Biology subjects

Hester, E. R.

Publications and source records attributed to Hester, E. R..

4 recordsLinked to original sources

bioRxiv2026

Prebiotic ALPINA GOS produced from whey permeate has a bifidogenic effect on the adult fecal microbiota in vitro, including stimulation of organic acids production

Functional oligosaccharides, such as galacto-oligosaccharides (GOS), are valued for modulating gut microbiota and promoting health. This study aimed to produce a high-purity GOS ingredient (ALPINA GOS) via nanofiltration/diafiltration and assess its prebiotic efficacy using an in vitro fermentation model. GOS-rich syrup was obtained from transgalactosylation of lactose in concentrated whey permeate (30% lactose) and processed by diafiltration/nanofiltration to reduce monosaccharides and enrich oligosaccharide content. Carbohydrate composition was analyzed by HPAEC-PAD. Prebiotic activity was evaluated using a MicroColon model with fecal inocula from healthy adults, measuring pH, short-chain fatty acids (SCFAs), and microbiota shifts. Membrane processing increased oligosaccharides from 55.5% to 70.2% (dry basis) and reduced monosaccharides from 25.2% to 5.1%. ALPINA GOS induced a dose-dependent pH reduction and significantly enhanced lactate and acetate production, with stronger effects at 10 mg/mL. Microbiota profiling showed increased abundance of beneficial bacteria, especially Bifidobacterium, versus control. The findings confirm that GOS can be sustainably produced from whey permeate and exhibits potent prebiotic activity, supporting its application in functional foods aimed at gut health.

microbiology↗

bioRxiv2019

Metabolic overlap in environmentally diverse microbial communities

The majority of microbial communities consist of hundreds to thousands of species, creating a massive network of organisms competing for available resources within an ecosystem. In natural microbial communities it appears that many microbial species have highly redundant metabolisms and seemingly are capable of utilizing the same substrates. This is paradoxical, as theory indicates that species requiring a common resource should outcompete one another. To better understand why microbial species can co-exist, we developed Metabolic Overlap (MO) as a new metric to survey the functional redundancy of microbial communities at the genome scale across a wide variety of ecosystems. Using metagenome-assembled genomes, we surveyed over 1200 studies across ten ecosystem types. We found the highest MO in extreme (i.e., low pH/high temperature) and aquatic environments, while the lowest MO was observed in communities associated with animal hosts, or the built/engineered environment. In addition, different metabolism subcategories were explored for their degree of metabolic overlap. For instance, overlap in nitrogen metabolism was among the lowest in Animal and Engineered ecosystems, while the most was in species from the Built environment. Together, we present a metric that utilizes whole genome information to explore overlapping niches of microbes. This provides a detailed picture of potential metabolic competition and cooperation between species present in an ecosystem, indicates the main substrate types sustaining the community and serves as a valuable tool to generate hypotheses for future research.

microbiology↗

bioRxiv2019

Comparison of the bacterial and methanotrophic diversities between an Italian paddy field and its neighboring meadow

Methane is a potent greenhouse gas that contributes to global warming. However, under certain conditions, its release into the atmosphere can be mitigated by methane-oxidizing microorganisms. Typically, cultivated wetlands (i.e., paddy fields) are a major source of methane (CH4) while forests and meadow uplands are considered to be CH4 sinks. As the global need for rice production increases each year, more uplands are converted to inundated paddy fields. To investigate soils that may be converted into productive land for rice production, we investigated a paddy field and adjacent meadow in Northern Italy. Using a combination of 16S rRNA gene amplicon sequencing to analyze the bacterial community, and gas flux measurements to quantify CH4 emissions, we looked for differences between classically defined CH4 sinks (meadow soils) and CH4 sources (paddy fields). Analysis of the total bacterial community revealed that the family Fimbriimonadaceae, which belongs to the phylum Armatimonadetes, was significantly higher in paddy field soils driving the difference between paddy and meadow soils. Whereas, we found that the methylotrophic families Methyloligellaceae and Methylomirabilaceae were also present in higher relative abundance in the paddy field. Despite these major differences, CH4 fluxes were highly variable between the two sites with no significant differences observed. Furthermore, we found the Methylomonaceae family to be more abundant at the center of a neighboring paddy field compared to the edge of the paddy field from the current study, hinting at methanotrophic variation based on location. Taking these results into account, we propose a conceptual model to explain possible scenarios that may result in paddy and meadow fields not exhibiting classical source/sink properties. These findings call for caution when including paddy and meadow areas separately into global CH4 flux calculations, and urge further research to discern drivers of CH4 cycling under a range of environmental conditions rather than relying on assumptions.

microbiology↗

bioRxiv2017

Linking nitrogen load to the structure and function of wetland soil and rhizosphere microbial communities

Wetland ecosystems are important reservoirs of biodiversity and significantly contribute to emissions of the greenhouse gases CO2, NO2 and CH4. High anthropogenic nitrogen (N) inputs from agriculture and fossil fuel combustion have been recognized as a severe threat to biodiversity and ecosystem functioning such as control of greenhouse gas emissions. Therefore it is important to understand how increased N input into pristine wetlands affects the composition and activity of micro-organisms, especially in interaction with dominant wetland plants. In a series of incubations analyzed over 90 days, we disentangle the effects of N fertilization on the microbial community in bulk soil and the rhizosphere of Juncus acutiflorus, a common and abundant graminoid wetland plant. We observed an increase in greenhouse gas emissions when N is increased in incubations with J. acutiflorus, changing the system from a greenhouse gas sink to a source. Using 16S rRNA amplicon sequencing and metagenomics, we determined that the bacterial orders Opitutales, Subgroup-6 Acidobacteria and Sphingobacteriales significantly responded to high N availability and we hypothesize that these groups are contributing to the increased greenhouse gas emissions. These results indicated that increased N input leads to shifts in microbial activity within the rhizosphere, severely altering N cycling dynamics. Our study provides a framework for connecting environmental conditions of wetland bulk and rhizosphere soil to the structure and metabolic output of microbial communities.

microbiology↗