Biology subjects

Susanti, D.

Publications and source records attributed to Susanti, D..

3 recordsLinked to original sources

bioRxiv2022

SMbiot: A Shared Latent Model for Microbiomes and their Hosts

The collective nature of the variation in host associated microbial communities suggest that they exhibit low dimensional characteristics. To identify these lower dimensional descriptors, we propose SMbiot (pronounced SIM BY OT): a Shared Latent Model for Microbiomes and their hosts. In SMbiot, latent variables embed host-specific microbial communities in a lower dimensional space and the corresponding features reflect controlling axes that dictate community compositions. Using data from different animal hosts, organ sites, and microbial kingdoms of life, we show that SMbiot identifies a small number of host-specific latent variables that accurately capture the compositional variation in host associated microbial communities. By using the same latents to describe hosts phenotypic states and the host-associated microbiomes, we show that the latent space embedding is informed by host physiology as well as the associated microbiomes. Importantly, SMbiot enables the quantification of host phenotypic differences associated with altered microbial community compositions in a host-specific manner, underscoring the context specificity of host-microbiome associations. SMbiot can also predict missing host metadata or microbial community compositions. This way, SMbiot is a concise quantitative method to understand the low dimensional collective behavior of host-associated microbiomes.

systems biology↗

bioRxiv2022

Interactions between time on diet, antibiotic treatment, and liver abscess development on the fecal microbiome of beef cattle

Liver abscesses caused by polymicrobial infections of the liver are a widespread problem in feedlot cattle production. There are currently no effective methods for the early detection of liver abscesses or to predict antibiotic efficacy. Although gene expression and microbiome differences have been reported in the rumen of abscessed and normal animals, liver abscess biomarkers using less invasive tools can facilitate managing of the disease in the field. Here we report the results of two studies measuring the fecal microbiome composition of steers that did or did not develop liver abscesses, with or without antibiotic treatment, along a 7-month feeding period on a high-concentrate diet. Our results indicate a limited impact of liver abscesses or tylosin on fecal microbiome composition, with time on diet explaining most variance in the fecal microbiome. Interestingly, in both studies, antibiotic treatment led to larger differences in both the composition and variance of the fecal microbiomes between abscessed and normal animals compared to controls. These differences were limited to specific sampling times in each of the two studies. Although multiple amplicon sequence variants with differential abundances according to liver abscess state were identified, there was no overlap between the two studies. Our results suggests that early fecal biomarkers of liver abscess susceptibility might be developed, especially for animals receiving preventative antibiotics, but the fecal abundance of individual microorganisms may not be a robust predictor across different sampling times or diet regimes.

microbiology↗

bioRxiv2020

Dominant Remodeling of Cattle Rumen Microbiome by Schedonorus arundinaceus (Tall Fescue) KY-31 Carrying a Fungal Endophyte

Tall fescue KY-31 feeds ~20% of the beef cattle in the United States. It carries a fungal endophyte that produces ergovaline, which causes toxicosis in cattle, leading to $2 billion revenue loss annually. The MaxQ cultivar of the grass is non-toxic, but less attractive economically. To develop ways of mitigating the toxicity, the rumen microbiome of cattle consuming KY-31 and MaxQ have been analyzed, principally for identifying ergovaline transforming microorganisms and often using fecal microbiome as a surrogate. We have hypothesized that KY-31 not only causes toxicosis, but also impacts rumen metabolism broadly, and tested the hypothesis by analyzing rumen microbiome compositions of cattle that grazed MaxQ with an intervening KY-31 grazing period with 16S rRNA-V4 element as identifier. We found that KY-31 remodeled the cellulolytic and saccharolytic communities substantially. This effect was not evident at whole microbiome levels but in the compositions of sessile and planktonic fractions. A move from MaxQ to KY-31 lowered the Firmicutes abundance in the sessile fraction and increased it in planktonic part and caused an opposite effect for Bacteroidetes, although the total abundances of these dominant rumen organisms remained unchanged. In the sessile fraction, the abundances of Fibrobacter, which degrades less degradable fibers, and certain cellulolytic Firmicutes such as Pseudobutyrivibrio and Butyrivibrio 2, dropped, and these losses were apparently compensated by increased occurrences of Eubacterium and specific Ruminococcaceae and Lachnospiraceae. In planktonic fraction the Tenericutes abundance increased as saccharolytic Bacteroidetes level dropped. Several potential ergovaline degraders were enriched. A return to MaxQ restored the original Firmicutes and Bacteroidetes distributions. However, the Fibrobacter and Butyrivibrio 2 abundances remained low and their substitutes maintained significant presence. The rumen microbiome was influenced minimally by animals fescue toxicosis and was distinct from previously reported fecal microbiomes in composition. In summary, KY-31 and MaxQ cultivars of tall fescue were digested in the cattle rumen with distinct consortia and the KY-31-specific features were dominant. The study highlighted the importance of analyzing sessile and planktonic fractions separately.

microbiology↗