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A cross-sectional study was conducted to determine the prevalence and risk factors of Cryptosporidium infection and identify species of the parasite in cattle in central Ethiopia. Faecal samples, collected from 392 dairy cattle managed under intensive and extensive production system, were analyzed by the Modified Ziehl-Neelsen (MZN) microscopy, Nested PCR, PCR-RFLP and sequence analyses of the SSU rRNA gene of Cryptosporidium. The overall prevalence, the prevalence in the extensive and intensive farms was 18.6%, 11% and 21%, respectively. The infection was detected in 37.7% of the investigated farms with prevalence range of 7.4% -100%, and all of the six surveyed districts with significant (P = 0.000) prevalence difference. Restriction digestion and sequence analysis showed Cryptosporidium parvum and C. andersoni in 27% and 73% of the infections, respectively, showing an age related distribution pattern, C. parvum exclusively occurring in calves, Highlights • Cryptosporidium infection, due to C. parvum and C. andersoni, is widespread in cattle in central Ethiopia. • C parvum and C andersoni exclusively occurred in calves

Cryptosporidium spp. are common intestinal protozoan parasites that causes diarrhoea in neonates and young calves. This longitudinal study was conducted at two large dairy cattle farms in central Ethiopia during February/2014 to June/2015 to determine the age-related distribution of Cryptosporidium species, to identify risk factors of the disease and to assess the public health significance of the parasite. Thirty calves born to these dairy farms were followed-up from birth to three months of age, and 270 faecal samples were collected and examined by the Modified Ziehl-Neelsen, PCR-RFLP and Sequencing. Cryptosporidium was detected from week 1 to 3 months of age with an overall prevalence of 14.8%, Peak of the infection was at two weeks of age when 12 of the 30 calves (40%) shedded oocysts. Cryptosporidium parvum and C. andersoni were identified in pre-weaned and post-weaned calves, respectively. Phylogenetic analysis showed clustering of the C. parvum isolates from this study with GenBank sequences for C. parvum bovine genotype IIa and IId subtypes. This study showed the predominance of the zoonotic C. parvum species in pre-weaned calves and demonstrated that this age group of calves pose the greatest risk for human infection. Due attention on the management of pre-weaned calves is recommended to prevent transmission of the infection to humans and lessen contamination of the environment by oocysts.

Background: Analysis of shotgun metagenomic data generated from next generation sequencing platforms can be done through a variety of bioinformatic pipelines. These pipelines employ different sets of sophisticated bioinformatics algorithms which may affect the results of this analysis. Furthermore, no conventional assessment technique for estimating the precision of each pipeline exists and few studies have been carried out to compare the characteristics, benefits and disadvantages of each pipeline. In this study we compared two commonly used pipelines for shotgun metagenomic analysis: MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST) and Kraken, in terms of taxonomic classification, diversity analysis and usability using their primarily default parametersResults: Overall, the two pipelines detected similar abundance distributions in the three most abundant taxa Proteobacteria, Firmicutes and Bacteroidetes. Within bacterial domain, 497 genera were identified by both pipelines, while an additional 694 and 98 genera were solely identified by Kraken and MG-RAST respectively. 933 species were detected by the two algorithms. Kraken solely detected 3550 species, while MG-RAST identified 557 species uniquely. For archaea, Kraken generated 105 and 236 genera and species respectively while MG-RAST detected 60 genera and 88 species. 54 genera and 72 species were commonly detected by the two methods. Kraken had a quicker analysis time (~4 hours) while MG-RAST took approximately 2 days per sample.Conclusions: This study revealed that Kraken and MG-RAST generate comparable results and that a reliable high-level overview of sample is generated irrespective of the pipeline selected. The observed variations at the genus level show that a main restriction is using different databases for classification of the metagenomic data. Specifically, the pipelines could have been limited because some rumen microbes lack reference genomes. The results of this research indicate that a more inclusive and representative classification of microbiomes may be achieved through creation of combined pipelines.

Figure S2. Size and frequency of de novo-assembled representative contigs with high similarity to known viruses. In total 68 samples were sequenced and analyzed. Contig size is represented in 0.5 Kb increments in the X axis. The Y axis represents the number of contigs per size class. For each virus, the number of samples categorized as infected is indicated. a MCMV. b SCMV. c MSV. d MYDV-RMV. (PDF 278Â kb)

Figure S3. Partial nucleotide sequence alignment of Kenya samples in group 1, 2 and 3 relative to the Ohio isolate of SCMV (JX188385.1). The coat protein detected in the original description of maize lethal necrosis in Kenya was used for comparison (JX286708.1) [6]. Alignment was generate using MAFFT. NIb and coat protein coding sequences are color coded blue and red, respectively. Coordinates are based on the Ohio isolate (JX188385.1). In group 1 no nucleotide insertions or deletions were observed. Nucleotide substitutions resulted in amino acid substitutions. Group two, had a 39Â nt deletion (8487 to 8525) that resulted in an in-frame deletion of 13 amino acids. Group 3, had low similarity and a 45Â nt deletion between nt 8487 to 8676 that resulted in a 15-amino acid deletion. (PDF 256Â kb)

Los microorganismos constituyen el grupo de organismos más diverso de nuestro planeta dando lugar a comunidades muy dinámicas y con capacidades metabólicas extraordinarias (Brock y Madigan, 2000). Además, los microorganismos también tienen la capacidad de adaptarse rápidamente a condiciones nuevas (Cases y otros, 2002). Sin embargo, hoy en día se considera que aún sólo se conoce un mínimo porcentaje del total de las especies microbianas existentes (Curtis y otros, 2002). Las teorías actuales sobre la distribución de microorganismos en los diferentes ecosistemas se asientan sobre la cita de Baas- Becking (“Everything is everywhere, but, the environment selects”) según la cual los microorganismos pueden encontrarse en cualquier sitio, pero el ambiente los selecciona (Baas-Becking 1934; Van der Gast y otros, 2005). Estudios sobre la biodiversidad y biogeografía microbianas (Garcia-Pichel y otros, 1996; Zwart y otros, 1998; Richards y otros, 2005) han utilizado este principio para explicar la estructura de comunidades microbianas y su organización en micronichos., Proyecto europeo MARIE CURIE ACTION (EARLY STAGE TRAINING) “Advanced Research Training on the Conservation of Cultural Heritage” MEST-CT2004-513915 y gracias a la Conserjería de Cultura, Dirección General de Bienes Culturales, Convenio para el estudio de la cueva de Ardales.

2 páginas, 9 referencias. Póster publicado en el Libro de Resúmenes de la 9ª Reunión de la Red Temática del CSIC de Patrimonio Histórico y Cultural. Sevilla, 4 y 5, marzo, 2008., La Cueva de Doña Trinidad (Ardales, Málaga) fue descubierta en 1821 tras un gran terremoto. Tiene una edad geológica de dos millones y medio de años y una altitud sobre el nivel del mar de 550-560 m. En 1860 la señora Trinidad Grund compró la cueva e inició su explotación turística. En el interior de la cueva se encuentran laberintos de columnas, formaciones de estalactitas y estalagmitas, lagos permanentes y sobre todo pinturas rupestres y grabados del Paleolítico Superior. El primer gran estudioso de la cueva fue Henry Breuil, quien en 1921 describió sus pinturas y grabados.

Póster presentado a la citada conferencia, celebrada del 28 noviembre-1 diciembre, 2007, Sevilla, España.

4 pages, 1 figure, 13 references. Electronic Newsletter. CSIC Thematic Network on Cultural Heritage and Network on Science and Technology for the Conservation of Cultural Heritage Instituto de Recursos Naturales y Agrobiología de Sevilla, CSIC, Apartado de Correos 1052, 41080 Sevilla (Spain). The facilities and support provided by the Consejería de Cultura, Junta de Andalucía are gratefully acknowledged., Caves often contain rock art paintings some of them dated from the Palaeolithic period, over 20,000 years old. At present, most known rock art paintings are affected by progressive biodeterioration (Holden 2002, 2003, Allemand and Bahn 2005, Sire 2006) and the control and preservation of these environments is a serious problem gathering the interest of scientists and conservators. In the Mediterranean area, several examples of Palaeolithic paintings have been found in caves such as La Pileta and Doña Trinidad, both in Malaga (Spain)., This work was supported by the European Commission, Marie Curie Actions MEST-CT2004-513915.

Comunicación oral presentada al citado congreso, celebrado del 18-22, octubre, en Palermo, Italia.