Rumen and fecal microbiomes are related to diet and production traits in Bos indicus beef cattle.

Background: Ruminants harbor a complex microbial community within their gastrointestinal tract, which plays major roles in their health and physiology. Brazil is one of the largest producers of beef in the world and more than 90% of the beef cattle herds are composed of pure and crossbred Nelore (Bos indicus). Despite its importance to the Brazilian economy and human feeding, few studies have characterized the Nelore microbiome. Therefore, using shotgun metagenomics, we investigated the impact of diet on the composition and functionality of the Nelore microbiome, and explored the associations between specific microbial taxa and their functionality with feed efficiency and methane emission. Results: The ruminal microbiome exhibited significantly higher microbial diversity, distinctive taxonomic profile and variations in microbial functionality compared to the fecal microbiome, highlighting the distinct contributions of the microbiomes of these environments. Animals subjected to different dietary treatments exhibited significant differences in their microbiomes' archaeal diversity and in the abundance of 89 genera, as well as in the functions associated with the metabolism of components of each diet. Moreover, depending on the diet, feed-efficient animals and low methane emitters displayed higher microbial diversity in their fecal microbiome. Multiple genera were associated with an increase or decrease of the phenotypes. Upon analyzing the functions attributed to these taxa, we observed significant differences on the ruminal taxa associated with feed efficient and inefficient cattle. The ruminal taxa that characterized feed efficient cattle stood out for having significantly more functions related to carbohydrate metabolism, such as monosaccharides, di-/oligosaccharides and amino acids. The taxa associated with methane emission had functions associated with methanogenesis and the production of substrates that may influence methane production, such as hydrogen and formate. Conclusion: Our findings highlight the significant role of diet in shaping Nelore microbiomes and how its composition and functionality may affect production traits such as feed efficiency and methane emission. These insights provide valuable support for the implementation of novel feeding and biotechnological strategies.

Heavy metal resistance in the Yanomami and Tunapuco microbiome

BACKGROUND The Amazon Region hosts invaluable and unique biodiversity as well as mineral resources. Consequently, large illegal and artisanal gold mining areas exist in indigenous territories. Mercury has been used in gold mining, and some has been released into the environment and atmosphere, primarily affecting indigenous people such as the Yanomami. In addition, other heavy metals have been associated with gold mining and other metal-dispersing activities in the region. OBJECTIVE Investigate the gut microbiome of two semi-isolated groups from the Amazon, focusing on metal resistance. METHODS Metagenomic data from the Yanomami and Tunapuco gut microbiome were assembled into contigs, and their putative proteins were searched against a database of metal resistance proteins. FINDINGS Proteins associated with mercury resistance were exclusive in the Yanomami, while proteins associated with silver resistance were exclusive in the Tunapuco. Both groups share 77 non-redundant metal resistance (MR) proteins, mostly associated with multi-MR and operons with potential resistance to arsenic, nickel, zinc, copper, copper/silver, and cobalt/nickel. Although both groups harbour operons related to copper resistance, only the Tunapuco group had the pco operon. CONCLUSION The Yanomami and Tunapuco gut microbiome shows that these people have been exposed directly or indirectly to distinct scenarios concerning heavy metals.

Phylogenetic analyses of chikungunya virus among travelers in Rio de Janeiro, Brazil, 2014-2015

Chikungunya virus (CHIKV) is a mosquito-borne pathogen that emerged in Brazil by late 2014. In the country, two CHIKV foci characterized by the East/Central/South Africa and Asian genotypes, were established in North and Northeast regions. We characterized, by phylogenetic analyses of full and partial genomes, CHIKV from Rio de Janeiro state (2014-2015). These CHIKV strains belong to the Asian genotype, which is the determinant of the current Northern Brazilian focus, even though the genome sequence presents particular single nucleotide variations. This study provides the first genetic characterisation of CHIKV in Rio de Janeiro and highlights the potential impact of human mobility in the spread of an arthropod-borne virus.

Parvovirus B19 1A complete genome from a fatal case in Brazil

Parvovirus B19 (B19V) infects individuals worldwide and is associated with an ample range of pathologies and clinical manifestations. B19V is classified into three distinct genotypes, all identified in Brazil. Here, we report a complete sequence of a B19V genotype 1A that was obtained by high-throughput metagenomic sequencing. This genome provides information that will contribute to the studies on B19V epidemiology and evolution.

Metagenômica na investigação de agentes infecciosos em amostras clínicas humanas / Metagenomics in the investigation of infectious agents in human clinical samples

O vírus dengue infecta um número estimado de 50-100 milhões de pessoasanualmente em todo o mundo e no Brasil, dengue foi relatada pela primeira vez em1981, desde então, a infecção tornou-se hiper-endêmica. As práticas atuais dediagnóstico não detectam o vírus em cerca de 50% dos casos suspeitos.Metagenômica é uma estratégia que pode ser aplicada na identificação de qualquerorganismo em uma amostra, uma vez que recupera sequências de ácidos nucléicosque são analisadas contra bases de dados. Neste estudo, o nosso objetivo foiaplicar abordagens de metagenômica para analisar casos fatais de pacientes queapresentaram sintomas similares a dengue, mas com teste negativo para este víruse também amostras de pacientes com suspeita de febre amarela. DNA e RNAgenômico foram extraídos, amplificados com iniciadores randômicos e processadosno sequenciador Illumina HiSeq2500. Em seguida, aplicamos um pipeline debioinformática para filtragem de sequências de baixa qualidade e remoção desequências humanas. Vários programas foram utilizados para classificar as readsmetagenômicas: Kraken, GOTTCHA, SURPI, Metaphlan2, Taxoner e Blastn. Asanálises in silico identificaram patógenos que foram posteriormente confirmados porensaios in vitro aplicando reagentes específicos. Deste modo, identificamos vírus ebactérias em 13% das amostras. Quatro desses vírus, com potencial depatogenicidade estavam em amostras distintas: Parvovírus B19, vírus da hepatite A,vírus da hepatite G e vírus Torque-teno. Todos eles, com exceção do vírus daHepatite A estavam nos casos fatais. O Parvovírus B19 é um agente patogênico quetem sido associado a casos fatais. As bactérias identificadas foram N. meningitidis do serogrupo C em duas amostras e S...

Dengue virus infects an estimated 50–100 million people annually worldwide and inBrazil, dengue was first reported in 1981, since then the infection became hyperendemic.The current diagnostic practices cannot detect the virus in around 50% ofsuspected cases. Metagenomic is a strategy that can be applied to recover anyorganism in a sample. In this study, our aim was to apply metagenomic approachesto analyse fatal cases of patients presenting dengue-like symptoms, but testingnegative for this virus and samples of patients with suspected yellow fever. GenomicDNA and RNA were extracted, amplified with random primers and sequenced in theIllumina HiSeq2500 sequencer. We then followed a bioinformatic filtering pipeline toremove both low-quality sequences and human sequences. Several tools were usedto classify the metagenome reads: Kraken, GOTTCHA, SURPI, Metaphlan2, Taxonerand Blastn. The in silico analysis identified pathogens that were further confirmed byin vitro assays applying specific reagents. In this way, we were able to detect virusesand bacteria in 13% of the samples. Four viruses, with pathogenicity potential wereidentified in distinct samples: Parvovirus B19, Hepatitis A virus, Hepatitis G virus andTorque-teno virus. All of them, except Hepatitis A virus were present in fatal cases.The Parvovirus B19 is in fact a pathogen that has been eventually associated to fatalcases. The bacteria identified were N. meningitidis serogroup C in two samples andS. pneumoniae in two other samples...