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Methanogens, reductive acetogens and sulfate-reducing bacteria play an important role in disposing of hydrogen in gut ecosystems. However, how they interact with each other remains largely unknown. This in vitro study cocultured Blautia hydrogenotrophica (reductive acetogen), Desulfovibrio piger (sulfate reducer) and Methanobrevibacter smithii (methanogen). Results revealed that these three species coexisted and did not compete for hydrogen in the early phase of incubations. Sulfate reduction was not affected by B. hydrogenotrophica and M. smithii. D. piger inhibited the growth of B. hydrogenotrophica and M. smithii after 10 h incubations, and the inhibition on M. smithii was associated with increased sulfide concentration. Remarkably, M. smithii growth lag phase was shortened by coculturing with B. hydrogenotrophica and D. piger. Formate was rapidly used by M. smithii under high acetate concentration. Overall, these findings indicated that the interactions of the hydrogenotrophic microbes are condition-dependent, suggesting their interactions may vary in gut ecosystems.
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Microbioma Gastrointestinal, Methanobrevibacter, Methanobrevibacter/fisiologia, Ecossistema, Hidrogênio, SulfatosRESUMO
Background: Infusion of short-chain fatty acids (SCFA) to the distal colon beneficially affects human substrate and energy metabolism. Here, we hypothesized that the combination of 2'-fucosyllactose (2'-FL) with resistant starch (RS) increases distal colonic SCFA production and improves metabolic parameters. Methods: In this randomized, crossover study, 10 lean (BMI 20-24.9 kg/m2) and nine men with prediabetes and overweight/obesity (BMI 25-35 kg/m2) were supplemented with either 2'-FL, 2'-FL+RS, or placebo one day before a clinical investigation day (CID). During the CID, blood samples were collected after a overnight fast and after intake of a liquid high-fat mixed meal to determine plasma SCFA (primary outcomes). Secondary outcomes were fasting and postprandial plasma insulin, glucose, free fatty acid (FFA), glucagon-like peptide-1, and peptide YY concentrations. In addition, fecal SCFA and microbiota composition, energy expenditure and substrate oxidation (indirect calorimetry), and breath hydrogen excretion were determined. Results: In lean men, supplementation with 2'-FL increased postprandial plasma acetate (P = 0.017) and fasting H2 excretion (P = 0.041) compared to placebo. Postprandial plasma butyrate concentration increased after 2'-FL and 2'-FL+RS as compared to placebo (P < 0.05) in lean men and men with prediabetes and overweight/obesity. Additionally, 2'-FL+RS decreased fasting and postprandial plasma FFA concentrations compared to placebo (P < 0.05) in lean men. Conclusion: Supplementation of 2'-FL with/without RS the day before investigation increased systemic butyrate concentrations in lean men as well as in men with prediabetes and obesity, while acetate only increased in lean men. The combination of 2'-FL with RS showed a putatively beneficial metabolic effect by lowering plasma FFA in lean men, indicating a phenotype-specific effect. Clinical trial registration: nr. NCT04795804.
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Yield for biofuel crops is measured in terms of biomass, so measurements throughout the growing season are crucial in breeding programs, yet traditionally time- and labor-consuming since they involve destructive sampling. Modern remote sensing platforms, such as unmanned aerial vehicles (UAVs), can carry multiple sensors and collect numerous phenotypic traits with efficient, non-invasive field surveys. However, modeling the complex relationships between the observed phenotypic traits and biomass remains a challenging task, as the ground reference data are very limited for each genotype in the breeding experiment. In this study, a Long Short-Term Memory (LSTM) based Recurrent Neural Network (RNN) model is proposed for sorghum biomass prediction. The architecture is designed to exploit the time series remote sensing and weather data, as well as static genotypic information. As a large number of features have been derived from the remote sensing data, feature importance analysis is conducted to identify and remove redundant features. A strategy to extract representative information from high-dimensional genetic markers is proposed. To enhance generalization and minimize the need for ground reference data, transfer learning strategies are proposed for selecting the most informative training samples from the target domain. Consequently, a pre-trained model can be refined with limited training samples. Field experiments were conducted over a sorghum breeding trial planted in multiple years with more than 600 testcross hybrids. The results show that the proposed LSTM-based RNN model can achieve high accuracies for single year prediction. Further, with the proposed transfer learning strategies, a pre-trained model can be refined with limited training samples from the target domain and predict biomass with an accuracy comparable to that from a trained-from-scratch model for both multiple experiments within a given year and across multiple years.
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Hydrogenotrophic microbes, primarily including the three functional groups methanogens, sulfate-reducing bacteria, and reductive acetogens, use hydrogen as an energy source and play an important role in maintaining the hydrogen balance in gut ecosystems. A distorted hydrogen balance has been associated with irritable bowel syndrome (IBS). However, the role of hydrogenotrophic microbes in overall microbiota composition and function remains largely unknown. This study aims to assess the distribution and stability of hydrogenotrophic functional groups in healthy adults (HAs) and IBS patients and their association with overall microbiota composition and IBS symptoms. A two-time-point study with 4 weeks in between was performed with 27 HAs and 55 IBS patients included. Our observations revealed that methanogens showed a bimodal distribution across samples. A high-level methanogen microbiota was consistently associated with higher alpha diversity, and its composition was significantly different from that of individuals with a low-level methanogen microbiota. In general, these associations were more pronounced in IBS patients than in HAs. The differences in the copy numbers of genes indicative of total bacteria and acetogens between HAs and IBS patients and their correlations with IBS symptom severity, anxiety, depression, and quality of life (QoL) were sampling time dependent. Hydrogenotrophic functional groups did not show negative abundance correlations with each other in HAs and IBS patients. These findings suggest that methanogen levels in the gut have a pronounced association with microbiota alpha diversity and composition, and the interactions between hydrogenotrophic functional groups are complex in gut ecosystems. IMPORTANCE Hydrogenotrophic microbes play an essential role in the disposal of hydrogen and the maintenance of the hydrogen balance in gut ecosystems. Their abundances vary between individuals and have been reported to be associated with human gut disorders such as irritable bowel disease. This study confirms that methanogen levels show a bimodal distribution. Moreover, a high-level methanogen microbiota was associated with higher alpha diversity, and its composition was different from that of individuals with a low-level methanogen microbiota. These associations are more pronounced in IBS patients than in healthy subjects. In addition, associations between hydrogenotrophic microbes and IBS symptom scores vary over time, which argues for the use of longitudinal study designs. Last but not least, this study suggests that the different hydrogenotrophic microbes coexist with each other and do not necessarily compete for hydrogen in the gut. The findings in this study highlight the impact of methanogens on overall microbiota composition and function.
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Microbioma Gastrointestinal, Síndrome do Intestino Irritável, Microbiota, Humanos, Adulto, Síndrome do Intestino Irritável/microbiologia, Qualidade de Vida, Estudos Longitudinais, Microbioma Gastrointestinal/genética, Fezes/microbiologia, HidrogênioRESUMO
Constipation can greatly impact the quality of life (QoL), which can be relieved by dietary fibres; however, preserving a higher fibre intake remains a challenge. We investigated the effects of a personalised dietary advice (PDA) on fibre intake and mild constipation complaints. A total number of twenty-five adults with mild constipation complaints were included in a 4-week observation period followed by a 4-week personalised intervention. The PDA provided high-fibre alternatives via a web tool. In weeks 1, 4 and 8, dietary intake, constipation complaints and QoL were assessed. Furthermore, participants collected a faecal sample at weeks 1, 4 and 8 to determine microbiota diversity and composition, and short-chain fatty acids (SCFA). Participants completed questions daily for 8 weeks regarding abdominal complaints, stool frequency and stool consistency. Fibre intake in week 8 was significantly higher compared to week 1 (Δ = 5·7 ± 6·7 g, P < 0·001) and week 4 (Δ = 5·2 ± 6·4 g, P < 0·001). Constipation severity and QoL significantly improved at week 8 compared to the observation period (P < 0·001). A higher fibre intake significantly reduced constipation severity (ß = -0·031 (-0·05; -0·01), P = 0·001) and the QoL (ß = -0·022 (-0·04; -0·01), P = 0·009). Stool consistency (P = 0·040) and abdominal pain (P = 0·030) improved significantly during the intervention period (P = 0·040), but stool frequency did not. Average microbial alpha diversity and composition and SCFA concentrations did not change over time, but indicated individual-specific dynamics. Several SCFAs were associated with constipation complaints. To conclude, a PDA effectively increased fibre intake and subsequently reduced constipation complaints, indicating that guided dietary adjustments are important and feasible in the treatment of mild constipation complaints.
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Constipação Intestinal, Qualidade de Vida, Adulto, Constipação Intestinal/prevenção & controle, Fibras na Dieta, Fezes, Educação em Saúde, HumanosRESUMO
BACKGROUND: Irritable bowel syndrome (IBS) is the most prevalent functional bowel disorder, but its pathophysiology is still unknown. Although a microbial signature associated with IBS severity has been suggested, its association with IBS severity still remains largely unknown. AIMS: This study aims to assess longitudinal dynamics of fecal microbiota and short-chain fatty acids (SCFAs) in different IBS severity groups and study the association with stool pattern, diet, depression, anxiety, and quality of life (QoL). METHODS: A longitudinal study was performed, including n = 91 IBS patients and n = 28 matched controls. All participants collected fecal samples for microbiota composition and SCFA analysis and completed validated questionnaires regarding IBS severity, stool pattern, depression, anxiety, and IBS-QoL at two timepoints with four weeks in-between. Diet was assessed at the first timepoint. RESULTS: Over time, 36% of IBS patients changed in severity group, and 53% changed in predominant stool pattern. The largest proportion of microbiota variation was explained by the individual (R2 = 70.07%). Microbiota alpha diversity and composition, and SCFAs did not differ between IBS severity groups, nor between IBS and controls. Relative abundances of Bifidobacterium, Terrisporobacter, and Turicibacter consistently differed between IBS and controls, but not between IBS severity groups. Large dynamics over time were observed in the association of microbiota composition with questionnaire data where IBS symptom severity was associated at T1 but not at T2. CONCLUSIONS: Fecal microbiota and SCFA signatures were not consistently associated with IBS severity over time, indicating the importance of repeated sampling in IBS research.
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Síndrome do Intestino Irritável, Microbiota, Humanos, Qualidade de Vida, Estudos Longitudinais, Fezes/química, Ácidos Graxos VoláteisRESUMO
OBJECTIVE: A high-fibre diet is associated with a lower risk for diseases. However, few adults meet the dietary fibre recommendation. Therefore, the effects and acceptance of an algorithm-generated personalised dietary advice (PDA) compared with general advice (GA) on fibre intake were investigated. DESIGN: A 6-week, single-blind randomised controlled trial with a 3-month follow-up. SETTING: PDA was based on habitual intake and provided fibre-rich alternatives using a website; GA contained brochures. Dietary intake was assessed at baseline, week 1, week 6 and 3-month follow-up. Both groups evaluated their advice at week 6. All participants had access to PDA from week 7 until 3-month follow-up. PARTICIPANTS: Two groups of healthy adults: PDA (n 34) and GA (n 47). For 3-month follow-up analysis, participants were re-divided into visitors (n 52) and non-visitors (n 26) of the PDA. RESULTS: At week 6, energy intake remained stable in both groups, but fibre intake per 1000 kcal increased non-significantly in both groups (PDA = Δ0·5 ± 2·8; GA = Δ0·8 ± 3·1, P = 0·128). Importantly, a significantly higher percentage of PDA participants adhered to the recommendation compared with week 1 (PDA = 21 % increase; GA = 4 % increase, P ≤ 0·001). PDA participants evaluated the advice significantly better compared with GA participants. At 3-month follow-up, fibre intake increased compared with baseline (visitors = Δ2·2 ± 2·6, P < 0·001; non-visitors = Δ1·5 ± 1·9, P = 0·001), but was insignificantly different between groups. Visitors had a decrease and non-visitors had an increase in energy intake (visitors =Δ - 132 ± 525; non-visitors = Δ109 ± 507, P = 0·055). CONCLUSIONS: The algorithm-generated PDA was well accepted and stimulated adherence to the recommendations more than GA, indicating to be a suitable and cost-efficient method for improving dietary fibre intake in healthy adults.
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Fibras na Dieta, Ingestão de Energia, Adulto, Aconselhamento, Educação em Saúde, Humanos, Método Simples-CegoRESUMO
In this study, the changes in microbial communities of lamb meat packaged in the air (plastic tray, PT) and in a vacuum pouch (VAC) were assessed by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) during the storage at 4°C. For the PT lamb, the total viable count (TVC) was 107 CFU/g on Day 5, and the dominated bacteria were Pseudomonas fragi, P. fluorescens, and Acinetobacter spp. For the VAC lamb, the TVC was 107 CFU/g on Day 9, and the dominated bacteria were lactic acid bacteria, including Carnobacterium divergens, C. maltaromaticum, and Lactococcus piscium. One strain of Pseudomonas spp. also appeared in VAC lamb. The relative abundance of Enterobacteriaceae in VAC lamb was higher than that PT lamb, indicating a more important role of Enterobacteriaceae in spoilage for VAC lamb than that of PT lamb. The microbial compositions changed faster in the lamb stored in a PT than that stored in a VAC, and microbial community compositions of the late storage period were largely different from those of the early storage period for both the conditions. The findings of this study may guide improve the lamb hygiene and prolong the shelf life of the lamb.
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Changes in the microbiota of lamb were investigated under vacuum packaging (VP) and under 20% CO2/80% N2 (LC), 60% CO2/40% N2 (MC), and 100% CO2 (HC) modified atmosphere packaging (MAP) during chilled storage. Viable counts were monitored, and the total microbial communities were assessed by high-throughput sequencing. The starting community had the highest microbial diversity, after which Lactococcus and Carnobacterium spp. outcompeted during the 28-day storage. The relative abundances of Brochothrix spp. in the LC atmosphere were much higher than those of the other groups on days 7 and 28. The bacterial inhibiting effect of the MAP environments on microbial growth was positively correlated with the CO2 concentration. The HC atmosphere inhibited microbial growth and delayed changes in the microbial community composition, extending the lamb's shelf life by approximately 7days compared with the VP atmosphere. Lamb packaged in the VP atmosphere had a more desirable colour but a higher weight loss than lamb packaged in the MAP atmospheres.
