Biology subjects

Mills, D. A.

Publications and source records attributed to Mills, D. A..

8 recordsLinked to original sources

bioRxiv2025

Indoor environmental conditions shape the microbial landscape of food production facilities across space and time

The microbial communities inhabiting food production environments are distinguished from those of other built environments in their capacity to influence food quality and safety, impacting consumer health. However, how indoor environmental conditions drive the bacterial and fungal communities of food production facilities remains largely unknown. In this study of five commercial food production facilities, we employed remote wireless sensors paired with marker-gene amplicon sequencing (bacterial 16S rRNA genes and fungal ITS) of processing equipment and non-processing built environment surfaces (N=2,329) to profile spatial and longitudinal changes in bacterial and fungal communities, and their association with indoor climate. We identify multiple associations between indoor environmental conditions and microbial community structure, demonstrating the role of the indoor environment in shaping microbial communities on food processing and non-processing surfaces. This suggests that indoor climate could be manipulated to rationally modify surface communities, with the aim of enhancing food quality and safety.

microbiology↗

bioRxiv2025

Spatial heterogeneity and microbial terroir: balancing dispersal limitation and cultivar as drivers of microbial diversity in viticulture

The microbial communities inhabiting grapevines and wines exhibit spatiotemporal patterns linked to region, climate, and cultivar. However, the degree of spatial heterogeneity within and between vineyards and its relationship to cultivar-associated biodiversity selection has not been studied previously. We combined high-density sampling of grapevine microbiota (N = 230) with spatial modeling and satellite imagery in two experiments: (i) two monoclonal Chardonnay vineyards to examine spatial heterogeneity in a genetically homogenous population; and (ii) three old-vine vineyards interplanted with mixed cultivars to investigate the relative effects of spatial distance and cultivar on the microbiota. Contrary to expectations based on monoclonal vineyards, cultivar effects were not apparent in mixed-cultivar vineyards. Instead, we demonstrate extensive spatial variation in the bacterial and fungal communities inhabiting individual grapevines and vineyards, and that community similarity is correlated with spatial distance within and between vineyards. This suggests that dispersal limitation may play an important role in shaping grapevine microbiota, as well as cumulative diversity within the vineyard ecosystem (gamma diversity), with implications for both plant health and wine quality. Spatial models can identify abnormalities in microbial communities, such as contaminant sources within vineyards, and future studies examining microbiota in agricultural settings should account for spatial variation within the study design, e.g., by sufficiently dense spatial sampling or collection of grape musts to avoid undersampling bias. These findings add to the complicated story of microbial biogeography associated with winegrowing and wine quality (microbial terroir), highlighting the roles of dispersal and potential microclimate effects in agricultural settings.

microbiology↗

bioRxiv2025

Whey Protein Phospholipid Concentrate Supplementation Prevents High-Fat Diet Induced Cognitive Impairment in Wistar Rats by Promoting Brain Neuronal Connectivity and Sphingolipid Clearance

Whey protein phospholipid concentrate (WPPC), a byproduct of whey protein processing, is high in phospholipids and glycoconjugates which serve as substrates for fatty acids and sugar monomers (e.g. sialic acid) critical to neuronal myelin synthesis in the brain. This led us to hypothesize that WPPC will improve cognitive impairment induced by a high fat (HF) diet by promoting myelin turnover and improving myelin-dependent processes associated with encoding and storing memory. Male Wistar rats were randomized to one of four diets starting at weaning to [~]6.5 months on age: a low-fat (LF) diet containing 10% fat by weight, a HF diet containing 45% fat by weight to induce cognitive impairment, and a HF diet containing either 1.6% or 10% WPPC by weight (n=12 per diet). Rats were subjected to cognitive testing after 2 and 4 months of dietary intervention and then implanted with chronic bipolar electrodes to measure axonal evoked responses within the entorhinal cortex-hippocampal circuitry. Phospholipid and sphingolipid components of myelin were quantified in the hippocampus. There were no significant differences in cognition measured by novel object recognition after 2 months of supplementation. At 4 months, rats on the HF diet performed significantly worse than rats on the LF, HF1.6 and HF10 diets. The beneficial effects of WPPC on cognition were due to a partial reversal in evoked response impairments in hippocampal memory storage. Additionally, hippocampus sphingolipids were higher in rats on the HF diet compared to the LF, HF1.6 and HF10 groups. These findings demonstrate that WPPC prevented cognitive impairment induced by a HF diet by regulating entorhinal cortex-hippocampal circuitries associated with memory storage, though modulating myelin turnover.

neuroscience↗

bioRxiv2025

A Milk Fat Globule Membrane-enriched dairy co-product modulates gut Faecalibaculum rodentium metabolism in association with the prevention of cognitive impairment in aging male Wistar rats

Consumption of the milk fat globule membrane (MFGM) by infants is linked to enhanced neurodevelopment and sustained cognitive improvements later in life. Aging, by contrast, is often marked by neurodegeneration and cognitive decline-a growing concern in the U.S. as 6.9 million Americans live with Alzheimers disease (AD). As such, identifying interventions to prevent cognitive impairment are imperative. The whey protein phospholipid concentrate (WPPC), a dairy co-product, is enriched in MFGM glycoconjugates. Given the cognitive health benefits conferred by MFGM consumption in early life, we previously found that high-fat (HF) diet induced cognitive impairment in aging male Wistar rats was prevented by supplementating with a 1.6% or 10% WPPC in the diet, compared to control rats fed a low-fat (LF) diet. We hypothesized that WPPC exerts protective effects against cognitive impairment through the gut-brain axis by modulating gut microbial composition and metabolism. To test this, we analyzed 16S rRNA sequencing data from fecal samples of aged male Wistar rat (4 months old) fed a LF, HF, HF + 1.6% WPPC, or HF + 10% WPPC diet (n=9-10/group). Compared to LF, the HF diet reduced the abundance of the Erysipelotrichaceae family, particularly the species Faecalibaculum rodentium, which increased numerically with the 10% WPPC diet. Interestingly, Erysipelotrichaceae relative abundance correlated with hippocampal memory storage (spearman correlation=0.4, p=0.034). In vitro growth assays confirmed that F. rodentium grew robustly in isolation on WPPC glycoconjugates and on constituent WPPC components (p<0.05). RNA sequencing of F. rodentium grown on the WPPC MFGM glycoconjugates versus glucose (n=3/group) revealed significant upregulation of genes involved in in amino acid metabolism and fatty acid oxidation (FDR<0.05). Collectively this data suggests a potential role for F. rodentium in preventing cognitive impairment through the gut-brain axis by metabolizing the WPPC that may act on the host.

microbiology↗

bioRxiv2025

A tale of two vineyards: parsing site-specific differences in bacterial and fungal communities of wine grapes from proximal vineyards, and their changes during processing in a single winery

Wine is a microbial product, naturally transformed through fermentation by a consortium of fungi and bacteria that originate from the vineyard and the cellar, in addition to any microorganisms that are intentionally inoculated. Previous work has shown that grapevine-associated microbiota follow distinct biogeographic patterns, associated with climate and soil properties, and that even neighboring vineyards can harbor distinct microbial communities, but it is unclear whether these differences persist when controlling for variations in farming practices, cultivar, and climate, and whether site-specific microbial profiles change during processing in the winery. Here we investigated the bacterial and fungal microbiota of fruit pre- and post-harvest from two nearby vineyards planted to a single variety, geographically close to one another, and farmed the same way, and then processed in a single winery. These communities subtly changed during processing yet retained distinct site-specific signatures, indicating a partial contribution of the winery environment to the microbiota of grape must and juice pre-fermentation. We also profiled the microbiota of key microbial sources in the winery environment, including fruit flies and processing equipment, demonstrating that the microbiota at these sites reflect contact with plant material, harbor communities distinct from fruit, and appear to partially contribute to the fermentation assemblage, especially via the contribution of fermentative yeasts that are rare or missing in the vineyard environment. These results bolster previous reports of site-specific microbial signatures in winegrowing and make a first estimation of the changes to the grape-associated microbiome during early processing. ImportanceNative wine fermentations are driven by microbes carried over from the vineyard or introduced in the winery. In this study, we tracked the microbiome dynamics of wine fermentations from two Chardonnay vineyards planted in close proximity to examine the relative contribution of vineyard- and winery-resident microbiota on microbial succession during wine fermentation. By tracking microbial changes from vineyard to winery, we show that the winery environment, including processing equipment and fruit flies, contributes to the fermentation microbiome but does not override vineyard-specific microbial differences. These findings support the concept of microbial terroir and highlight the importance of vineyard microbiomes in shaping wine fermentation. This work advances our understanding of how microbial diversity influences wine production and provides insight into the ecological dynamics of fermentation. By identifying key microbial sources and their contributions, this study lays the groundwork for future microbiome research in viticulture and wine making.

microbiology↗

bioRxiv2023

Plant-based production of diverse human milk oligosaccharides

Human milk oligosaccharides (HMOs) are a diverse class of carbohydrates that aid in the health and development of infants. The vast health benefits of HMOs have made them a commercial target for microbial production; however, producing the [~]130 structurally diverse HMOs at scale has proven difficult. Here, we produce a vast diversity of HMOs by leveraging the robust carbohydrate anabolism of plants. This diversity includes high value HMOs, such as lacto-N-fucopentaose I, that have not yet been commercially produced using state-of-the-art microbial fermentative processes. HMOs produced in transgenic plants provided strong bifidogenic properties, indicating their ability to serve as a prebiotic supplement. Technoeconomic analyses demonstrate that producing HMOs in plants provides a path to the large-scale production of specific HMOs at lower prices than microbial production platforms. Our work demonstrates the promise in leveraging plants for the cheap and sustainable production of HMOs.

plant biology↗

bioRxiv2019

Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes

BackgroundShotgun metagenomes are often assembled prior to annotation of genes which biases the functional capacity of a community towards its most abundant members. For an unbiased assessment of community function, short reads need to be mapped directly to a gene or protein database. The ability to detect genes in short read sequences is dependent on pre- and post-sequencing decisions. The objective of the current study was to determine how library size selection, read length and format, protein database, e-value threshold, and sequencing depth impact gene-centric analysis of human fecal microbiomes when using DIAMOND, an alignment tool that is up to 20,000 times faster than BLASTX.\n\nResultsUsing metagenomes simulated from a database of experimentally verified protein sequences, we find that read length, e-value threshold, and the choice of protein database dramatically impact detection of a known target, with best performance achieved with longer reads, stricter e-value thresholds, and a custom database. Using publicly available metagenomes, we evaluated library size selection, paired end read strategy, and sequencing depth. Longer read lengths were acheivable by merging paired ends when the sequencing library was size-selected to enable overlaps. When paired ends could not be merged, a congruent strategy in which both ends are independently mapped was acceptable. Sequencing depths of 5 million merged reads minimized the error of abundance estimates of specific target genes, including an antimicrobial resistance gene.\n\nConclusionsShotgun metagenomes of DNA extracted from human fecal samples sequenced using the Illumina platform should be size-selected to enable merging of paired end reads and should be sequenced in the PE150 format with a minimum sequencing depth of 5 million merge-able reads to enable detection of specific target genes. Expecting the merged reads to be 180-250bp in length, the appropriate e-value threshold for DIAMOND would then need to be more strict than the default. Accurate and interpretable results for specific hypotheses will be best obtained using small databases customized for the research question.

bioinformatics↗

bioRxiv2017

SAMSA2: A standalone metatranscriptome analysis pipeline

BackgroundComplex microbial communities are an area of rapid growth in biology. Metatranscriptomics allows one to investigate the gene activity in an environmental sample via high-throughput sequencing. Metatranscriptomic experiments are computationally intensive because the experiments generate a large volume of sequence data and the sequences must be compared with many references.\n\nResultsHere we present SAMSA2, an upgrade to the original Simple Annotation of Metatranscriptomes by Sequence Analysis (SAMSA) pipeline that has been redesigned for use on a supercomputing cluster. SAMSA2 is faster due to the use of the DIAMOND aligner, and more flexible and reproducible because it uses local databases. SAMSA2 is available with detailed documentation, and example input and output files along with examples of master scripts for full pipeline execution.\n\nConclusionsUsing publicly available example data, we demonstrate that SAMSA2 is a rapid and efficient metatranscriptome pipeline for analyzing large paired-end RNA-seq datasets in a supercomputing cluster environment. SAMSA2 provides simplified output that can be examined directly or used for further analyses, and its reference databases may be upgraded, altered or customized to fit the specifics of any experiment.

bioinformatics↗