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Item Valorization of Sacha Inchi press cake: Technological advances, market, and regulatory considerations for sustainable food applications(Elsevier B.V., 2025-12) Njoroge JW; Phonphimai P; Khatmorn P; Ketnawa S; Tonkla P; Vong V; Singh J; Kaur L; Donlao NSacha Inchi (Plukenetia volubilis L.) press cake (SP), the nutrient-dense by-product of oil extraction, is rich in high quality proteins, essential fatty acids, and bioactive compounds. However, its use remains constrained by processing, regulatory and market acceptance barriers. This review summarizes recent advances in processing strategies to improve SP's nutritional, functional, and sensory qualities. Physical treatments (dry/wet fractionation, steaming, autoclaving, roasting and extrusion) increase protein digestibility and solubility while reducing heat-stable antinutrients. Emerging methods, including high-pressure processing, high-pressure homogenization, ultrasonication, microwave treatment, electroconductivity (Ohmic/PEF), and cold plasma technologies enhance extractability and bioactivity while preserving sensitive compounds. Chemical and chemo-enzymatic approaches (e.g., alkaline soaking, cyclodextrin complexation) suppress flavor precursors, whereas enzymatic hydrolysis and fermentation improve bioactive peptide release, digestibility, and functionality. Functional additives (sweeteners, salts, polysaccharides, flavor enhancers) help mask bitterness, while paired with consumer-preferred flavors increase acceptance. Beyond processing, safety approvals (e.g., Thai FDA, EU novel food approval) and consumer perception on sensory, nutritional, and sustainability factors shape its market potential. Currently, SP shows potential across a wide range of food applications and its valorization supports sustainable protein supply chains. Future opportunities depend on integrating processing, safety, and regulatory strategies with consumer-driven innovation.Item Fish sauce fermentation technology using New Zealand raw materials : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy (PhD) at at Massey University, New Zealand(Massey University, 2025) Sharim, Nur SyazwanaDespite abundant raw material, industrial fish sauce production is absent in New Zealand, partly due to a paucity of prior research on how well cold-climate South Pacific fish ferment under temperate conditions with local solar salt. The present study investigates the effect of different fish sauce fermentation conditions using New Zealand raw materials (Hoki and snapper heads and frames as well as green-shell mussel), New Zealand solar salts (stoved and unstoved salts) and different temperatures on volatile fatty acid (VFA) production as well as bacterial composition and diversity. Four different fermentation set-ups were conducted to investigate different aims: 1. Laboratory scale fermentation to investigate the influence of different variables (including seafood material, type of salt and temperature) on fermentation. 2. Pilot scale fermentation to investigate the influence of sampling depth on fermentation. 3. Shell-on mussel fermentation to investigate the influence of mussel shell on mussel fermentation 4. Snapper fermentation with mussel shell added to investigate the influence of mussel shell on snapper fermentation. Four VFA were quantified in all fermentation in this study: acetic acid, propionic acid, butanoic acid and 3-methylbutanoic acid. Butanoic acid was detected only in fermentations with unstoved solar salt regardless of seafood material and fermentation temperature. The presence of butanoic acid exclusively in unstoved fermentations may be associated with the presence or abundance of bacterial groups associated with butanoic acid production in these fermentations. The current study found that VFA concentrations generally increased as the fermentation time increased. Salt type had more influence on VFA production than any other single variable including seafood material used, fermentation temperature and sampling depth. It was also revealed that seafood material had more influence on bacterial compositions than any other variable and seafood material appeared to be the primary determinant of the predominant bacterial family groups for the fermentations (Hoki paste – Micrococcaceae and Moraxellaceae; snapper paste – Carnobacteriaceae, Moraxellaceae and Pseudomonadaceae; and mussel paste – Flavobacteriaceae, Moraxellaceae, Paracoccaceae, Pseudomonadaceae and Roseobacteriaceae). Halobacteriales were found only in unstoved salt fermentations suggesting that salt type may be responsible for these results. However, this postulate could not be validated since insufficient intact nucleic acid could be recovered from the salts used to generate adequate bioinformatics information. Shell-on mussel and snapper plus shell fermentation revealed that the presence of mussel shell was associated with high pH in fish sauce fermentation, an observation not previously reported. However, no significant difference in pH was found in fermentations with different shell contents. In pilot scale snapper fermentation, sampling depth did not have a major influence on VFA production. However, sampling depth may influence the growth of some bacterial families to become the predominant groups by the end of the fermentation.Item Effects of defatted rice bran-fortified bread on gut microbiome, cardiovascular risk, gut discomfort, wellbeing and gut physiology in healthy adults with low dietary fibre intake(Elsevier Ltd on behalf of the European Society for Clinical Nutrition and Metabolism, 2025-06) Ng HM; Maggo J; Wall CL; Bayer SB; Mullaney JA; Cabrera D; Fraser K; Cooney JM; Günther CS; McNabb WC; Foster M; Frampton C; Gearry RB; Roy NCBackground & aims: Inadequate dietary fibre (DF) intake is associated with suboptimal gut function and increased risk of several human diseases. Bread is commonly consumed and is ideal to incorporate cereal bran to increase DF content. No human studies have investigated the effects of defatted rice bran (DRB) in bread, which has triple the DF of white bread, purported hypo-allergenicity and a unique nutrient profile, as a dietary intervention in healthy adults. This study aims to assess the relative abundances of a composite of key faecal microbial genera and species involved in DF fermentation and metabolism following the habitual intake of DRB-fortified bread and its influence on other biological markers of host and microbial interactions, cardiovascular risk profile, patient-reported outcomes, total DF intake, and gut physiology in healthy adults with low baseline DF intake. Methods: Fifty-six healthy adults with low baseline DF intake (<18 g/day (females), <22 g/day (males)) completed a two-arm, placebo-controlled, double-blind, randomised, crossover study. Participants consumed three (females) or four (males) slices of DRB-fortified bread or control bread daily as part of their usual diet for four weeks, with the intervention periods separated by a two-week washout. Outcomes included faecal microbiota composite (primary outcome); relative abundances (taxa and gene); faecal moisture content and bile acid concentrations; plasma and faecal organic acid concentrations; cardiovascular risk profile; gut comfort, psychological wellbeing parameters; total DF intake; whole gut transit time, and were measured at baseline and following each intervention phase. Additionally, in a sub-study, 15 participants ingested gas-sensing capsules to assess whole and regional gut transit times, and total and regional colonic hydrogen and carbon dioxide concentrations at the same timepoints. Results: DRB-fortified bread consumption significantly increased total DF intake from 20.7 g/day to 43.4 g/day (p < 0.001). No significant differences were observed in the primary outcome, microbial taxa composite within and between groups (False Discovery Rate (FDR) correction, p > 0.10). As compared to control, the DRB group had increased relative abundances of Faecalibacterium prausnitzii (unadjusted p = 0.04), Bifidobacterium longum (unadjusted p = 0.12), and Bacteroides ovatus (unadjusted p = 0.10); lower relative abundances in Coprococcus genus (unadjusted p = 0.09), Roseburia faecis (unadjusted p = 0.02) and Prevotella copri species (unadjusted p = 0.05). However, no significant differences were observed in the relative abundances of these taxa within and between groups (FDR correction p > 0.10) and for most of the other outcomes between groups (p > 0.05). Only mean serum high-density lipoprotein (HDL) concentrations significantly increased (p = 0.006), and mean total cholesterol (TC) to HDL concentration ratio significantly lowered (p = 0.02) in the DRB group compared to the control group. Conclusion: This is the first human study to show that a high-DF DRB-fortified bread improved DF intake, HDL cholesterol profiles, and may affect the gut microbiota composition in healthy adults with low DF intake. These findings support the substitution of white bread with DRB-fortified bread as an effective method to improve DF intake, which may have subsequent benefits on gut physiology and metabolic health.Item Rumen Epithelial Development- and Metabolism-Related Genes Regulate Their Micromorphology and VFAs Mediating Plateau Adaptability at Different Ages in Tibetan Sheep.(MDPI (Basel, Switzerland), 2022-12-16) Sha Y; He Y; Liu X; Zhao S; Hu J; Wang J; Li S; Li W; Shi B; Hao Z; Martinez-Pastor FThe rumen is an important hallmark organ of ruminants and plays an important role in the metabolism and immune barrier of Tibetan sheep on the Plateau. However, there are few studies on rumen development and metabolism regulation in Tibetan sheep at different ages. Here, we comprehensively analyzed the immune function, fermentation function, rumen epithelial micromorphology and transcriptome profile of Tibetan sheep at different ages. The results showed that the concentration of IgG decreased and the concentration of IgM increased with age (p < 0.05), and the highest concentration of IgA was observed at 1.5 and 3.5 years of age. In terms of rumen fermentation characteristics, VFAs of 4-month-old lambs were the highest, followed by VFAs and NH3-N of Tibetan sheep at 3.5 years of age. Hematoxylin-eosin staining and transmission electron microscopy section examination of rumen epithelial tissue showed that the rumen papilla width increased with age (p < 0.001), the thickness of the stratum corneum decreased, the cells in the stratum corneum showed accelerated migration and the thickness of the rumen muscle layer increased (p < 0.001). Desmosomal junctions between the layers of rumen epithelium increased at 1.5 and 3.5 years old, forming a compact barrier structure, and the basal layer had more mitochondria involved in the regulation of energy metabolism. RNA-seq analysis revealed that a total of 1006 differentially expressed genes (DEGs) were identified at four ages. The DEGs of Tibetan sheep aged 4 months and 6 years were mainly enriched in the oxidation−reduction process and ISG15-protein conjugation pathway. The 1.5 and 3.5-year-olds were mainly enriched in skeletal muscle thin filament assembly, mesenchyme migration and the tight junction pathway. WGCNA showed that DEGs related to rumen microbiota metabolite VFAs and epithelial morphology were enriched in “Metabolism of xenobiotics by cytochrome P450, PPAR signaling pathway, Butanoate metabolism pathways” and participated in the regulation of rumen epithelial immune and fermentation metabolism functions of Tibetan sheep at different ages. This study systematically revealed the regulatory mechanism of rumen epithelial development and metabolism in the plateau adaptation of Tibetan sheep, providing a new approach for the study of plateau adaptation.Item A period of 10 weeks of increased protein consumption does not alter faecal microbiota or volatile metabolites in healthy older men: a randomised controlled trial(Cambridge University Press on behalf of The Nutrition Society, 2020-07-02) Mitchell SM; McKenzie EJ; Mitchell CJ; Milan AM; Zeng N; D'Souza RF; Ramzan F; Sharma P; Rettedal E; Knowles SO; Roy NC; Sjödin A; Wagner K-H; O'Sullivan JM; Cameron-Smith DDiet has a major influence on the composition and metabolic output of the gut microbiome. Higher-protein diets are often recommended for older consumers; however, the effect of high-protein diets on the gut microbiota and faecal volatile organic compounds (VOC) of elderly participants is unknown. The purpose of the study was to establish if the faecal microbiota composition and VOC in older men are different after a diet containing the recommended dietary intake (RDA) of protein compared with a diet containing twice the RDA (2RDA). Healthy males (74⋅2 (sd 3⋅6) years; n 28) were randomised to consume the RDA of protein (0⋅8 g protein/kg body weight per d) or 2RDA, for 10 weeks. Dietary protein was provided via whole foods rather than supplementation or fortification. The diets were matched for dietary fibre from fruit and vegetables. Faecal samples were collected pre- and post-intervention for microbiota profiling by 16S ribosomal RNA amplicon sequencing and VOC analysis by head space/solid-phase microextraction/GC-MS. After correcting for multiple comparisons, no significant differences in the abundance of faecal microbiota or VOC associated with protein fermentation were evident between the RDA and 2RDA diets. Therefore, in the present study, a twofold difference in dietary protein intake did not alter gut microbiota or VOC indicative of altered protein fermentation.Item Biotransformation of Rutin in In Vitro Porcine Ileal and Colonic Fermentation Models(American Chemical Society, 2023-08-23) Ulluwishewa D; Montoya CA; Mace L; Rettedal EA; Fraser K; McNabb WC; Moughan PJ; Roy NCQuercetin, a polyphenol antioxidant, is widely distributed in food in the form of glycoside rutin, which is not readily absorbed in the gastrointestinal tract. The microbiota of the colon is known to biotransform rutin, generating quercetin aglycones that can be absorbed. We investigated the role of the ileal and colonic microbiota in rutin biotransformation using established in vitro fermentation models. Overall, a higher rate of rutin biotransformation was observed during colonic fermentation compared with ileal fermentation. The colonic microbiome showed higher potential for rutin conversion to quercetin through an increased abundance of α-rhamnosidase- and β-glucosidase-encoding genes compared to the ileal microbiome. Nonetheless, rutin metabolism occurred rapidly during ileal fermentation (∼20% rutin disappearance after 1 h). The appearance of quercetin varied depending on the ileal inoculum and correlated with an increased abundance of Firmicutes, suggesting that quercetin absorption could be improved via modulation of the ileal microbiota.Item In Vitro Fermentation of Sheep and Cow Milk Using Infant Fecal Bacteria(MDPI (Basel, Switzerland), 2020-06-17) Ahlborn N; Young W; Mullaney J; Samuelsson LMWhile human milk is the optimal food for infants, formulas that contain ruminant milk can have an important role where breastfeeding is not possible. In this regard, cow milk is most commonly used. However, recent years have brought interest in other ruminant milk. While many similarities exist between ruminant milk, there are likely enough compositional differences to promote different effects in the infant. This may include effects on different bacteria in the large bowel, leading to different metabolites in the gut. In this study sheep and cow milk were digested using an in vitro infant digestive model, followed by fecal fermentation using cultures inoculated with fecal material from two infants of one month and five months of age. The effects of the cow and sheep milk on the fecal microbiota, short-chain fatty acids (SCFA), and other metabolites were investigated. Significant differences in microbial, SCFA, and metabolite composition were observed between fermentation of sheep and cow milk using fecal inoculum from a one-month-old infant, but comparatively minimal differences using fecal inoculum from a five-month-old infant. These results show that sheep milk and cow milk can have differential effects on the gut microbiota, while demonstrating the individuality of the gut microbiome.Item Effect of 3-nitrooxypropanol on enteric methane emissions of feedlot cattle fed with a tempered barley-based diet with canola oil(Oxford University Press on behalf of the American Society of Animal Science, 2023-07-10) Almeida AK; Cowley F; McMeniman JP; Karagiannis A; Walker N; Tamassia LFM; McGrath JJ; Hegarty RSA dose-response experiment was designed to examine the effect of 3-nitrooxypropanol (3-NOP) on methane (CH4) emissions, rumen function and performance of feedlot cattle fed a tempered barley-based diet with canola oil. Twenty Angus steers of initial body weight (BW) of 356 ± 14.4 kg were allocated in a randomized complete block design. Initial BW was used as the blocking criterion. Cattle were housed in individual indoor pens for 112 d, including the first 21 d of adaptation followed by a 90-d finishing period when five different 3-NOP inclusion rates were compared: 0 mg/kg dry matter (DM; control), 50 mg/kg DM, 75 mg/kg DM, 100 mg/kg DM, and 125 mg/kg DM. Daily CH4 production was measured on day 7 (last day of starter diet), day 14 (last day of the first intermediate diet), and day 21 (last day of the second intermediate diet) of the adaptation period and on days 28, 49, 70, 91, and 112 of the finisher period using open circuit respiration chambers. Rumen digesta samples were collected from each steer on the day prior to chamber measurement postfeeding, and prefeeding on the day after the chamber measurement, for determination of rumen volatile fatty acids (VFA), ammonium-N, protozoa enumeration, pH, and reduction potential. Dry matter intake (DMI) was recorded daily and BW weekly. Data were analyzed in a mixed model including period, 3-NOP dose and their interaction as fixed effects, and block as a random effect. Our results demonstrated both a linear and quadratic (decreasing rate of change) effect on CH4 production (g/d) and CH4 yield (g/kg DMI) as 3-NOP dose increased (P < 0.01). The achieved mitigation for CH4 yield in our study ranged from approximately 65.5% up to 87.6% relative to control steers fed a finishing feedlot diet. Our results revealed that 3-NOP dose did not alter rumen fermentation parameters such as ammonium-N, VFA concentration nor VFA molar proportions. Although this experimental design was not focused on the effect of 3-NOP dose on feedlot performance, no negative effects of any 3-NOP dose were detected on animal production parameters. Ultimately, the knowledge on the CH4 suppression pattern of 3-NOP may facilitate sustainable pathways for the feedlot industry to lower its carbon footprint.Item Genomic insights into the physiology of Quinella, an iconic uncultured rumen bacterium.(Nature Portfolio, 2022-10-20) Kumar S; Altermann E; Leahy SC; Jauregui R; Jonker A; Henderson G; Kittelmann S; Attwood GT; Kamke J; Waters SM; Patchett ML; Janssen PHQuinella is a genus of iconic rumen bacteria first reported in 1913. There are no cultures of these bacteria, and information on their physiology is scarce and contradictory. Increased abundance of Quinella was previously found in the rumens of some sheep that emit low amounts of methane (CH4) relative to their feed intake, but whether Quinella contributes to low CH4 emissions is not known. Here, we concentrate Quinella cells from sheep rumen contents, extract and sequence DNA, and reconstruct Quinella genomes that are >90% complete with as little as 0.20% contamination. Bioinformatic analyses of the encoded proteins indicate that lactate and propionate formation are major fermentation pathways. The presence of a gene encoding a potential uptake hydrogenase suggests that Quinella might be able to use free hydrogen (H2). None of the inferred metabolic pathways is predicted to produce H2, a major precursor of CH4, which is consistent with the lower CH4 emissions from those sheep with high abundances of this bacterium.Item Extracellular Polysaccharide Extraction from Streptococcus thermophilus in Fermented Milk.(American Society for Microbiology, 2022-04-27) Wa Y; Chanyi RM; Nguyen HTH; Gu R; Day L; Altermann E; Cocolin LLactic acid bacteria such as Streptococcus thermophilus are known to produce extracellular polysaccharide (EPS) in fermented foods that enhance the creaminess and mouthfeel of the product, such as yogurt. Strains producing larger amounts of EPS are highly sought-after, and therefore, robust and accurate quantification methodologies are important. This study found that two commonly used methodologies significantly underestimated the amount of EPS produced as measured using a milk matrix. To this end, a proteolytic step was implemented prior to EPS extraction (Method C). An initial proteolytic step using xanthan gum-spiked milk significantly increased recovery yield to 64%, compared to 27.8% for Method A and 34.3% for Method B. Method C showed no improvement when assessed using a chemically defined medium. Method C was further validated using three strains of S. thermophilus with varying EPS-production capabilities (STLOW, STMID, STHIGH). Overall, Method C demonstrated significant improvements in the EPS extraction yield for all three S. thermophilus strains in fermented milk. On average, Method C improved isolation yield by ∼3- to 6-fold compared with Method A and by ∼2- to 3-fold compared with method B. There were no significant differences between samples when they were grown in a chemically defined medium, highlighting the importance of a proteolytic step specifically for fermented milk samples. In commercial applications, accurate quantification of EPS-production is an important aspect when finding new strains. IMPORTANCE Extracellular polysaccharide (EPS) production by milk-fermenting microorganisms is a highly sought-after trait in improving the perceived thickness, creaminess, and mouthfeel of yogurt. Streptococcus thermophilus are commonly isolated and their EPS production is quantified in the search for higher-producing strains. In this study, we demonstrated that two commonly used methods for isolating EPS from milk samples significantly underestimated the true amount of EPS present. We demonstrated that the addition of a proteolytic step prior to EPS extraction isolated over 2-fold more EPS than identical samples processed using the traditional protocols. We further validated this method in fermented milk samples from three strains of S. thermophilus that included a low-, mid-, and high-EPS producing strain. Again, we showed significant improvements in EPS isolation using a proteolytic step. In the search for new S. thermophilus strains with enhanced EPS production, accurate quantification in an optimal medium is essential.