryptic gland epithelia, primarily in the jejune and ileum, suggesting that eimeriosis is likely a triggering or predisposing factor for the development of enterotoxemia. The microbiological studies allowed the design and progressive improvement of an inactivated enterotoxemia vaccine containing primarily the bacterial component plus exotoxins of types A, Aβ2 and C isolated from natural fatal cases of the disease. During six years of field tests in southern Peru, the vaccine has steadily reduced specific neonatal mortality rates due to enterotoxemia from 19.5% (2000, without vaccine) to less than 5% in 2006.Se revisan las investigaciones recientes realizadas por nuestro grupo de investigadores sobre enterotoxemia de las alpacas en el Perú. Estudios microbiológicos y moleculares demostraron que la mayoría de las cepas aisladas fueron de Clostridium perfringens y estas contienen únicamente el gen cpa de la toxina α (C. perfringens genotipo A) y solamente el 0.4% tienen genes cpa y cpb de las toxinas α y β (genotipo C). En análisis paralelo, se encontró que el 8.5% de los genotipos A contenían, adicionalmente, el gen cpb2, pero ninguna cepa tenía el gen cpe de la enterotoxina. Estos resultados evidencian que las exotoxinas secretadas, y no las endotoxinas (cpe), serían los probables factores de virulencia clostridiales en la enterotoxemia de la alpaca. Adicionalmente, en el análisis histopatológico de intestinos infectados, el 30.6% de las muestras presentó abundantes estructuras parasitarias inmaduras correspondientes a Eimeria macusaniensis, afectando la mucosa y epitelio de las glándulas crípticas intestinales, sugiriendo a las infecciones coccidiales como uno de los posibles factores desencadenantes o predisponentes de la enterotoxemia. Estos resultados microbiológicos permitieron diseñar, preparar y mejorar una vacuna convencional inactivada que contiene, mayoritariamente, componentes bacterianos y exotoxinas A, Aβ2 y C aislados de casos fatales de la enfermedad. Desde su introducción en una empresa alpaquera del sur peruano en 2001, la vacuna ha logrado reducir progresivamente los índices de mortalidad por enterotoxemia de 19.5% (2000, sin vacuna) hasta alcanzar tasas menores al 5% en 2006

Comparing genetic diversity and demographic history in co-distributed wild South American camelids

Vicuñas and guanacos are two species of wild South American camelids that are key ruminants in the ecosystems where they occur. Although closely related, these species feature differing ecologies and life history characters, which are expected to influence both their genetic diversity and population differentiation at different spatial scales. Here, using mitochondrial and microsatellite genetic markers, we show that vicuña display lower genetic diversity within populations than guanaco but exhibit more structure across their Peruvian range, which may reflect a combination of natural genetic differentiation linked to geographic isolation and recent anthropogenic population declines. Coalescent based demographic analyses indicate that both species have passed through a strong bottleneck, reducing their effective population sizes from over 20,000 to less than 1,000 individuals. For vicuña this bottleneck is inferred to have taken place ~3,300 years ago, but to have occurred more recently for guanaco at ~2,000 years ago. These inferred dates are considerably later than the onset of domestication (when the alpaca was domesticated from the vicuña while the llama was domesticated from the guanaco), coinciding instead with a major human population expansion following the mid-Holocene cold period. As importantly, they imply earlier declines than the well-documented Spanish conquest, where major mass mortality events were recorded for Andean human and camelid populations. We argue that underlying species’ differences and recent demographic perturbations have influenced genetic diversity in modern vicuña and guanaco populations, and these processes should be carefully evaluated in the development and implementation of management strategies for these important genetic resources

Phenotypic characterization and 16S rDNA identification of culturable non-obligate halophilic bacterial communities from a hypersaline lake, La Sal del Rey, in extreme South Texas (USA)

Background: La Sal del Rey ( the King’s Salt”) is one of several naturally-occurring salt lakes in Hidalgo County, Texas and is part of the Lower Rio Grande Valley National Wildlife Refuge. The research objective was to isolate and characterize halophilic microorganisms from La Sal del Rey. Water samples were collected from the lake and a small creek that feeds into the lake. Soil samples were collected from land adjacent to the water sample locations. Sample salinity was determined using a refractometer. Samples were diluted and cultured on a synthetic saline medium to grow halophilic bacteria. The density of halophiles was estimated by viable plate counts. A collection of isolates was selected, gram-stained, tested for catalase, and characterized using API 20E® test strips. Isolates were putatively identified by sequencing the 16S rDNA. Carbon source utilization by the microbial community from each sample site was examined using EcoPlate™ assays and the carbon utilization total activity of the community was determined. Results: Results showed that salinity ranged from 4 parts per thousand (ppt) at the lake water source to 420 ppt in water samples taken just along the lake shore. The density of halophilic bacteria in water samples ranged from 1.2 × 102 - 5.2 × 103 colony forming units per ml (cfu ml-1) whereas the density in soil samples ranged from 4.0 × 105 - 2.5 × 106 colony forming units per gram (cfu g-1). In general, as salinity increased the density of the bacterial community decreased. Microbial communities from water and soil samples were able to utilize 12 - 31 carbon substrates. The greatest number of substrates utilized was by water-borne communities compared to soil-based communities, especially at lower salinities. The majority of bacteria isolated were gram-negative, catalase-positive, rods. Biochemical profiles constructed from API 20E® test strips showed that bacterial isolates from low-salinity water samples (4 ppt) showed the greatest phenotypic diversity with regards to the types and number of positive tests from the strip. Isolates taken from water samples at the highest salinity (420 ppt) tended to be less diverse and have only a limited number of positive tests. Sequencing of 16S DNA displayed the presence of members of bacterial genera Bacillus, Halomonas, Pseudomonas, Exiguobacterium and others. The genus Bacillus was most commonly identified. None of the isolates were members of the Archaea probably due to dilution of salts in the samples. Conclusions: The La Sal del Rey ecosystem supports a robust and diverse bacterial community despite the high salinity of the lake and soil. However, salinity does appear to a limiting factor with

Diversity of Haloquadratum and other haloarchaea in three, geographically distant, Australian saltern crystallizer ponds

Haloquadratum walsbyi is frequently a dominant member of the microbial communities in hypersaline waters. 16S rRNA gene sequences indicate that divergence within this species is very low but relatively few sites have been examined, particularly in the southern hemisphere. The diversity of Haloquadratum was examined in three coastal, but geographically distant saltern crystallizer ponds in Australia, using both culture-independent and culture-dependent methods. Two 97%-OTU, comprising Haloquadratum- and Halorubrum-related sequences, were shared by all three sites, with the former OTU representing about 40% of the sequences recovered at each site. Sequences 99.5% identical to that of Hqr. walsbyi C23T were present at all three sites and, overall, 98% of the Haloquadratum-related sequences displayed ≤2% divergence from that of the type strain. While haloarchaeal diversity at each site was relatively low (9–16 OTUs), seven phylogroups (clones and/or isolates) and 4 different clones showed ≤90% sequence identity to classified taxa, and appear to represent novel genera. Six of these branched together in phylogenetic tree reconstructions, forming a clade (MSP8-clade) whose members were only distantly related to classified taxa. Such sequences have only rarely been previously detected but were found at all three Australian crystallizers

Denitrification likely catalyzed by endobionts in an allogromiid foraminifer

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in The ISME Journal 6 (2012): 951–960, doi:10.1038/ismej.2011.171.Nitrogen can be a limiting macronutrient for carbon uptake by the marine biosphere. The process of denitrification (conversion of nitrate to gaseous compounds, including N2) removes bioavailable nitrogen, particularly in marine sediments, making it a key factor in the marine nitrogen budget. Benthic foraminifera reportedly perform complete denitrification, a process previously considered nearly exclusively performed by bacteria and archaea. If the ability to denitrify is widespread among these diverse and abundant protists, a paradigm shift is required for biogeochemistry and marine microbial ecology. However, to date, the mechanisms of foraminiferal denitrification are unclear and it is possible that the ability to perform complete denitrification is due to symbiont metabolism in some foraminiferal species. Using sequence analysis and GeneFISH, we show that for a symbiont-bearing foraminifer, the potential for denitrification resides in the endobionts. Results also identify the endobionts as denitrifying pseudomonads and show that the allogromiid accumulates nitrate intracellularly, presumably for use in denitrification. Endobionts have been observed within many foraminiferal species, and in the case of associations with denitrifying bacteria, may provide fitness for survival in anoxic conditions. These associations may have been a driving force for early foraminiferal diversification, which is thought to have occurred in the Neoproterozoic when anoxia was widespread.This research was supported by NSF grant EF-0702491 to JMB, KLC and VPE; some ship support was provided by NSF MCB-0604084 to VPE and JMB.2012-06-0

From community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic Bacteroidetes generalists

The microbiota of multi-pond solar salterns around the world has been analyzed using a variety of culture-dependent and molecular techniques. However, studies addressing the dynamic nature of these systems are very scarce. Here we have characterized the temporal variation during 1 year of the microbiota of five ponds with increasing salinity (from 18% to >40%), by means of CARD-FISH and DGGE. Microbial community structure was statistically correlated with several environmental parameters, including ionic composition and meteorological factors, indicating that the microbial community was dynamic as specific phylotypes appeared only at certain times of the year. In addition to total salinity, microbial composition was strongly influenced by temperature and specific ionic composition. Remarkably, DGGE analyses unveiled the presence of most phylotypes previously detected in hypersaline systems using metagenomics and other molecular techniques, such as the very abundant Haloquadratum and Salinibacter representatives or the recently described low GC Actinobacteria and Nanohaloarchaeota. In addition, an uncultured group of Bacteroidetes was present along the whole range of salinity. Database searches indicated a previously unrecognized widespread distribution of this phylotype. Single-cell genome analysis of five members of this group suggested a set of metabolic characteristics that could provide competitive advantages in hypersaline environments, such as polymer degradation capabilities, the presence of retinal-binding light-activated proton pumps and arsenate reduction potential. In addition, the fairly high metagenomic fragment recruitment obtained for these single cells in both the intermediate and hypersaline ponds further confirm the DGGE data and point to the generalist lifestyle of this new Bacteroidetes group.This work was supported by the projects CGL2012-39627-C03-01 and 02 of the Spanish Ministry of Economy and Competitiveness, which were also co-financed with FEDER support from the European Union. TG group research is funded in part by a grant from the Spanish Ministry of Economy and Competitiveness (BIO2012-37161), a grant from the Qatar National Research Fund grant (NPRP 5-298-3-086) and a grant from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC (grant agreement no. ERC-2012-StG-310325)

Arqueas Halófilas productoras de Betacaroteno aisladas de las salinas solares de Huacho-Lima

Throughout the world, interest toward the search of natural sources of betacarotene has beenincreased due to its wide use as a colorant and antioxidant agent in pharmaceutical, cosmetic and food industries. In order to isolate Archaea halophilics betacarotene producers, salt samples from solar saltems located in Huacho were taken and cultured in sea water agar (SWA) supplemented with 20% NaCl and 0.5% yeast extract.. From the 25 microorganisms isolated, 12 which presented difierent reddish cellular pigmentation were chosen. Selected isolates were analyzed to determine their cellular growth and ability to produce betacarotene, being the isolate W2 which obtained the highest cellular pigmentation index. Besides, optimal concentration of NaCl and yeast extract to increase the production of betacarotene was determined. Isolate W2 was identified as Haloferax gibbonsii of the Archaea domain by amplification and parcial sequencing of the 16S ribosomal genes. This strain produced 0.6042 mg of betacarotene/ml of culture with 25% NaCl and 0.5% yeast extract.A nivel mundial se ha incrementado el interés hada h búsqueda de fuentes naturales de betacaroteno debido a su amplio uso como agente colorante y antioxidante en las industrias farmacéutica, alimentaria y cosmética. Con la finalidad de aislar arqueas halófilas productoras de betacaroteno se tomaron muestras de sales de las salinas solares de Huacho y se sembraron en agar sea water (SWA) suplementado con NaCl al 20% y extracto de levadura al 0.5%. De los 25 microorganismos aislados se seleccionaron 12 por presentar tonos rojizos de pigmentación celular. Los aislados seleccionados fueron analizados para determinar su crecimiento celular y su capacidad de producir betacaroteno, siendo el aislado denominado W2 el que produjo el mayor índice de pigmentación celular; adicionalmente, se determinó la concentración óptima de NaCl y extracto de levadura para incrementar la producción de betacaroteno. El aislado W2 fue identificado por amplificación y secuenciación de la región variable de los genes ribosómicos 165 como Haloferax gibbonsii perteneciente al dominio Archaea, éste llegó a producir 0.6042 mg de betacaroteno/ml de cultivo a 25% de NaCl y 0.5% de extracto de levadura