Biology subjects

Sprockett, D. D.

Publications and source records attributed to Sprockett, D. D..

5 recordsLinked to original sources

bioRxiv2024

Hackflex library preparation enables low-cost metagenomic profiling

Shotgun metagenomic sequencing provides valuable insights into microbial communities, but the high cost of library preparation with standard kits and protocols is a barrier for many. New methods such as Hackflex use diluted commercially available reagents to greatly reduce library preparation costs. However, these methods have not been systematically validated for metagenomic sequencing. Here, we evaluate Hackflex performance by sequencing metagenomic libraries from known mock communities as well as mouse fecal samples prepared by Hackflex, Illumina DNA Prep, and Illumina TruSeq methods. Hackflex successfully recovered all members of the Zymo mock community, performing best for samples with DNA concentrations <1 ng/uL. Furthermore, Hackflex was able to delineate microbiota of individual inbred mice from the same breeding stock at the same mouse facility, and statistical modeling indicated that mouse ID explained a greater fraction of the variance in metagenomic composition than did library preparation method. These results show that Hackflex is suitable for generating inventories of bacterial communities through metagenomic sequencing.

microbiology↗

bioRxiv2022

Local adaptation of host-species specific gut microbiota

Mammalian species harbor compositionally distinct gut microbial communities, but the mechanisms that maintain specificity of symbionts to host species remain unclear. Here we show that natural selection within house mice (Mus musculus domesticus) drives deterministic assembly of the house-mouse gut microbiota from mixtures of native and non-native microbiotas. Competing microbiotas from wild-derived lines of house mice and other mouse species (Mus and Peromyscus spp.) within germ-free wildtype (WT) and Rag1-knockout (Rag1-/-) house mice revealed widespread fitness advantages for native gut bacteria. Certain native Bacteriodetes and Firmicutes favored by selection in WT hosts were not favored or disfavored in Rag1-/- hosts, which lack adaptive immunity, indicating that Rag1 mediates fitness advantages of these strains. This study demonstrates local adaptation of gut microbiota to a mammalian species. One-Sentence SummaryAdaptive advantages for native bacteria underlie the assembly of the mouse gut microbiota.

evolutionary biology↗

bioRxiv2022

Spatial and social structure of rewilded laboratory mice

Social behavior and social organization have major influences on individual health and fitness. Yet, biomedical research focuses on studying a few genotypes under impoverished social conditions. Understanding how lab conditions have modified social organizations of model organisms, such as lab mice, relative to natural populations is a missing link between socioecology and biomedical science. Using a common garden design, we describe the formation of social structure in the well-studied laboratory mouse strain, C57BL/6J, in replicated mixed-sex populations over 10-day trials compared to control trials with wild-derived outbred house mice in outdoor field enclosures. We focus on three key features of mouse social systems: (i) territory establishment in males, (ii) female social relationships, and (iii) the social networks formed by the populations. Male territorial behaviors were similar but muted in C57 compared to wild-derived mice. Female C57 sharply differed from wild-derived females, showing little social bias toward cage mates and exploring substantially more of the enclosures compared to all other groups. Female behavior consistently generated denser social networks in C57 than in wild-derived mice. The repeatable societies formed under field conditions highlights opportunities to experimentally study the interplay between society and individual biology using model organisms.

animal behavior and cognition↗

bioRxiv2021

Influential factors of saliva microbiota composition

BackgroundThe oral microbiota is emerging as an influential factor of host physiology and disease state. Factors influencing oral microbiota composition have not been well characterised. In particular, there is a lack of population-based studies. We undertook a large hypothesis-free study of the saliva microbiota, considering potential influential factors of host health (frailty; diet; periodontal disease), demographics (age; sex; BMI) and sample processing (storage time), in a sample (n=679) of the TwinsUK cohort of adult twins. ResultsAlpha and beta diversity of the saliva microbiota was associated most strongly with frailty (alpha diversity: Q = 0.003, Observed; Q=0.002, Shannon; Q=0.003, Simpson; Beta diversity: Q = 0.002, Bray Curtis dissimilarity) and age (alpha diversity: Q=0.006, Shannon; Q=0.003, Simpson; beta diversity: Q=0.002, Bray Curtis dissimilarity; Q= 0.032, Weighted UniFrac) in multivariate models including age, frailty, sex, BMI, frailty and diet, and adjustment for multiple testing. Those with a more advanced age were more likely to be dissimilar in the saliva microbiota composition than younger participants (P = 5.125e-06, ANOVA). In subsample analyses, including consideration of periodontal disease (total n=138, periodontal disease n=66), the association with frailty remained for alpha diversity (Q=0.002, Observed ASVs; Q= 0.04 Shannon Index), but not beta diversity, whilst age was not demonstrated to associate with alpha or beta diversity in this subsample, potentially due to insufficient statistical power. Length of time that samples were stored prior to sequencing was associated with beta diversity (Q = 0.002, Bray Curtis dissimilarity). Six bacterial taxa were associated with age after adjustment for frailty and diet. ConclusionsFrailty and age emerged as the most influential factors of saliva microbiota composition. Whilst frailty and age are correlates, the associations were independent of each other, suggesting that both biological and chronological ageing are key drivers of saliva microbiota composition.

microbiology↗

bioRxiv2019

Microbiota Assembly, Structure, and Dynamics Among Tsimane Horticulturalists of the Bolivian Amazon

Little is known about the relative contributions of selective and neutral forces on human-associated microbiota assembly. Here, we characterize microbial community assembly in 52 Tsimane infant-mother pairs, using longitudinally collected stool and tongue swab samples profiled with 16S rRNA gene amplicon sequencing. The Tsimane are an indigenous Bolivian population who practice infant care associated behaviors expected to increase mother-infant dispersal. Infant consumption of dairy products, vegetables, and chicha (a fermented drink inoculated with oral microbes) was significantly associated with gut microbiota composition. At both body sites, maternal microbes at higher relative abundance were more likely to be shared. Shared microbes were also higher in abundance in infants at both body sites, but decreased in average relative abundance with age and were not significantly higher by 12 months of age. Infant microbiotas were modeled using a neutral community model of assembly, which showed that the prevalence of more than two thirds of infant-colonizing microbes could be explained using neutral processes alone. The same method was applied to datasets from Finnish and Bangladeshi infants, confirming that the majority of microbes colonizing infants from different countries were neutrally distributed. Among the Tsimane infant and adult gut microbiota samples, neutral processes were less prominent in villages with more market access. These results underscore the importance of neutral processes during infant microbiota assembly, and suggest that cultural changes associated with market integration may be affecting traditional modes of microbiota assembly by decreasing the role of these neutral processes, perhaps through changes in diet, sanitation, or access to medical care.

microbiology↗