An important factor in quality control of non-invasive prenatal screening (NIPS) or testing (NIPT) is a sufficient percentage of fetal DNA to avoid false-negative results. Here we evaluate 14,379 shallow whole-genome sequenced diagnostic NIPS samples, as well as negative controls, for both technical and biological factors that can influence fetal fraction and its assessment. Technically, bioinformatics analyses can have a profound impact on fetal fraction determination. We found best performance for fetal fraction determination with the Y chromosome based tool DEFRAG for male fetuses and the count based tool SeqFF for female fetuses. Biologically, gestational age of up to 21 weeks and maternal age had no influence on fetal fraction, while an increase in weight and BMI had a negative influence on fetal fraction. While a trend was observed, no statistically significant difference in fetal fraction was found between trisomy and normal samples. Overall, these results confirm the influence of biological factors and give insight into technical factors that can affect fetal fractions in NIPS.

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We carried out a comparative analysis between the bacterial microbiota composition of zoo-housed western lowland gorillas and their wild counterparts through 16S rRNA gene amplicon sequencing. In addition, we characterised the carbohydrate-active and methanogenic potential of the zoo-housed gorilla (ZHG) microbiome through shotgun metagenomics and RNA sequencing. The ZHG microbiota showed increased alpha diversity in terms of bacterial species richness and a distinct composition from that of the wild gorilla microbiota, including a loss of abundant fibre-degrading and hydrogenic Chloroflexi. Metagenomic analysis of the CAZyome indicated predominant oligosaccharide-degrading activity, while RNA sequencing revealed diverse cellulase and hemi-cellulase activities in the ZHG gut, contributing to a total of 268 identified carbohydrate-active enzymes. Metatranscriptome analysis revealed a substantial contribution of 38% of the transcripts from anaerobic fungi and archaea to the gorilla microbiome. This activity originates from cellulose-degrading and hydrogenic fungal species belonging to the class Neocallimastigomycetes, as well as from methylotrophic and hydrogenotrophic methanogenic archaea belonging to the classes Thermoplasmata and Methanobacteria, respectively. Our study shows the added value of RNA sequencing in a multiomics approach and highlights the contribution of eukaryotic and archaeal activities to the gut microbiome of gorillas.

We carried out a comparative analysis between the microbiota composition of zoo-housed western lowland gorillas (Gorilla gorilla gorilla) and their counterparts living in the wild through 16s rRNA gene amplicon sequencing. In addition, we characterized the carbohydrate active potential and activity of the zoo-housed gorilla microbiome through shotgun metagenomics and RNA-seq. Alpha and beta-diversity indices significantly decreased in the zoo-housed gorilla microbiota compared to those of their wild fellow species. Abundant fiber-degrading native bacterial taxa of the wild gorilla gut, Chloroflexi andOlsenella, vanished, whereas oligosaccharide-consumingLactobacillusspecies blossomed in presumably, the upper gastro-intestinal-tract of the zoo-housed gorilla. Metagenomic analysis of the CAZyome indicated predominant oligosaccharide-degrading activity, while RNA-sequencing revealed diverse cellulase and hemi-cellulase activities in the zoo-housed gorilla gut, contributing to a total of 268 identified carbohydrate active enzymes. We demonstrated for the first-time major activity of the cellulose-degrading fungi Neocallimastigomycetes and methanogenic archaea in the gorilla gut, the latter known to feed on hydrogen produced by the anaerobic fungi. We propose that the zoo-housed gorilla microbiome is adapted in composition and reduced in bacterial diversity due to lifestyle effects, while a previously unacknowledged fiber-degrading capacity is sustained by anaerobic gut fungi. Our study shows the added value of RNA-seq in a multiomics approach and highlights the contribution of eukaryotic and archaeal activity to the gorilla gut microbiome.