Questing microbioticks : Interactions of microbes, ticks, vertebrates, and the environment

Krawczyk, Aleksandra I.

doi:10.18174/542129

Cited by 1 publication

(1 citation statement)

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“…We also observed a negative correlation between the total number of reads per sample and the Shannon diversity index, which indicates that samples with low numbers of reads (roughly <1000 reads) show profiles that are indicative of contamination or that those bacteria are present in very low concentrations. This negative correlation is the opposite result of studies performed on the gut microbiome (Willis, 2019) but in‐line with other studies performed on low microbial biomass samples (Karstens et al., 2019; Krawczyk, 2021). Although low numbers of reads are to be expected in low microbial biomass samples such as kidney, the low number of reads complicates distinguishing between DNA from bacteria truly present in the sample (although in low numbers) and DNA from contaminants.…”

Section: Discussionsupporting

confidence: 84%

Screen the unforeseen: Microbiome‐profiling for detection of zoonotic pathogens in wild rats

Cock

Fonville

Vries

et al. 2022

Transbounding Emerging Dis

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Wild rats can host various zoonotic pathogens. Detection of these pathogens is commonly performed using molecular techniques targeting one or a few specific pathogens. However, this specific way of surveillance could lead to (emerging) zoonotic pathogens staying unnoticed. This problem may be overcome by using broader microbiome-profiling techniques, which enable broad screening of a sample's bacterial or viral composition. In this study, we investigated if 16S rRNA gene amplicon sequencing would be a suitable tool for the detection of zoonotic bacteria in wild rats. Moreover, we used virome-enriched (VirCapSeq) sequencing to detect zoonotic viruses. DNA from kidney samples of 147 wild brown rats (Rattus norvegicus) and 42 black rats (Rattus rattus) was used for 16S rRNA gene amplicon sequencing of the V3-V4 hypervariable region. Blocking primers were developed to reduce the amplification of rat host DNA. The kidney bacterial composition was studied using alphaand beta-diversity metrics and statistically assessed using PERMANOVA and SIM-PER analyses. From the sequencing data, 14 potentially zoonotic bacterial genera were identified from which the presence of zoonotic Leptospira spp. and Bartonella tribocorum was confirmed by (q)PCR or Sanger sequencing. In addition, more than 65% of all samples were dominated (>50% reads) by one of three bacterial taxa:Streptococcus (n = 59), Mycoplasma (n = 39) and Leptospira (n = 25). These taxa also showed the highest contribution to the observed differences in beta diversity. Vir-CapSeq sequencing in rat liver samples detected the potentially zoonotic rat hepatitis E virus in three rats. Although 16S rRNA gene amplicon sequencing was limited in its capacity for species level identifications and can be more difficult to interpret due to the influence of contaminating sequences in these low microbial biomass samples, we believe it has potential to be a suitable pre-screening method in the This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

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Section: Discussionsupporting

confidence: 84%