Browsing by Subject "FOOD"

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  • Linkens, Armand M. A.; van Best, Niels; Niessen, Petra M.; Wijckmans, Nicole E. G.; de Goei, Erica E. C.; Scheijen, Jean L. J. M.; van Dongen, Martien C. J. M.; van Gool, Christel C. J. A. W.; de Vos, Willem M.; Houben, Alfons J. H. M.; Stehouwer, Coen D. A.; Eussen, Simone J. M. P.; Penders, John; Schalkwijk, Casper G. (2022)
    Dietary advanced glycation endproducts (AGEs), abundantly present in Westernized diets, are linked to negative health outcomes, but their impact on the gut microbiota has not yet been well investigated in humans. We investigated the effects of a 4-week isocaloric and macronutrient-matched diet low or high in AGEs on the gut microbial composition of 70 abdominally obese individuals in a double-blind parallel-design randomized controlled trial (NCT03866343). Additionally, we investigated the cross-sectional associations between the habitual intake of dietary dicarbonyls, reactive precursors to AGEs, and the gut microbial composition, as assessed by 16S rRNA amplicon-based sequencing. Despite a marked percentage difference in AGE intake, we observed no differences in microbial richness and the general community structure. Only the Anaerostipes spp. had a relative abundance >0.5% and showed differential abundance (0.5 versus 1.11%; p = 0.028, after low- or high-AGE diet, respectively). While the habitual intake of dicarbonyls was not associated with microbial richness or a general community structure, the intake of 3-deoxyglucosone was especially associated with an abundance of several genera. Thus, a 4-week diet low or high in AGEs has a limited impact on the gut microbial composition of abdominally obese humans, paralleling its previously observed limited biological consequences. The effects of dietary dicarbonyls on the gut microbiota composition deserve further investigation.
  • McCrackin, Michelle L.; Muller-Karulis, Baerbel; Gustafsson, Bo G.; Howarth, Robert W.; Humborg, Christoph; Svanbäck, Annika; Swaney, Dennis P. (2018)
    There is growing evidence that the release of phosphorus (P) from legacy stores can frustrate efforts to reduce P loading to surface water from sources such as agriculture and human sewage. Less is known, however, about the magnitude and residence times of these legacy pools. Here we constructed a budget of net anthropogenic P inputs to the Baltic Sea drainage basin and developed a three-parameter, two-box model to describe the movement of anthropogenic P though temporary (mobile) and long-term (stable) storage pools. Phosphorus entered the sea as direct coastal effluent discharge and via rapid transport and slow, legacy pathways. The model reproduced past waterborne P loads and suggested an similar to 30-year residence time in the mobile pool. Between 1900 and 2013, 17 and 27 Mt P has accumulated in the mobile and stable pools, respectively. Phosphorus inputs to the sea have halved since the 1980s due to improvements in coastal sewage treatment and reductions associated with the rapid transport pathway. After decades of accumulation, the system appears to have shifted to a depletion phase; absent further reductions in net anthropogenic P input, future waterborne loads could decrease. Presently, losses from the mobile pool contribute nearly half of P loads, suggesting that it will be difficult to achieve substantial near-term reductions. However, there is still potential to make progress toward eutrophication management goals by addressing rapid transport pathways, such as overland flow, as well as mobile stores, such as cropland with large soil-P reserves.
  • Ahlberg, Sara; Grace, Delia; Kiarie, Gideon; Kirino, Yumi; Lindahl, Johanna (2018)
    Aflatoxin M1 (AFM1), a human carcinogen, is found in milk products and may have potentially severe health impacts on milk consumers. We assessed the risk of cancer and stunting as a result of AFM1 consumption in Nairobi, Kenya, using worst case assumptions of toxicity and data from previous studies. Almost all (99.5%) milk was contaminated with AFM1. Cancer risk caused by AFM1 was lower among consumers purchasing from formal markets (0.003 cases per 100,000) than for low-income consumers (0.006 cases per 100,000) purchasing from informal markets. Overall cancer risk (0.004 cases per 100,000) from AFM1 alone was low. Stunting is multifactorial, but assuming only AFM1 consumption was the determinant, consumption of milk contaminated with AFM1 levels found in this study could contribute to 2.1% of children below three years in middle-income families, and 2.4% in low-income families, being stunted. Overall, 2.7% of children could hypothetically be stunted due to AFM1 exposure from milk. Based on our results AFM1 levels found in milk could contribute to an average of −0.340 height for age z-score reduction in growth. The exposure to AFM1 from milk is 46 ng/day on average, but children bear higher exposure of 3.5 ng/kg bodyweight (bw)/day compared to adults, at 0.8 ng/kg bw/day. Our paper shows that concern over aflatoxins in milk in Nairobi is disproportionate if only risk of cancer is considered, but that the effect on stunting children might be much more significant from a public health perspective; however, there is still insufficient data on the health effects of AFM1.
  • Sabet, Saman; Kirjoranta, Satu; Lampi, Anna-Maija; Lehtonen, Mari Johanna; Pulkkinen, Elli Eva; Valoppi, Fabio (2022)
    The interest on the digestive fate of oleogels, i.e., substitutes for solid fats rich in liquid oil, have pushed re-searchers to use the widely adopted INFOGEST protocol for static in vitro digestion. However, this protocol was originally designed to simulate the digestibility of conventional foods and to accommodate the large fraction of oil in oleogels, researchers have deliberately modified the INFOGEST protocol, inadvertently leading to results difficult to be compared. In this study, we highlighted possible problems that may arise during oleogel simulated digestion such as under-or overestimation of oleogel lipolysis. The effect of oleogel amount, oleogelator type and concentration, and shear applied during digestion on the rate and extent of oleogel digestion was studied. The release of fatty acids during the application of INFOGEST protocol was monitored using the pH-stat method and compared to those analyzed by HPLC-ELSD. Oleogels' structural information was obtained using brightfield, polarized, and fluorescence microscopy, and DSC. We determined that lipolysis of ethylcellulose oleogels follow the "interaction with enzymes and bile salts " pattern, whereas that of wax oleogels follow the "disintegration of oleogel and interaction with enzymes and bile salts ". We also observed that the chemical composition of wax, crystal morphology, and crystal distribution do not alter the lipolysis of oil entrapped inside the wax crystals. We finally recommended a few minimal but fundamental modifications to the INFOGEST protocol to achieve more reliable results from the static in vitro digestion of oleogels and possibly other lipid-based systems.
  • Järviö, Natasha; Maljanen, Netta-Leena; Kobayashi, Yumi; Ryynänen, Toni; Tuomisto, Hanna (2021)
    Novel food production technologies are being developed to address the challenges of securing sustainable and healthy nutrition for the growing global population. This study assessed the environmental impacts of microbial protein (MP) produced by autotrophic hydrogen-oxidizing bacteria (HOB). Data was collected from a company currently producing MP using HOB (hereafter simply referred to as MP) on a small-scale. Earlier studies have performed an environmental assessment of MP on a theoretical basis but no study yet has used empirical data. An attributional life cycle assessment (LCA) with a cradle-to-gate approach was used to quantify global warming potential (GWP), land use, freshwater and marine eutrophication potential, water scarcity, human (non-)carcinogenic toxicity, and the cumulative energy demand (CED) of MP production in Finland. A Monte Carlo analysis was performed to assess uncertainties. The impacts of alternative production options and locations were explored. The impacts were compared with animal- and plant-based protein sources for human consumption as well as protein sources for feed. The results showed that electricity consumption had the highest contribution to environmental impacts. Therefore, the source of energy had a substantial impact on the results. MP production using hydropower as an energy source yielded 87.5% lower GWP compared to using the average Finnish electricity mix. In comparison with animal-based protein sources for food production, MP had 53-100% lower environmental impacts depending on the reference product and the source of energy assumed for MP production. When compared with plant-based protein sources for food production, MP had lower land and water use requirements, and eutrophication potential but GWP was reduced only if low-emission energy sources were used. Compared to protein sources for feed production, MP production often resulted in lower environmental impact for GWP (FHE), land use, and eutrophication and acidification potential, but generally caused high water scarcity and required more energy.
  • Bui, Thi Phuong Nam; Troise, Antonio Dario; Fogliano, Vincenzo; de Vos, Willem M. (2019)
    Modifications of lysine contribute to the amount of dietary advanced glycation end-products reaching the colon. However, little is known about the ability of intestinal bacteria to metabolize dietary N-epsilon-carboxymethyllysine (CML). Successive transfers of fecal microbiota in growth media containing CML were used to identify and isolate species able to metabolize CML under anaerobic conditions. From our study, only donors exposed to processed foods degraded CML, and anaerobic bacteria enrichments from two of them used 77 and 100% of CML. Oscillibacter and Cloacibacillus evryensis increased in the two donors after the second transfer, highlighting that the bacteria from these taxa could be candidates for anaerobic CML degradation. A tentative identification of CML metabolites produced by a pure culture of Cloacibacillus evryensis was performed by mass spectrometry: carboxymethylated biogenic amines and carboxylic acids were identified as CML degradation products. The study confirmed the ability of intestinal bacteria to metabolize CML under anoxic conditions.
  • Becker, Daniel J.; Hall, Richard J.; Forbes, Kristian M.; Plowright, Raina K.; Altizer, Sonia (2018)
  • Taar, Jaana; Palojoki, Päivi (2022)
    In this paper, we seek to determine the relationship between home economics education and 21stcentury skills (critical thinking, creativity, communication and collaboration) in the context of social learning. We see potential in students' discussions while working together with different group members and practicing the essential skills necessary for coping in the contemporary world. Using a socio-cultural framework, we focused on students' talk and language use as a tool in an educational setting. In addition, interthinking was analysed to obtain an overview of language use for thinking together while solving learning assignments requiring thinking-in-action in the context of home economics lessons. The results demonstrate how interthinking emerges in students' group work discussions during gap-closing processes in various collaborative home economics tasks (n = 11). As a result, interthinking was determined to be as a good medium for the development of 21st-century skills in school lessons. Based on the empirical data, we argue that interthinking is well-suited to the aims and context of home economics education, as it enables the promotion of students' action competence so that the knowledge and skills learned in school can become a reality in students' lives.
  • Kaljonen, Minna; Peltola, Taru; Salo, Marja; Furman, Eeva (2019)
    The critical role of everyday practices in climate change mitigation has placed experimental approaches at the top of the environmental policy agenda. In this paper we discuss the value of behavioural approaches, practice theories, pragmatic tinkering and speculative thinking with respect to experimentation. Whereas the first two have been much discussed within sustainability science and transition research, the notions of pragmatic tinkering and speculative thinking radically broaden the scope of experimental research and its contribution to sustainable everyday practices. Pragmatism brings to the fore the need to coordinate multiple practices and understandings of good eating, as these may clash in practice. Through this lens, the value of experimental research lies in revealing frictions that need to be resolved, or tinkered, in practice. Speculative experimentation, in turn, refers to the power of experiments to challenge the experimental setting itself and force thinking about new possibilities and avenues. We investigate the value of all four approaches in relation to our experiments with sustainable eating in the Finnish and Nordic context. Our elaboration justifies the need to broaden the conception of experimental research in order to capture the multiplicity of sustainable eating. Hence, we call for attentive, speculative experimental research aimed not only at testing solutions for sustainable everyday practice, but also at reflecting on the practice of experimentation itself.
  • Chamlagain, Bhawani; Peltonen, Liisa; Edelmann, Minnamari; Ramos-Diaz, Jose Martin; Kemppinen, Asmo; Jouppila, Kirsi; Varmanen, Pekka; Piironen, Vieno (2021)
    The bioaccessibility of vitamin B12 (B12) in plant-based products fortified using wheat bran extract fermented with B12-producing food-grade Propionibacterium freudenreichii was studied by applying a standard static in vitro model. At first, a culture of P. freudenreichii, fresh or heat-treated, was subjected to in vitro assays. Then, food ingredients or products were evaluated for their in vitro bioaccessibility: spray-dried wheat bran extract powder, pasta made with an extruder using fermented bran extract and breads made with spray-dried powder or with added cyanocobalamin. B12 bioaccessibility from the fresh P. freudenreichii culture was only ca. 53%, which, when heated, increased to 73%. The bioaccessibility of B12 from the food products varied from 75% (spray-dried powder) to 95% (breads). B12 from the fortified bread was as bioaccessible as from the bread made with added cyanocobalamin (99%). The in vitro results suggest that B12 synthesized by P. freudenreichii, when fortified in the studied cereal-based products, is largely bioaccessible and could be available for absorption. Plant-based products fortified using fermentation with P. freudenreichii could thus be considered excellent sources of bioaccessible B12.
  • Ali-Kovero, Kirsi; Pietilainen, Olli; Mauramo, Elina; Jäppinen, Sauli; Rahkonen, Ossi; Lallukka, Tea; Kanerva, Noora (2020)
    Retirement is a major life transition affecting health and health behaviour, but evidence on how this transition contributes to changes in healthy food habits is scarce. We examined whether the consumption of fruit and vegetables as well as fish changes after transition into statutory retirement. The data were derived from the prospective Helsinki Health Study. At phase 1 in 2000-2002, all participants were 40- to 60-year-old employees of the City of Helsinki, Finland (n 8960, response rate 67 %). Follow-up surveys were conducted in 2007, 2012 and 2017 (response rates 79-83 %). Using the four phases, we formed three nested cohorts in which the participants either continued working or moved to statutory retirement. The final analytical sample consisted of 6887 participants (14 357 observations). Frequency of fruit, vegetable and fish consumption was calculated from a twenty-two-item FFQ. Analyses of repeated measures of food consumption before and after retirement transition were conducted with a negative binomial mixed model, adjusting for age, marital status, limiting long-standing illness and household income. During the follow-up, altogether 3526 participants retired. Transition to retirement was associated with a decrease in vegetable consumption among women and, contrarily, with an increase in fruit consumption among men (P <0 center dot 05 for interaction between time and employment status). Fish consumption did not differ by the change in employment status. Statutory retirement can have mixed effects on healthy food habits, and these can differ between food groups and sex. Healthy food habits should be promoted among employees transitioning to retirement.
  • Vuorinen, Anna-Leena; Erkkola, Maijaliisa; Fogelholm, Mikael; Kinnunen, Satu; Saarijärvi, Hannu; Uusitalo, Liisa; Näppilä, Turkka; Nevalainen, Jaakko (2020)
    Background: To date, the evaluation of diet has mostly been based on questionnaires and diaries that have their limitations in terms of being time and resource intensive, and a tendency toward social desirability. Loyalty card data obtained in retailing provides timely and objective information on diet-related behaviors. In Finland, the market is highly concentrated, which provides a unique opportunity to investigate diet through grocery purchases. Objective: The aims of this study were as follows: (1) to investigate and quantify the selection bias in large-scale (n=47,066) loyalty card (LoCard) data and correct the bias by developing weighting schemes and (2) to investigate how the degree of loyalty relates to food purchases. Methods: Members of a loyalty card program from a large retailer in Finland were contacted via email and invited to take part in the study, which involved consenting to the release of their grocery purchase data for research purposes. Participants' sociodemographic background was obtained through a web-based questionnaire and was compared to that of the general Finnish adult population obtained via Statistics Finland. To match the distributions of sociodemographic variables, poststratification weights were constructed by using the raking method. The degree of loyalty was self-estimated on a 5-point rating scale. Results: On comparing our study sample with the general Finnish adult population, in our sample, there were more women (65.25%, 30,696/47,045 vs 51.12%, 2,273,139/4,446,869), individuals with higher education (56.91%, 20,684/36,348 vs 32.21%, 1,432,276/4,446,869), and employed individuals (60.53%, 22,086/36,487 vs 52.35%, 2,327,730/4,446,869). Additionally, in our sample, there was underrepresentation of individuals aged under 30 years (14.44%, 6,791/47,045 vs 18.04%, 802,295/4,446,869) and over 70 years (7.94%, 3,735/47,045 vs 18.20%, 809,317/4,446,869), as well as retired individuals (23.51%, 8,578/36,487 vs 31.82%, 1,414,785/4,446,869). Food purchases differed by the degree of loyalty, with higher shares of vegetable, red meat & processed meat, and fat spread purchases in the higher loyalty groups. Conclusions: Individuals who consented to the use of their loyalty card datafor research purposes tended to diverge from the general Finnish adult population. However, the high volume of data enabled the inclusion of sociodemographically diverse subgroups and successful correction of the differences found in the distributions of sociodemographic variables. In addition, it seems that food purchases differ according to the degree of loyalty, which should be taken into account when researching loyalty card data. Despite the limitations, loyalty card data provide a cost-effective approach to reach large groups of people, including hard-to-reach population subgroups.
  • Lienemann, Taru; Kyyhkynen, Aino; Halkilahti, Jani; Haukka, Kaisa; Siitonen, Anja (2015)
    Background: Salmonella enterica spp. enterica serotype Typhimurium (STM) is the most common agent of domestically acquired salmonellosis in Finland. Subtyping methods which allow the characterization of STM are essential for effective laboratory-based STM surveillance and for recognition of outbreaks. This study describes the diversity of Finnish STM isolates using phage typing, antimicrobial susceptible testing, pulsed-field gel electrophoresis (PFGE) and multilocus variable-number tandem repeat analysis (MLVA), and compares the discriminatory power and the concordance of these methods. Results: A total of 375 sporadic STM isolates were analysed. The isolates were divided into 31 definite phage (DT) types, dominated by DT1 (47 % of the isolates), U277 (9 % of the isolates) and DT104 (8 % of the isolates). Of all the isolates, 62 % were susceptible to all the 12 antimicrobials tested and 11 % were multidrug resistant. Subtyping resulted in 83 different XbaI-PFGE profiles and 111 MLVA types. The three most common XbaI-PFGE profiles (STYM1, STYM7 and STYM8) and one MLVA profile with three single locus variants accounted for 56 % and 49 % of the STM isolates, respectively. The studied isolates showed a genetic similarity of more than 70 % by XbaI-PFGE. In MLVA, 71 % of the isolates lacked STTR6 and 77 % missed STTR10p loci. Nevertheless, the calculated Simpson's diversity index for XbaI-PFGE was 0.829 (95 % CI 0.792-0.865) and for MLVA 0.867 (95 % CI 0.835-0.898). However, the discriminatory power of the 5-loci MLVA varied among the phage types. The highest concordance of the results was found between XbaI-PFGE and phage typing (adjusted Wallace coefficient was 0.833 and adjusted Rand coefficient was 0.627). Conclusions: In general, the calculated discriminatory power was higher for genotyping methods (MLVA and XbaI-PFGE) than for phenotyping methods (phage typing). Overall, comparable diversity indices were calculated for PFGE and MLVA (both DI > 0.8). However, MLVA was phage type dependent providing better discrimination of the most common phage types. Furthermore, 5-loci MLVA was a less laborious method and easier to interpret than XbaI-PFGE. Thus, the laboratory-based surveillance of the Finnish human STM infections has been conducted with a combination of phage typing, antimicrobial susceptibility testing and 5-loci MLVA since January 2014.
  • Mehlig, Kirsten; Bogl, Leonie H.; Hunsberger, Monica; Ahrens, Wolfgang; De Henauw, Stefaan; Iguacel, Isabel; Jilani, Hannah; Molnar, Denes; Pala, Valeria; Russo, Paola; Tornaritis, Michael; Veidebaum, Toomas; Kaprio, Jaakko; Lissner, Lauren (2018)
    Objective: The present study investigated the association between sugar and fat intake in childhood in relation to alcohol use in adolescence. We hypothesized that early exposure to diets high in fat and sugar may affect ingestive behaviours later in life, including alcohol use. Design/Setting/Subjects: Children from the European IDEFICS/I.Family cohort study were examined at ages 5-9 years and followed up at ages 11-16 years. FFQ were completed by parents on behalf of children, and later by adolescents themselves. Complete data were available in 2263 participants. Children's propensities to consume foods high in fat and sugar were calculated and dichotomized at median values. Adolescents' use of alcohol was classified as at least weekly v. less frequent use. Log-binomial regression linked sugar and fat consumption in childhood to risk of alcohol use in adolescence, adjusted for relevant covariates. Results: Five per cent of adolescents reported weekly alcohol consumption. Children with high propensity to consume sugar and fat were at greater risk of later alcohol use, compared with children with low fat and low sugar propensity (relative risk = 2.46; 95% CI 1.47, 4.12), independent of age, sex and survey country. The association was not explained by parental income and education, strict parenting style or child's health-related quality of life and was only partly mediated by sustained consumption of sugar and fat into adolescence. Conclusions: Frequent consumption of foods high in fat and sugar in childhood predicted regular use of alcohol in adolescence.
  • Lubbers, Ronnie J. M.; Dilokpimol, Adiphol; Navarro, Jorge; Peng, Mao; Wang, Mei; Lipzen, Anna; Ng, Vivian; Grigoriev, Igor V.; Visser, Jaap; Hildén, Kristiina S.; de Vries, Ronald P. (2019)
    Cinnamic acid is an aromatic compound commonly found in plants and functions as a central intermediate in lignin synthesis. Filamentous fungi are able to degrade cinnamic acid through multiple metabolic pathways. One of the best studied pathways is the non-oxidative decarboxylation of cinnamic acid to styrene. In Aspergillus niger, the enzymes cinnamic acid decarboxylase (CdcA, formally ferulic acid decarboxylase) and the flavin prenyltransferase (PadA) catalyze together the non-oxidative decarboxylation of cinnamic acid and sorbic acid. The corresponding genes, cdcA and padA, are clustered in the genome together with a putative transcription factor previously named sorbic acid decarboxylase regulator (SdrA). While SdrA was predicted to be involved in the regulation of the non-oxidative decarboxylation of cinnamic acid and sorbic acid, this was never functionally analyzed. In this study, A. niger deletion mutants of sdrA, cdcA, and padA were made to further investigate the role of SdrA in cinnamic acid metabolism. Phenotypic analysis revealed that cdcA, sdrA and padA are exclusively involved in the degradation of cinnamic acid and sorbic acid and not required for other related aromatic compounds. Whole genome transcriptome analysis of ΔsdrA grown on different cinnamic acid related compounds, revealed additional target genes, which were also clustered with cdcA, sdrA, and padA in the A. niger genome. Synteny analysis using 30 Aspergillus genomes demonstrated a conserved cinnamic acid decarboxylation gene cluster in most Aspergilli of the Nigri clade. Aspergilli lacking certain genes in the cluster were unable to grow on cinnamic acid, but could still grow on related aromatic compounds, confirming the specific role of these three genes for cinnamic acid metabolism of A. niger.
  • Rodriguez, C.; Taminiau, B.; Bouchafa, L.; Romijn, S.; Rajamaki, M. M.; Van Broeck, J.; Delmee, M.; Clercx, C.; Daube, G. (2019)
    Zoonotic transmission of Clostridium difficile has been largely hypothesised to occur after direct or indirect contact with contaminated animal faeces. Recent studies have reported the presence of the bacterium in the natural environment, including in soils and rivers. If C. difficile spores are scattered in the environment, they can easily enter the respiratory tract of dogs, and therefore, dog nasal discharge could be a direct route of transmission not previously investigated. This study reports for the first time the presence of C. difficile in the respiratory tracts of dogs. The bacterium was isolated from 6 (17.1%) out of 35 nasal samples, with a total of 4 positive dogs (19%). C. difficile was recovered from both proximal and distal nasal cavities. All isolates were toxigenic and belonged to PCR- ribotype 014, which is one of the most predominant types in animals and in community- acquired C. difficile infections in recent years. The findings of this study demonstrate that the nasal cavity of dogs is contaminated with toxigenic C. difficile, and therefore, its secretions could be considered as a new route by which bacteria are spread and transmitted.
  • Xie, Chong; Coda, Rossana; Chamlagain, Bhawani; Varmanen, Pekka; Piironen, Vieno; Katina, Kati (2019)
    The present study investigated the effect of co-fermentation on vitamin B12 content and microbiological composition of wheat bran. Propionibacterium freudenreichii DSM 20271 was used as the producer of vitamin while Lactobacillus brevis ATCC 14869 was selected to ensure the microbial safety of the bran dough. Fermentation trials were conducted in bioreactors to monitor and adjust the pH of the ferments. Vitamin B12 level reached 357 +/- 8 ng/g dry weight (dw) after 1 day of pH-controlled fermentation with P. freudenreichii monoculture and remained stable thereafter. In co-fermentation with L. brevis, slightly less vitamin B12 (255 +/- 31 ng/g dw) was produced in 1 day and an effective inhibition of the growth of total Enterobacteriaceae and Bacillus cereus was obtained. On day 3, vitamin B12 content in pH-controlled co-fermentation increased to 332 +/- 44 ng/g dw. On the other hand, without a pH control, co-fermentation resulted in a stronger inhibition of Enterobacteriaceae and B. cereus but a lower level of vitamin B12 (183 +/- 5 ng/g dw on day 3). These results demonstrated that wheat bran fermented by P. freudenreichii and L. brevis can be a promising way to produce vitamin B12 fortified plant-origin food ingredients, which could reduce cereal waste streams and contribute to a more resilient food chain.
  • Williamson, Charles H. D.; Sahl, Jason W.; Smith, Theresa J.; Xie, Gary; Foley, Brian T.; Smith, Leonard A.; Fernandez, Rafael A.; Lindström, Miia; Korkeala, Hannu; Keim, Paul; Foster, Jeffrey; Hill, Karen (2016)
    Background: Clostridium botulinum is a diverse group of bacteria characterized by the production of botulinum neurotoxin. Botulinum neurotoxins are classified into serotypes (BoNT/A-G), which are produced by six species/Groups of Clostridia, but the genetic background of the bacteria remains poorly understood. The purpose of this study was to use comparative genomics to provide insights into the genetic diversity and evolutionary history of bacteria that produce the potent botulinum neurotoxin. Results: Comparative genomic analyses of over 170 Clostridia genomes, including our draft genome assemblies for 59 newly sequenced Clostridia strains from six continents and publicly available genomic data, provided in-depth insights into the diversity and distribution of BoNT-producing bacteria. These newly sequenced strains included Group I and II strains that express BoNT/A,/B,/E, or/F as well as bivalent strains. BoNT-producing Clostridia and closely related Clostridia species were delineated with a variety of methods including 16S rRNA gene, concatenated marker genes, core genome and concatenated multi-locus sequencing typing (MLST) gene phylogenies that related whole genome sequenced strains to publicly available strains and sequence types. These analyses illustrated the phylogenetic diversity in each Group and the diversity of genomic backgrounds that express the same toxin type or subtype. Comparisons of the botulinum neurotoxin genes did not identify novel toxin types or variants. Conclusions: This study represents one of the most comprehensive analyses of whole genome sequence data for Group I and II BoNT-producing strains. Read data and draft genome assemblies generated for 59 isolates will be a resource to the research community. Core genome phylogenies proved to be a powerful tool for differentiating BoNT-producing strains and can provide a framework for the study of these bacteria. Comparative genomic analyses of Clostridia species illustrate the diversity of botulinum-neurotoxin-producing strains and the plasticity of the genomic backgrounds in which bont genes are found.
  • Byholm, Patrik; Burgas, Daniel; Virtanen, Tarmo; Valkama, Jari (2012)
  • Lehtinen, Sami O.; Geritz, Stefanus A.H. (2019)
    We investigate the evolution of timidity in a prey species whose predator has cannibalistic tendencies. The ecological model is derived from individual-level processes, in which the prey seeks refuge after detecting a predator, and the predator cannibalises on the conspecific juveniles. Bifurcation analysis of the model reveals ecological bistability between equilibrium and periodic attractors. Using the framework of adaptive dynamics, we classify ten qualitatively different evolutionary scenarios induced by the ecological bistability. These scenarios include ecological attractor switching through catastrophic bifurcations, which can reverse the direction of evolution. We show that such reversals often result in evolutionary cycling of the level of timidity. In the absence of cannibalism, the model never exhibits ecological bistability nor evolutionary cycling. We conclude that cannibalistic predator behaviour can completely change both the ecological dynamics and the evolution of prey. (C) 2019 The Authors. Published by Elsevier Ltd.