To realize the potential of materials comprising living organisms, bioengineers require a holistic understanding of the reciprocal relationship between environmental conditions and the biochemical and biophysical processes that influence development and behaviour. Mathematical modelling has a critical part to play in managing the complexity of biological dynamical systems and attaining higher degrees of control over their trajectories and endpoints. To support the development of mycelium-based engineered living materials, this paper reviews the literature of growth models for filamentous fungi with emphasis on the connection between morphogenesis and metabolism.

Aflatoxins in contaminated corn do not degrade in corn fermentation solution (CFS) during biofuel production; rather, they are enriched in the co-product, dried distillers grain. Aflatoxin B1 (AfB1) is the most toxic form of all aflatoxins. Removing AfB1 from CFS is desirable to minimize its toxicity to animals. Smectites can adsorb AfB1 from aqueous solutions and, therefore, inactivate the toxin, but proteins in CFS inhibit the adsorption of AfB1 by smectites. The current study aimed to minimize the interference by CFS in adsorption of AfB1 on smectite by modifying a calcium-smectite (Ca-3MS) with a small nutritive organic compound, e.g. carnitine, choline, arginine, histidine, or tryptophan. The organo-smectites were characterized by X-ray diffraction (XRD) and Fourier-transform infrared (FTIR) spectroscopy, and adsorption of AfB1 in CFS by these composites was examined. Various degrees of intercalation of the organic nutrients into the smectites were observed with XRD and FTIR. After immersing the smectite and organo-smectites in the CFS, the d001 values of Ca-3MS expanded to ~1.82 nm due to protein interaction, but the organo-smectites were confined to ~1.39 nm, which indicated that the protein had limited access to the organo-smectite interlayers. The IR bands at ~1652, 1544, 1538, and 1454 cm–1 from the organo-smectites revealed, however, that complete protein inhibition was not achieved. The organo-smectites were capable of adsorbing AfB1 in simple aqueous solution with maximal adsorption capacity up to 0.55 mol kg–1. Significantly greater (p ≤ 0.05) AfB1 adsorption was achieved by choline- and carnitine-modified smectites compared with the original Ca-3MS in the presence of competing protein (pepsin) in simple aqueous solution. In real CFS, both AfB1 adsorption capacities (Qmax) and affinities (K) by all organo-smectites were greater (Qmax = up to 0.45 mol kg–1 and K = up to 0.165 μM–1) than those by Ca-3MS (Qmax = 0.22 mol kg–1 and K = 0.031 μM–1). The study suggested that using smectites modified with an organic nutritive compound could be an effective, economical, and safe strategy for removing mycotoxins, including aflatoxins, during biofuel production.

Lemongrass essential oil (LEO) has been evaluated as a silage additive to improve silage fermentation and reduce fermentative losses. The present study aimed to evaluate the effects of increasing levels of LEO on whole-plant sorghum silage (WPSS) fermentation profile, fermentation losses, chemical composition, dry matter (DM) and neutral detergent fibre (NDF) in vitro degradation and aerobic stability. Five cultivars and fifty experimental silos were used to evaluate the following LEO levels: 0, 1, 2, 3 and 4 ml kg−1 DM of WPSS. The material was compacted (650 kg m−2) and the silos were sealed, weighed and stored at room temperature for 167 days. The addition of LEO linearly decreased butyric acid content and the ratio between lactic and acetic acids. Intermediate levels of LEO increased NH3-N and reduced lactic and acetic acids content. LEO linearly decreased silage gas losses. However, LEO did not affect total silage losses and DM recovery. Intermediate levels of LEO addition decreased organic matter and crude protein in the WPSS. The addition of LEO did not affect other chemical composition parameters, DM and NDF in vitro degradation, and pH and temperature of the silage after aerobic exposure. Thus, LEO supply in WPSS reduces gas losses, butyric acid concentration, and the ratio between lactic and acetic acids. However, LEO does not improve the chemical composition, in vitro degradation, and aerobic stability of WPSS.

The present study aimed to evaluate the effects of chitosan instead of microbial inoculants on fermentation profile, losses, chemical composition, in vitro degradation, and aerobic stability of sugarcane silage (SS). Forty experimental silos (PVC tubes with 28 cm i.d., 25 cm height) were used in a randomized block design to evaluate the following treatments: (I) Control (CON): SS with no additive; (II) LB: SS ensiled with 5.0 × 105 colony forming units (CFU) of Lactobacillus buchneri (NCIM 40788)/g as-fed; (III) LPPA: SS ensiled with 1.6 × 105 CFU of L. plantarum and 1.6 × 105 CFU of Pediococcus acidilactici/g as-fed; and (IV) Chitosan (CHI): SS ensiled with 6 g/kg dry matter (DM) of chitosan. Microbial inoculation of SS reduced (P ≤ 0.05) silage pH relative to CON and CHI treatment. The LPPA decreased ammonia-nitrogen and LB decreased (P ≤ 0.05) ethanol content and increased acetic acid content relative to other treatments. The LPPA-silos had higher (P ≤ 0.05) gas losses and lower (P ≤ 0.05) DM recovery than other treatment silos. Consequently, LPPA reduced (P ≤ 0.05) DM and non-fibre carbohydrates and increased (P ≤ 0.05) neutral detergent fibre (NDF) silage content compared to other treatments. Treatments did not affect (P ≥ 0.212) DM and NDF in vitro degradation and silage pH after aerobic exposure. However, LB reduced silage temperature after aerobic exposure. Thus, LB reduces alcoholic fermentation and improves SS aerobic stability. Inoculation of LPPA reduces DM recovery and negatively affects SS chemical composition. Although CHI positively affects SS conservation relative to CON, it shows higher gas losses and decreased SS temperature after aerobic exposure compared to LB.

Resistant starch 2 (RS2) may offer therapeutic value to irritable bowel syndrome (IBS) patients particularly in combination with minimally fermented fibre, but tolerability data are lacking. The present study evaluated the tolerability of RS2, sugarcane bagasse and their combination in IBS patients and healthy controls. Following baseline, participants consumed the fibres in escalating doses lasting 3 d each: RS2 (10, 15 and 20 g/d); sugarcane bagasse (5, 10 and 15 g/d); and their combination (20, 25 and 30 g/d). Gastrointestinal symptoms were assessed daily. Six IBS patients and five controls were recruited. No differences in overall symptoms from baseline were found across the fibre doses (IBS, P = 0⋅586; controls, P = 0⋅687). For IBS patients, all RS2 doses led to increased bloating. One IBS patient did not tolerate the low combination dose and another the high sugarcane bagasse dose. Supplementation of RS2 ≤ 20 g/d caused mild symptoms and was generally tolerated in IBS patients even when combined with minimally fermented fibre.

Our previous studies have shown that the nutritional properties of peanut meal after fermentation are markedly improved. In this study, in order to facilitate the further utilisation of peanut meal, we investigated the effects of its fermentation extract by Bacillus natto (FE) on cognitive ability, antioxidant activity of brain and protein expression of hippocampus of ageing rats induced by d-galactose. Seventy-two female sd rats aged 4–5 months were randomly divided into six groups: normal control group, ageing model group, FE low-dose group, FE medium-dose group, FE high-dose group and vitamin E positive control group. Morris water maze (MWM) test was performed to evaluate their effects on learning and memory ability in ageing rats. Superoxide dismutase (SOD) activity and malondialdehyde (MDA) content of brain, HE staining and the expression of γ-aminobutyric acid receptor 1 (GABABR1) and N-methyl-d-aspartic acid 2B receptor in the hippocampus of rats were measured. The results show that FE supplementation can effectively alleviate the decrease of thymus index induced by ageing, decrease the escape latency of MWM by 66·06 %, brain MDA by 28·04 %, hippocampus GABABR1 expression by 7·98 % and increase brain SOD by 63·54 % in ageing model rats. This study provides evidence for its anti-ageing effects and is a research basis for potential nutritional benefits of underutilised food by-products.

The revitalization of fermentation projects during COVID-19 raises questions about the preservation of the pandemic’s material and ephemeral effects – a topic that heritage policy is well equipped to engage. These activities also emphasize the necessity of engaging with heritage practices as a kind of care, encompassing both methods of safekeeping and practices of empathy. In addition, heritage ferments prove “good to think” around themes of loss and preservation, the interpretation of novel viruses through traditional food practices, and the coupling of heritage to microbes. Connecting microbes with heritage allows us to consider points of overlap: as bearers of patrimony with cultural and material lineages, as central to heritage tastes, and as open to geographical indications or other protections to further a kind of microbial resource management. Despite the pandemic’s devastating impact, consideration of heritage ferments points to both emancipatory and constraining outcomes for our post-pandemic future.

This study aimed to examine the effects of re-ensiling time and Lactobacillus buchneri on the fermentation profile, chemical composition and aerobic stability of sugarcane silages. The experiment was set up as a repeated measure design consisting of four air-exposure periods (EP)(0, 6, 12, and 24 h) microbial additive (A) (L. buchneri; or lack of there), with five replicates. Sugarcane was ground through a stationary forage chopper and ensiled in four plastic drums of 200-L capacity. After 210 days of storage, the drums were opened and half of the silage mass was treated with L. buchneri at the concentration of 105 cfu/g of forage. Subsequently, the silages were divided into stacks. The re-ensiling process was started immediately, at 0, 6, 12 and 24-hour intervals, by transferring the material to PVC mini-silos. Silos were opened after 120 days of re-ensiling. The use of L. buchneri reduced butyrate concentration but did not change ethanol or acetic acid concentrations and aerobic stability. An interaction effect between L. buchneri and re-ensiling time was observed for dry matter (DM) losses and composition. Lactobacillus buchneri is not effective in improving aerobic stability in re-ensiled sugarcane silages. However, less DM is lost in silages treated with L. buchneri and exposed to air for 24 h. Re-ensiling sugar cane in up to 24 h of exposure to air does not change final product quality.

The therapeutic value of specific fibres is partly dependent on their fermentation characteristics. Some fibres are rapidly degraded with the generation of gases that induce symptoms in patients with irritable bowel syndrome (IBS), while more slowly or non-fermentable fibres may be more suitable. More work is needed to profile a comprehensive range of fibres to determine suitability for IBS. Using a rapid in vitro fermentation model, gas production and metabolite profiles of a range of established and novel fibres were compared. Fibre substrates (n 15) were added to faecal slurries from three healthy donors for 4 h with gas production measured using real-time headspace sampling. Concentrations of SCFA and ammonia were analysed using GC and enzymatic assay, respectively. Gas production followed three patterns: rapid (≥60 ml/g over 4 h) for fructans, carrot fibre and maize-derived xylo-oligosaccharide (XOS); mild (30–60 ml/g) for partially hydrolysed guar gum, almond shell-derived XOS and one type of high-amylose resistant starch 2 (RS2) and minimal (no differences with blank controls) for methylcellulose, another high-amylose RS2, acetylated or butyrylated RS2, RS4, acacia gum and sugarcane bagasse. Gas production correlated positively with total SCFA (r 0·80, P < 0·001) and negatively with ammonia concentrations (r –0·68, P < 0·001). Proportions of specific SCFA varied: fermentation of carrot fibre, XOS and acetylated RS2 favoured acetate, while fructans favoured butyrate. Gas production and metabolite profiles differed between fibre types and within fibre classes over a physiologically relevant 4-h time course. Several fibres resisted rapid fermentation and may be candidates for clinical trials in IBS patients.

The successful ensiling of lucerne (Medicago sativa L.) depends on a rapid acidification in the silo and consequently relies on a sufficient proliferation of, particularly homofermentative, lactic acid bacteria. Similarly, growth of spoilage bacteria, such as enterobacteria and clostridia, must be suppressed and silage additives are therefore frequently applied to promote favourable conditions during ensiling. Three silage additives or soil were applied during lucerne ensiling and investigated for their effects on silage quality characteristics and abundances of total bacteria as well as the bacterial key players Lactobacillus spp., homofermentative Lact. plantarum, heterofermentative Lact. buchneri, Clostridium spp. and Enterobacteriaceae after 30 days of storage. Inoculation with viable Lact. plantarum resulted in highest concentration of this species and excellent silage quality, i.e. high lactic acid concentration coupled with low acetic acid and ammonia-nitrogen concentrations. A sodium nitrite and hexamine-based additive did not support growth of lactic acid bacteria, which was also apparent by higher pH and low lactic acid concentration. No effect of treatments was found on spoilage-related enterobacteria and clostridia, even not when adding soil to lucerne to increase initial clostridial contamination. However, soil treatment resulted in increased ammonia-nitrogen and acetic acid concentrations. Consequently, among the bacterial key players, lactic acid bacteria concentrations were related to silage quality. Regarding spoilage bacteria, however, alterations in silage quality characteristics were not reflected in the abundances of enterobacteria and clostridia. Future investigations should underpin the present findings and help to understand how silage additives affect microbial key players and silage fermentation.

Diet 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.

The rumen contains a great diversity of prokaryotic and eukaryotic microorganisms that allow the ruminant to utilize ligno-cellulose material and to convert non-protein nitrogen into microbial protein to obtain energy and amino acids. However, rumen fermentation also has potential deleterious consequences associated with the emissions of greenhouse gases, excessive nitrogen excreted in manure and may also adversely influence the nutritional value of ruminant products. While several strategies for optimizing the energy and nitrogen use by ruminants have been suggested, a better understanding of the key microorganisms involved and their activities is essential to manipulate rumen processes successfully. Diet is the most obvious factor influencing the rumen microbiome and fermentation. Among dietary interventions, the ban of antimicrobial growth promoters in animal production systems has led to an increasing interest in the use of plant extracts to manipulate the rumen. Plant extracts (e.g. saponins, polyphenol compounds, essential oils) have shown potential to decrease methane emissions and improve the efficiency of nitrogen utilization; however, there are limitations such as inconsistency, transient and adverse effects for their use as feed additives for ruminants. It has been proved that the host animal may also influence the rumen microbial population both as a heritable trait and through the effect of early-life nutrition on microbial population structure and function in adult ruminants. Recent developments have allowed phylogenetic information to be upscaled to metabolic information; however, research effort on cultivation of microorganisms for an in-depth study and characterization is needed. The introduction and integration of metagenomic, transcriptomic, proteomic and metabolomic techniques is offering the greatest potential of reaching a truly systems-level understanding of the rumen; studies have been focused on the prokaryotic population and a broader approach needs to be considered.

Rumen sensors provide specific information to help understand rumen functioning in relation to health disorders and to assist in decision-making for farm management. This review focuses on the use of rumen sensors to measure ruminal pH and discusses variation in pH in both time and location, pH-associated disorders and data analysis methods to summarize and interpret rumen pH data. Discussion on the use of rumen sensors to measure redox potential as an indication of the fermentation processes is also included. Acids may accumulate and reduce ruminal pH if acid removal from the rumen and rumen buffering cannot keep pace with their production. The complexity of the factors involved, combined with the interactions between the rumen and the host that ultimately determine ruminal pH, results in large variation among animals in their pH response to dietary or other changes. Although ruminal pH and pH dynamics only partially explain the typical symptoms of acidosis, it remains a main indicator and may assist to optimize rumen function. Rumen pH sensors allow continuous monitoring of pH and of diurnal variation in pH in individual animals. Substantial drift of non-retrievable rumen pH sensors, and the difficulty to calibrate these sensors, limits their application. Significant within-day variation in ruminal pH is frequently observed, and large distinct differences in pH between locations in the rumen occur. The magnitude of pH differences between locations appears to be diet dependent. Universal application of fixed conversion factors to correct for absolute pH differences between locations should be avoided. Rumen sensors provide high-resolution kinetics of pH and a vast amount of data. Commonly reported pH characteristics include mean and minimum pH, but these do not properly reflect severity of pH depression. The area under the pH × time curve integrates both duration and extent of pH depression. The use of this characteristic, as well as summarizing parameters obtained from fitting equations to cumulative pH data, is recommended to identify pH variation in relation to acidosis. Some rumen sensors can also measure the redox potential. This measurement helps to understand rumen functioning, as the redox potential of rumen fluid directly reflects the microbial intracellular redox balance status and impacts fermentative activity of rumen microorganisms. Taken together, proper assessment and interpretation of data generated by rumen sensors requires consideration of their limitations under various conditions.

Benzimidazole derivatives such as albendazole (ABZ) and mebendazole are important molecules used in helminthic treatment. Neurocysticercosis is the main cause of acquired epilepsy throughout the world and is currently treated with ABZ. New molecules have been studied in order to aid in the treatment of this neglected tropical disease, among them RCB15 and RCB20. The aim of this study was to evaluate the metabolic impact of RCB15 and RCB20 on Taenia crassiceps cysticerci intracranially inoculated in Balb/c mice. Thirty days after the inoculation the mice were treated with 50 mg kg−1 of RCB15, RCB20, ABZ or NaCl 0.9%. The euthanasia and cysticerci removal were performed 24 h after the treatment. The cysticerci were analysed through high performance liquid chromatography. After the treatments, there was an impairment in the main energetic pathways such as glycolytic pathway, homolactic fermentation or in mitochondrion energy production detected through the decrease in pyruvate, lactate, oxaloacetate, malate and fumarate concentrations. This induced the parasite to resort to alternative energetic pathways such as proteins catabolism, propionate fermentation and fatty acids oxidation. Therefore, benzimidazole derivatives are a promising alternative to ABZ use as they also reach the brain tissue and induce a metabolic stress in the cysticerci.

The micro-organisms which inhabit the human gut (i.e. the intestinal microbiota) influence numerous human biochemical pathways and physiological functions. The present review focuses on two questions, ‘Are intestinal microbiota effects measurable and meaningful?’ and ‘What research methods and variables are influenced by intestinal microbiota effects?’. These questions are considered with respect to doubly labelled water measurements of energy expenditure, heat balance calculations and models, measurements of RMR via indirect calorimetry, and diet-induced energy expenditure. Several lines of evidence suggest that the intestinal microbiota introduces measurement variability and measurement errors which have been overlooked in research studies involving nutrition, bioenergetics, physiology and temperature regulation. Therefore, we recommend that present conceptual models and research techniques be updated via future experiments, to account for the metabolic processes and regulatory influences of the intestinal microbiota.

Grains rich in starch constitute the primary source of energy for both pigs and humans, but there is incomplete understanding of physiological mechanisms that determine the extent of digestion of grain starch in monogastric animals including pigs and humans. Slow digestion of starch to produce glucose in the small intestine (SI) leads to undigested starch escaping to the large intestine where it is fermented to produce short-chain fatty acids. Glucose generated from starch provides more energy than short-chain fatty acids for normal metabolism and growth in monogastrics. While incomplete digestion of starch leads to underutilised feed in pigs and economic losses, it is desirable in human nutrition to maintain consistent body weight in adults. Undigested nutrients reaching the ileum may trigger the ileal brake, and fermentation of undigested nutrients or fibre in the large intestine triggers the colonic brake. These intestinal brakes reduce the passage rate in an attempt to maximise nutrient utilisation, and lead to increased satiety that may reduce feed intake. The three physiological mechanisms that control grain digestion and feed intake are: (1) gastric emptying rate; (2) interplay of grain digestion and passage rate in the SI controlling the activation of the ileal brake; and (3) fermentation of undigested nutrients or fibre in the large intestine activating the colonic brake. Fibre plays an important role in influencing these mechanisms and the extent of their effects. In this review, an account of the physiological mechanisms controlling the passage rate, feed intake and enzymatic digestion of grains is presented: (1) to evaluate the merits of recently developed methods of grain/starch digestion for application purposes; and (2) to identify opportunities for future research to advance our understanding of how the combination of controlled grain digestion and fibre content can be manipulated to physiologically influence satiety and food intake.

The effect of kiwi fruit at two dietary levels on the adaptation of intestinal fermentation over time in the growing pig was studied. A semi-synthetic fibre-free diet and two semi-synthetic diets containing kiwi fruit as a model fibre source (133 or 266 g/kg (DM basis); 28 or 48 g fibre/kg) were formulated and the diets contained titanium dioxide as an indigestible marker. A total of fourteen ileal cannulated pigs (41 kg body weight) were fed the fibre-free diet for 7 d followed by either the low or high kiwi fruit-containing diets (n 7/diet) for a further 44 d. Ileal digesta and faeces were collected at five times throughout the study. Ileal digesta were fermented (in vitro) with a standard pooled human faecal inoculum, while fresh pig faeces were used as inocula to ferment in vitro a standard purified fibre. Observations were normalised for diet DM intake using the marker. The 16S ribosomal RNA gene copy number of ileal and total faecal bacteria were high for the high-kiwi fruit level diet (P<0·05). The ileal bacteria tended to decrease over time (P<0·1), while the faecal bacteria increased (P<0·05), at the same rate for both diets. The amounts of crude protein and insoluble dietary fibre entering the hindgut changed over time similarly for both diets, whereas for starch it changed only for the low kiwi fruit-containing diet (P<0·05). Changes over time were also observed for the predicted hindgut valeric acid production and butyric acid absorption (P<0·05). In conclusion, adaptational changes over time of some characteristics of intestinal fermentation depended on the dietary level of kiwi fruit.

The objective of the studies reported in this research communication was to investigate the use of whey contaminated with antibiotics such as cephalosporins, quinolones and tetracyclines as a nutrient medium for the growth of Kluyveromyces marxianus with particular attention to the effect of thermal treatment used to overcome the inhibitory effects of antibiotic concentrations close to the Maximum Residue Limits. The heat treatments at 120 °C for 40 min, 120 °C for 83 min, and 120 °C for 91 min caused total inactivation of cephalosporins, tetracyclines and quinolone residues in whey respectively.