Biology subjects

Howell, K.

Publications and source records attributed to Howell, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Environmentally-mediated yield effects of vernalization and photoperiod alleles in historic winter wheat trials

In common wheat (Triticum aestivum L.), variation at the Vrn1 and Ppd1 loci changes plant phenology, resulting in differential adaptation useful to breeders. Because the effects of phenology on grain yield are conditional on environmental factors, the incorporation of markers for Vrn1 and Ppd1 alleles into breeding approaches has proven difficult. Historic phenotypic, genotypic, and environmental data can provide insight into the relationship between major phenology alleles and grain yield as mediated by environmental variables. Analyses of eight years of breeding trials (1,038 lines at 219 site-years) determined that weak vrn1 alleles and Ppd1 insensitivity alleles have variable effects. These effects change depending on an environment's winter temperature and latitude, respectively, but the environmentally-driven changes in effect of vrn1 alleles are much more variable than effects of Ppd1 alleles. Mediation analyses showed phenologically-dependent environmental variables are one mechanism through which phenological changes created by vrn1 and Ppd1 variants alter yield across multiple developmental stages. Environmentally-driven relationships between flowering time and yield were modeled to estimate yield allele effects as a function of effects on phenology and environmental variables. Weak winter alleles at vrn1 may play a stabilizing role on yield, due to the correlation of winter conditions that drive larger effects with later-season warm temperatures that penalize later maturity. A better mechanistic understanding of how these loci drive environment-specific yield effects may facilitate utilization of markers for these alleles and improve predictive modeling of yield.

genetics↗

bioRxiv2026

Seasonal dynamics of microbial communities mediate aroma and flavour formation during palm sap fermentation

In many tropical countries, fermentation of palm sap into palm wine is an important fermented beverage contributing to local economies, tradition, and culture. Traditionally made in villages and families, palm sap is not inoculated with starter cultures and fermentation commences spontaneously. It is therefore possible that fermentation is influenced by multiple ecological factors, which affect microbial dynamics and thus flavour outcomes. Here, we studied microbial communities during fermentation of palm sap from three different palm tree species (palmyra, coconut, and sugar palm) on the island of Bali, Indonesia in both the wet and dry seasons. Our results suggest that season of collection has a strong influence on microbial dynamics and succession, and these changes positively correlate to metabolite concentration. The change of the season from the dry to wet season led to the loss of microbial diversity with lower richness in the dry season. The dominance of Saccharomyces cerevisiae was not affected by season and fermentation time and was dominant in all samples. Potential spoilage species, such as Candida tropicalis were negatively correlated to ester production and more abundant in the dry season. As microbial species varied in incidence and thus biochemical activity, the chemical groups of esters from their metabolism related to the change of season and fermentation time, while volatile compounds and small molecules were highly discriminated by season in the resultant wines. Ethyl octanoate was consistently different across all variables through comparison by three-way ANOVA and is proposed as a biomarker of seasonal variation in palm sap fermentation. These findings improve our understanding of microbial dynamics in palm sap fermentation, revealing flavour differentiation within season and suggests that strategies for microbial management, product development and quality assurance will elevate this traditional product into the future.

microbiology↗

bioRxiv2026

Lactic acid bacterium Fructilactobacillus sanfranciscensis impairs fitness of yeast Maudiozyma humilis in synthetic wheat sourdough

Sourdough starters contain simple microbial communities typically consisting of a few bacterial species and one or two yeast species. The yeast Maudiozyma humilis and the lactic acid bacterium Fructilactobacillus sanfranciscensis often co-occur in sourdough starters and have been presumed to exist in a trophic relationship supported by glucose cross-feeding. However, previous research has highlighted a lack of evidence showing that yeast strains consume the glucose that F. sanfranciscensis produces. We have investigated the interaction between sourdough isolates of M. humilis and F. sanfranciscensis in a synthetic wheat sourdough medium, allowing us to control substrate composition and use flow cytometry to enumerate living and dead cells. M. humilis fitness was found to be lower in co-culture with F. sanfranciscensis than when grown alone. Analysis of spent medium composition highlighted the reliance of M. humilis on glucose rather than maltose for growth. Comparisons of predicted and measured co-culture metabolite content also revealed that F. sanfranciscensis consumed less maltose in co-culture than when grown alone. For the first time, we examined potential amino acid cross-feeding between M. humilis and F. sanfranciscensis, and found that within the pairing, F. sanfranciscensis was the main producer of amino acids. Our findings suggest that the M. humilis-F. sanfranciscensis interaction is likely to be neutral, or even competitive, with the strain identity of F. sanfranciscensis playing a defining role in the observed dominance of the bacteria and spent medium metabolite composition. ImportanceThe association of the yeast Maudiozyma humilis and the bacterium Fructilactobacillus sanfranciscensis in sourdough starters is well-documented, and together this pairing makes key functional and organoleptic contributions to the final bread product. Their relationship has historically been thought to be stabilised by cross-feeding of glucose to M. humilis. However, this theory has been drawn into question by recent research which found no evidence that M. humilis consumes the glucose produced by F. sanfranciscensis. Our understanding of cooperation, coexistence, and competition in microbial consortia affects approaches to ecosystem management in a broad variety of applied fields. The significance of our research is in demonstrating that this pairing does not interact mutualistically within a specified setting, providing support for neutral or competitive interactions as drivers of ecological stability.

microbiology↗

bioRxiv2026

A metagenomic exploration of the bacterial community composition of two deep-sea Pheronema carpenteri sponge aggregations from the North Atlantic; insights into ecosystem services

AimsSponge microbiomes have been extensively studied, in part due to their potential as sources of novel antimicrobials and other biologics, with most research focusing on Demosponges. Here, we investigate the Hexactinellid sponge Pheronema carpenteri, previously identified as a promising source of antibiotic-producing bacteria. MethodsUsing next-generation sequencing of bacterial 16S rRNA genes and a single sponge metagenome, we examined the composition of bacterial communities of P. carpenteri sponges recovered from the Porcupine Seabight, along with local water and sediment samples. ResultsOur results show that P. carpenteri harbours a microbiome abundant in Proteobacteria (47.1-59.4%) and Actinobacteria (11.5-27.5%), with consistent intra-aggregation similarities and structured intra-sponge communities. A metagenomic analysis revealed the presence of several nitrogen cycling genes (nirK, nosZ, nirS homologues of proteobacterial origin), supporting a suggestion that these sponges may play a role in nitrogen cycling, while biosynthetic gene clusters (BGCs) were limited (4 complete clusters). Notably, bacterial community structures within P. carpenteri aggregations resemble those observed in both low and high microbial abundance (LMA/HMA) sponges. ConclusionsHexactinellids are traditionally considered LMA sponges, so identifying species that deviate from this dichotomy provides new insights into sponge microbiome ecology. Integrating Hexactinellids into both culture-dependent and culture-independent studies will advance our broader understanding of sponge-associated microbial diversity and could inform biodiscovery programmes in marine environments. Impact StatementOur findings support the suggestion that a combination of culture-based and molecular analyses is required to generate a comprehensive picture of the biosynthetic potential of P. carpenteri sponges. We also reveal insights into the ecosystem services that sponge microbiomes may contribute towards. These observations could facilitate a deeper understanding of the biotechnological and environmental value of key marine resources.

microbiology↗

bioRxiv2026

Genotypic and phenotypic diversity of Maudiozyma humilis: the multiple evolutionary trajectories of a domesticated yeast

Maudiozyma humilis is the second most frequently encountered yeast species in sourdough bread. Despite its ecological and food relevance, little is known about its evolutionary trajectories and phenotype traits of interest. Here we investigated the genomic and phenotypic diversity of a world-wide collection of 55 M. humilis strains, including 52 from sourdough, by combining genomic analysis, flow cytometry and high-throughput phenotyping of fermentation kinetics and fitness. Population genomic analysis revealed six genetically distinct clades, three diploid and three triploid, with no geographical or substrate-specific structuring. Phylogenetic, loss of heterozygosity (LOH) distribution and allele specific analysis indicated that triploid strains originated from both recent and more ancient hybridization events involving multiple diploid lineages. The absence of the HO gene, and mating-type silent cassettes, revealed that M. humilis is not able to carry mating-type switching. In addition, high linkage disequilibrium (LD) and variable LOH accumulation were observed consistent with a predominantly clonal reproduction. Last, an exceptionally high level of heterozygosity was detected, suggesting that occasional hybridization is the major driver of genetic diversity. Phenotypic characterization in a synthetic sourdough medium revealed variation in fermentation kinetics and fitness statistically associated with the genetic clades. Interestingly, genetic distance between clades and strains better explain the phenotypic variation than difference in ploidy. Altogether, our findings highlight the complex evolutionary history of M. humilis, shaped by hybridization and ploidy variation and reveal that historical contingency, more than ploidy, shapes the phenotypic landscape of this species. Beyond providing the first analysis of M. humilis evolution, our result challenges the hypothesis that increases in ploidy are necessarily beneficial in domesticated species.

genomics↗

bioRxiv2026

Analysis of Organophosphate Insecticide Half-Lives in Foods Fermented with Lactic Acid Bacteria

There is a growing concern that chronic, low-level exposure to organophosphate insecticides is a threat to human health. These synthetic chemicals are used in crop and livestock production all over the world, and the general population are exposed to them through consuming the residues that remain in food. Evidence is emerging that fermentation with lactic acid bacteria may be an effective way of reducing organophosphate insecticide residues. However, while several studies have investigated this topic, outcome measures have varied, and there has been no research to date which has consolidated this data to better understand the half-lives of organophosphate insecticides in fermented foods and the factors affecting degradation. The aim of this review was to synthesise the evidence on organophosphate insecticide degradation during lactic acid fermentation, and analyse organophosphate insecticide half-lives, in order to determine the effectiveness of lactic acid fermentation in reducing organophosphate insecticide residues in food. Furthermore, the study aimed to explore the factors that impact the rate of degradation. CAB Abstracts, Food Science and Technology Abstracts, Scopus and Web of Science were searched for eligible laboratory-based studies, which were published after 2000. The literature search and screening process resulted in the inclusion of 14 eligible studies. Studies were screened for Risk of Bias (ROB) using the RoBDMAT tool. Collated results showed that organophosphate insecticides degraded over time, and this was irrespective of fermentation. However, out of the 249 experiments that involved a controlled fermentation, 232 demonstrated that fermentation with lactic acid bacteria could speed up the degradation of organophosphate insecticides in food, beyond the rate of inherent degradation in the food matrix, leading to shorter half-lives. The half-lives of organophosphate insecticides in apple juice, milk and wheat ranged from 9.5 hours to 21 days in fermented foods and ranged from 21.4 hours to 36.5 days in non-fermented foods. Single species of lactic acid bacteria that demonstrated strong potential for organophosphate insecticide degradation were Lpb.plantarum subsp.plantarum, Lab.delbrueckii subsp.bulgaricus and Lvb. brevis, where the median percentage change in organophosphate insecticide half-life during fermentation was -42.3%, -25.0% and -22.9%, respectively. Organophosphate insecticide degradation during natural fermentation was less clear because of fewer studies and less consistent results. Whilst the collated data shows that fermentation with lactic acid bacteria is an effective method to reduce organophosphate insecticide residues in food, reflected in shorter half-lives, the small number of studies and variability among studies does limit the conclusions that can be drawn, and further research is needed to strengthen these findings. The results of our analysis may help to inform more reliable organophosphate exposure assessments for the population as well as provide novel insights for both consumers and food manufacturers, expanding the market potential for fermented foods.

microbiology↗

bioRxiv2025

Deep Blueprint: A Literature Review and Guide to Automated Image Classification for Ecologists

O_LIDeep learning (DL) is a powerful tool to extract ecological information from large image datasets efficiently and consistently. However, applying these methods remains challenging, due in part to the complexity of DL workflows and the dynamic nature of available tools. C_LIO_LITo address this, we created a practical guide and review, focused on one of the fundamental tasks in automated image analysis: image classification. Our approach integrates commonly used software and highlights key steps - from image acquisition to annotated, model-ready datasets, to training, evaluation and deployment. It is modular and supported by a flexible code base (Python & R) and Graphical User Interfaces (GUIs), enabling adaptation to different models and ecological objectives. The goal is to empower ecologists to confidently incorporate computer vision into their research. C_LIO_LIWe illustrate this approach, using an open-source ROV dataset from the Norwegian Sea, featuring deep-sea biotopes defined by multivariate clusters of depth, substrate type, and associated species. To balance accessibility for users alongside performance, we focused on CNN models from the Ultralytics ML Platform (YOLO V.8 and V.11), comparing the full suite of architectures that range in complexity and efficiency. C_LIO_LICross-validation revealed high overall performances and that larger, more complex models are not always superior, with YOLO V.8m best (Accuracy = [~]0.98). Notably, high performances were achieved despite labels being based on both visual and external environmental predictors, suggesting visual features alone were sufficient for classification in this dataset. We highlight that the decision to deploy a model must be made in light of the studys objectives, with domain-based reasoning and experience guiding every stage of implementation. C_LIO_LIThis work offers a practical blueprint for implementing DL in ecological research, promoting broader adoption and supports reproducibility and more efficient, standardized, and sustainable monitoring; in this case of deep-sea biotopes, which is essential for marine spatial planning. C_LI

ecology↗

bioRxiv2025

Tibicos differentially affects faecal microbiota composition and short-chain fatty acid production in prediabetic and healthy adults in a simulated digestive tract

Prediabetes and obesity are increasingly prevalent chronic pro-inflammatory conditions driven by gut microbiota dysfunction. To assist in the management of such diseases, researchers are interested in gut-microbiota targeted dietary interventions. Tibicos is a plant-based fermented beverage shown to modulate gut microbiota, with anti-hyperglycaemic and anti-inflammatory effects in in vitro and in vivo human and animal studies. We investigated the effects of ginger-cayenne tibicos on healthy and prediabetic pooled faecal microbiota, with a static in vitro digestion/ colonic fermentation model using faeces from adult overweight/ obese donors with prediabetes, and healthy donors (n=3 per group). Changes in faecal microbiota composition and short-chain fatty acid (SCFA) production were determined. Baseline prediabetic faeces was less abundant in butyrate-producing bacterial taxa and SCFAs. In vitro colonic fermentation Time and Status (prediabetic vs. healthy) were the major determinants of shifts in faecal microbial community abundance and diversity. Tibicos reduced beneficial bacterial taxa loss in prediabetic faecal microbiota. However, tibicos improved the functional capacity of healthy faecal microbiota to a larger extent, with increased SCFA production and significant correlations between bacterial species and SCFAs. The differential shifts in composition and SCFAs observed during simulated gastrointestinal transit suggest that ginger-cayenne tibicos has the potential to beneficially modulate human faecal microbiota in both healthy and prediabetic participants. This study indicates that ginger-cayenne tibicos may be a useful tool in the management of prediabetes and obesity in humans and provides pilot data for the development of larger clinical trials.

microbiology↗

bioRxiv2024

Applying deconstructed sourdough communities and fermentation parameters to low-FODMAP wheat bread production

Despite being made with the same starting materials, standard and sourdough bread differ in terms of levels of fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs). This study aims to assess the impact of a selected yeast-bacteria co-culture isolated from sourdough starters in conjunction with varying bread-making process parameters on bread FODMAP content and overall quality. A survey of the microbial composition of sourdough starters found that many contain Maudiozyma humilis and Fructilactobacillus sanfranciscensis. A selected pairing was used for small-scale bread-making, and dough fermentation and bread quality parameters were assessed. The sourdough microbes exerted distinctive effects on dough gassing capacity and FODMAP composition in comparison to bakers yeast. To meet low-FODMAP cutoff values, the presence of a fermenting yeast and an extended dough fermentation time (> 6 h) were necessary. Sensory panellists preferred the sourdough co-culture bread fermented for 24 h over the 6 h treatment, and detected more complex aromas in the former. An extended, low-temperature dough fermentation regimen can be used to produce low-FODMAP bread with standard bread-making materials, and the use of sourdough fermentation microbes confers distinct textural and organoleptic properties.

microbiology↗

bioRxiv2024

A Human Brain-Chip for modelling brain pathologies and screening of BBB crossing therapeutic strategies

The limited translatability of preclinical experimental findings to human patients remains an obstacle for successful treatment of brain diseases. Relevant models to elucidate mechanisms behind brain pathogenesis, such as human cell-based systems, and support successful targeting and prediction of drug responses in humans are in urgent need given the species differences in brain and blood-brain barrier (BBB) functions. Here, we examined and advanced a Brain-Chip which recapitulates aspects of the human cortical parenchyma and the BBB in one model. We utilized human primary astrocytes and pericytes, hiPSC-derived cortical neurons, hiPSC-derived brain microvascular endothelial-like cells, and included for the first time on chip hiPSC-derived microglia. Using TNF to emulate neuroinflammation, we demonstrate that our model recapitulates in vivo-relevant responses. Importantly, we show microglia-derived responses, highlighting the ability of the model to capture cell-specific contributions in human disease associated pathology. We next tested BBB crossing of human transferrin receptor antibodies and conjugated adeno-associated viruses, and demonstrate successful in vitro/in vivo correlation in identifying crossing differences. These findings highlight the potential of the Brain-Chip as a time-saving and reliable model to support therapeutic development for brain diseases.

bioengineering↗

bioRxiv2024

The forgotten wine: understanding the fermentation and composition of palm wine

Palm wine is an alcoholic beverage that has existed for centuries and has important economic and socio-culture values in many tropical and sub-tropical countries. Lesser known than other types of wines, palm wine is made by spontaneous fermentation of palm sap by naturally occurring microbial communities. The palm sap ecosystem has unique microbial composition and diversity, which determines the composition of the eventual wine and is likely affected by geographical distinctiveness. While these features are well understood in grape and rice wine, these features have not been understood in palm wine. In this review, we gather information of microbial communities and metabolite profiles from published studies, covering a wide range of methodologies and regions, to better understand the causal links between the principal microbial species and major metabolites of palm wine. We assess palm wine quality across production regions and local practices to provide general characteristics of palm wine and identify specific regional information. These will provide better understandings to the function of microbial communities and metabolite diversity, the contribution of regional variations and to ensure product quality in this important and widespread, yet overlooked, fermented beverage. One sentence summaryreview and synthesis of microbial ecology and metabolites in palm wine fermentation across geography and their contribution to cultural food systems

microbiology↗

bioRxiv2024

Gli2 Facilitates Tumor Immune Evasion and Immunotherapeutic Resistance by Coordinating Wnt Ligand and Prostaglandin Signaling

Therapeutic resistance to immune checkpoint blockade has been commonly linked to the process of mesenchymal transformation (MT) and remains a prevalent obstacle across many cancer types. An improved mechanistic understanding for MT-mediated immune evasion promises to lead to more effective combination therapeutic regimens. Herein, we identify the Hedgehog transcription factor, Gli2, as a key node of tumor-mediated immune evasion and immunotherapy resistance during MT. Mechanistic studies reveal that Gli2 generates an immunotolerant tumor microenvironment through the upregulation of Wnt ligand production and increased prostaglandin synthesis. This pathway drives the recruitment, viability, and function of granulocytic myeloid-derived suppressor cells (PMN-MDSCs) while also impairing type I conventional dendritic cell, CD8+ T cell, and NK cell functionality. Pharmacologic EP2/EP4 prostaglandin receptor inhibition and Wnt ligand inhibition each reverses a subset of these effects, while preventing primary and adaptive resistance to anti-PD-1 immunotherapy, respectively. A transcriptional Gli2 signature correlates with resistance to anti-PD-1 immunotherapy in stage IV melanoma patients, providing a translational roadmap to direct combination immunotherapeutics in the clinic. SIGNIFICANCEGli2-induced EMT promotes immune evasion and immunotherapeutic resistance via coordinated prostaglandin and Wnt signaling.

cancer biology↗

bioRxiv2024

Stimulated saliva has a distinct composition that influences release of volatiles from wine

Saliva influences the release of aroma in the oral cavity. The composition of human saliva varies depending on stimulation and hosts origin; however, the compositional differences of saliva and their influences on aroma release have not been fully evaluated. In this study, we recruited 30 healthy adults (15 Australians and 15 Chinese) and collected saliva samples at three stages: before, during, and after stimulation. Salivary samples were characterised by flow rate, total protein concentration, esterase activity, microbiome composition by full-length 16S rRNA gene sequencing, and the ability to release aroma from wine by headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS). Differences in salivary composition and specific wine volatiles were found between Australian and Chinese participants, and amongst the three stimulation stages. Significant correlations between the relative abundance of 3 bacterial species and 10 wine volatiles were observed. Our results confirm the influence of participants geographic origin and stimulation on salivary composition, highlighting the role of salivary components, especially salivary bacteria, on the release of aroma from wine.

microbiology↗

bioRxiv2023

Variation of wine preference amongst consumers is influenced by the composition of salivary proteins

The preferences of consumers for different flavours and aromas in wine are varied and may be explained by inherent factors such as cultural background, wine education and personal taste of the wine consumer. Wine flavour as perceived in the mouth includes aroma compounds released through the retronasal pathway which are shaped by interactions with saliva. Saliva and wine interactions could provide an explanation as to why wine tasters express different preferences for wine. To test this hypothesis, 13 Western and 13 Chinese experienced wine tasters were recruited. Sensory evaluation was performed in formal surroundings to acquire free description-based and perceived sensory intensity data using the Pivot(R) Profile and continuous scale assessment, respectively. Participants saliva samples were collected before the sensory evaluation and spiked into a wine sample to investigate the impact on the wine volatile release using GCxGC-MS. Saliva samples were subjected to enzyme activity assays and protein composition profiling by Tandem Mass Tag (TMT) quantitative proteomics. The wine tasters showed differences in wine flavour perception, which was supported by the difference in wine volatile release resulting from the addition of saliva. The two groups of participants did not have significant differences in total salivary protein concentrations or the amounts of esterase and -amylase. However, statistically significant variations in the concentrations of specific proteins (proline-rich proteins (PRPs) and lipocalin-1 (LCN-1); p < 0.01) were found between the two groups. Significant correlations between perceived intensities of wine attributes and concentrations of PRPs and LCN-1 were observed. These results indicate that the composition of proteins in saliva are a factor that influences wine perception and preference. Our results provide a biochemical basis to understanding preference for food based on interactions between aroma compounds and salivary proteins and could be used to suggest foods or beverages to particular cultural groups.

biochemistry↗

bioRxiv2023

Bearded or Smooth? Awns Improve Yield when Wheat Experiences Heat Stress During Grain Fill

The presence or absence of awns - whether wheat heads are "bearded" or "smooth"- is the most visible phenotype distinguishing wheat cultivars. Previous studies suggest that awns may improve yields in heat or water-stressed environments, but the exact contribution of awns to yield differences remains unclear. Here we leverage historical phenotypic, genotypic, and climate data to estimate the yield effects of awns under different environmental conditions over a 12-year period in the Southeast US. Lines were classified as awned or awnless based on sequence data, and observed heading dates were used to associate grain fill periods of each line in each environment with climatic data and grain yield. In most environments, awn suppression was associated with higher yields, but awns were associated with better performance in heat-stressed environments more common at southern locations. Wheat breeders in environments where awns are only beneficial in some years may consider selection for awned lines to reduce year-to-year yield variability, and with an eye towards future climates.

genetics↗

bioRxiv2023

Comparison of metabarcoding taxonomic markers to describe fungal communities in fermented foods

AO_SCPLOWBSTRACTC_SCPLOWNext generation sequencing offers several ways to study microbial communities. For agri-food sciences, identifying species in diverse food ecosystems is key for both food sustainability and food security. The aim of this study was to compare metabarcoding pipelines and markers to determine fungal diversity in food ecosystems, from Illumina short reads. We built mock communities combining the most representative fungal species in fermented meat, cheese, wine and bread. Four barcodes (ITS1, ITS2, D1/D2 and RPB2) were tested for each mock and on real fermented products. We created a database, including all mock species sequences for each barcode to compensate for the lack of curated data in available databases. Four bioinformatics tools (DADA2, QIIME, FROGS and a combination of DADA2 and FROGS) were compared. Our results clearly showed that the combined DADA2 and FROGS tool gave the most accurate results. Most mock community species were not identified by the RPB2 barcode due to unsuccessful barcode amplification. When comparing the three rDNA markers, ITS markers performed better than D1D2, as they are better represented in public databases and have better specificity to distinguish species. Between ITS1 and ITS2, differences in the best marker were observed according to the studied ecosystem. While ITS2 is best suited to characterize cheese, wine and fermented meat communities, ITS1 performs better for sourdough bread communities. Our results also emphasized the need for a dedicated database and enriched fungal-specific public databases with novel barcode sequences for 118 major species in food ecosystems.

microbiology↗

bioRxiv2022

Vitamin-B12 enrichment in tempeh by co-culture with Propionibacterium freudenreichii during fermentation

Vitamin-B12, or cobalamin, is an essential human vitamin and most commonly acquired in the diet through consumption of animal products. Acquisition of the vitamin for people who follow strict plant-based diets is limited to supplementation via tablets or consumption of fortified foods. Tempeh -- an Indonesian food of soybeans fermented with a filamentous fungi, Rhizopus sp. is a potential dietary source of cobalamin, but its presence is under question based on difficult quantification of this trace vitamin. This study tested the presence and concentration of vitamin-B12 in commercially available tempeh and tempeh produced with deliberate inoculation of various bacteria and moulds. Vitamin-B12 was not detected in any commercially available tempeh. Tempeh made with filamentous fungi and Propionibacterium freudenreichii (ATCC 9617) consistently produced detectable levels of cobalamin. P. freudenreichii co-fermented with Rhizopus oligosporus (ATCC 22959) produced the highest concentration of cobalamin at 8.26 {+/-} 0.13 g/100g of wet weight of tempeh. Co-fermentation with a different tempeh mould significantly reduced the amount of cobalamin (P = 0.008). Results from this study suggest that incorporating nutrient-enhancing microbes into an existing fermentation stage of a product is an effective method to increase the nutritional density of food. The results of this study suggest that cheap, safe and easily cultured microbes can contribute to the nutritional diversity of people following plant-only diets.

microbiology↗

bioRxiv2021

A core salivary microbiome shows the high prevalence of bacterial members yet variability across human populations

Human saliva contains diverse bacterial communities, reflecting human health status, dietary patterns and contributing to variability in the sensory perception of food. Many descriptions of salivary microbiome diversity compare commonalities and differences with reference to a diseased state, but the composition of healthy saliva has not been described. Here, we use a meta-analysis approach to define and explore the core membership of the human salivary microbial community by collecting and re-analysing raw 16S rRNA amplicon sequencing data from 47 studies with 2206 saliva samples. We found 68 core bacterial taxa that were consistently detected. Differences induced by various host intrinsic and behaviour factors, including gender, age, geographic location, tobacco usage, and alcohol consumption, were evident. The core of the salivary microbiome was verified by collecting and analysing saliva in an independent study. These results suggest that the methods used can effectively define a core microbial community in human saliva with high prevalence. The core salivary microbiome demonstrated both stability and variability among populations. Geographic location was identified as the host factor with the largest effect in shaping salivary microbiota. The independent analysis underlined that the impact of geographic variation is likely due to diet.

microbiology↗