scholarly journals Metagenomic Analysis of the Enteric RNA Virome of Infants from the Oukasie Clinic, North West Province, South Africa, Reveals Diverse Eukaryotic Viruses

Viruses ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 1260
Author(s):  
Milton T. Mogotsi ◽  
Peter N. Mwangi ◽  
Phillip A. Bester ◽  
M. Jeffrey Mphahlele ◽  
Mapaseka L. Seheri ◽  
...  
Keyword(s):  
South Africa ◽  
Genomic Analysis ◽  
Illumina Miseq ◽  
Viral Population ◽  
Early Developmental Stage ◽  
Health State ◽  
North West ◽  
Viral Shedding ◽  
Healthy Infants ◽  
Miseq Platform

Establishing a diverse gut microbiota after birth is essential for preventing illnesses later in life. However, little knowledge exists about the total viral population (virome) present in the gut of infants during the early developmental stage, with RNA viruses being generally overlooked. Therefore, this small pilot longitudinal study investigated the diversity and changes in the enteric RNA virome in healthy infants from South Africa. Faecal samples (n = 12) were collected from four infants at three time points (on average at 8, 13, and 25 weeks), and then sequenced on an Illumina MiSeq platform. The genomic analysis revealed a diverse population of human enteric viruses from the infants’ stools, and changes in the enteric virome composition were observed over time. The Reoviridae family, more specifically the Rotavirus genus, was the most common and could be linked to viral shedding due to the administration of live-attenuated oral vaccines in South Africa, followed by the Picornaviridae family including parechoviruses, echoviruses, coxsackieviruses, enteroviruses, and polioviruses. Polioviruses were also linked to vaccine-related shedding. Astroviridae (astroviruses) and Caliciviridae (noroviruses) were present at low abundance. It is evident that an infant’s gut is colonized by distinct viral populations irrespective of their health state. Further characterization of the human virome (with a larger participant pool) is imperative to provide more conclusive insights into the viral community structure and diversity that has been shown in the current study, despite the smaller sample size.

scholarly journals Comparative Pathogenomics of Aeromonas veronii from Pigs in South Africa: Dominance of the Novel ST657 Clone

2020 ◽  
Vol 8 (12) ◽  
pp. 2008
Author(s):  
Yogandree Ramsamy ◽  
Koleka P. Mlisana ◽  
Daniel G. Amoako ◽  
Akebe Luther King Abia ◽  
Mushal Allam ◽  
...  
Keyword(s):  
South Africa ◽  
Orthologous Gene ◽  
Gene Clusters ◽  
Illumina Miseq ◽  
Aeromonas Veronii ◽  
Carbapenem Resistant ◽  
Kwazulu Natal ◽  
Miseq Platform ◽  
Differential Ability ◽  
Potential Pathogenicity

The pathogenomics of carbapenem-resistant Aeromonas veronii (A. veronii) isolates recovered from pigs in KwaZulu-Natal, South Africa, was explored by whole genome sequencing on the Illumina MiSeq platform. Genomic functional annotation revealed a vast array of similar central networks (metabolic, cellular, and biochemical). The pan-genome analysis showed that the isolates formed a total of 4349 orthologous gene clusters, 4296 of which were shared; no unique clusters were observed. All the isolates had similar resistance phenotypes, which corroborated their chromosomally mediated resistome (blaCPHA3 and blaOXA-12) and belonged to a novel sequence type, ST657 (a satellite clone). Isolates in the same sub-clades clustered according to their clonal lineages and host. Mobilome analysis revealed the presence of chromosome-borne insertion sequence families. The estimated pathogenicity score (Pscore ≈ 0.60) indicated their potential pathogenicity in humans. Furthermore, these isolates carried several virulence factors (adherence factors, toxins, and immune evasion), in different permutations and combinations, indicating a differential ability to establish infection. Phylogenomic and metadata analyses revealed a predilection for water environments and aquatic animals, with more recent reports in humans and food animals across geographies, making A. veronii a potential One Health indicator bacterium.

scholarly journals Draft Genomic Analysis of Pseudomonas sp. Strain OA3, a Potential Plant Growth-Promoting Rhizospheric Bacterium

2021 ◽  
Vol 10 (11) ◽  
Author(s):  
Olubukola Oluranti Babalola ◽  
Oluwaseun Adeyinka Fasusi ◽  
Adenike Eunice Amoo ◽  
Ayansina Segun Ayangbenro
Keyword(s):  
South Africa ◽  
Plant Growth ◽  
Genome Analysis ◽  
Genomic Analysis ◽  
Pseudomonas Sp ◽  
North West ◽  
North West Province ◽  
Plant Growth Promoting ◽  
Growth Promoting

ABSTRACT The genome analysis of the plant growth-promoting rhizospheric Pseudomonas sp. strain OA3, isolated from maize in North West Province, South Africa, is reported in this study. Pseudomonas sp. strain OA3 exhibits plant growth-promoting ability by enhancing maize and soybean growth.

scholarly journals Genome Sequence of Listeria innocua Strain MEZLIS26, Isolated from a Goat in South Africa

2019 ◽  
Vol 8 (44) ◽  
Author(s):  
Mohamed E. El Zowalaty ◽  
Rachel A. Hickman ◽  
Alexandra Moura ◽  
Marc Lecuit ◽  
Oliver T. Zishiri ◽  
...  
Keyword(s):  
South Africa ◽  
Genome Sequence ◽  
Dna Sequences ◽  
Draft Genome ◽  
Illumina Miseq ◽  
Listeria Innocua ◽  
Eastern Cape ◽  
Content Type ◽  
Transfer Rnas ◽  
Miseq Platform

Here, we report the draft genome sequence of Listeria innocua strain MEZLIS26, isolated from a healthy goat in Flagstaff, Eastern Cape Province, South Africa. The genome was sequenced using the Illumina MiSeq platform and had a length of 2,800,777 bp, with a G+C content of 37.4%, 2,755 coding DNA sequences (CDSs), 49 transfer RNAs (tRNAs), and 4 noncoding RNAs (ncRNAs).

scholarly journals PSIX-6 Gastrointestinal microbiome of calves fed solid diets containing different levels and sources of NDF

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 418-419
Author(s):  
Gercino F Virgínio Júnior ◽  
Milaine Poczynek ◽  
Ana Paula Silva ◽  
Ariany Toledo ◽  
Amanda Cezar ◽  
...  
Keyword(s):  
Illumina Miseq ◽  
Diversity Indices ◽  
Dairy Calves ◽  
Rrna Gene ◽  
Gastrointestinal Microbiome ◽  
Fecal Microbiome ◽  
Miseq Platform ◽  
Holstein Calves ◽  
Ad Libitum ◽  
Different Levels

Abstract Different levels and sources of NDF can modify the gastrointestinal microbiome. This study evaluated 18 Holstein calves housed in not-bedded suspended individual cages and fed one of three treatments: 22NDF - conventional starter containing 22% NDF (n = 7); 31NDF - starter with 31% NDF, replacing part of the corn by soybean hull (n = 6); and 22NDF+H - conventional starter with 22% NDF plus coast-cross hay ad libitum (n = 5). All animals received 4 L of milk replacer daily (24% CP; 18.5% fat; diluted to 12.5% solids), divided into two meals, being weaned at 8th week of age. After weaning, animals were housed in tropical shelters, fed with the respective solid diet and coast-cross hay ad libitum for all treatments. To evaluate the microbiome, ruminal fluid samples were collected using a modified Geishauser oral probe at weeks 2, 4, 6, 8 and 10, two hours after the morning feeding, and fecal samples were collected at birth (0) and at weeks 1, 2, 4, 8 and 10. The microbial community was determined by sequencing V3 and V4 region amplicons of the 16S rRNA gene that was amplified by PCR and sequenced by the Illumina MiSeq platform. Ruminal microbiome had no differences in diversity for the effects of weeks, treatments or interaction of both factors (Table 1). In feces, the diversity indices and evenness were higher for 22NDF+H when compared to 22NDF, with no difference for 31NDF. All indices were significantly affected by calves age. At birth, calves had the greatest diversity and richness. Week 1 and 2 had less evenness and diversity. Bacteroidota, Firmicutes_A and Firmicutes_C were the most abundant phylum in rumen and feces. The supply of hay was only effective in modifying the fecal microbiome of dairy calves, suggesting a resilience in the ruminal microbiome.

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