Pub Date : 2024-09-05DOI: 10.3390/microorganisms12091838
Lucy Hill, Stéphane Guyot, Lucie Bertheau, Hazel Davey
Experiments exposing Saccharomyces cerevisiae to glucose limitation (calorie restriction) are widely used to determine impacts on cell health as a model for aging. Using growth on plates and in liquid culture, we demonstrated that calorie restriction reduces fitness in subsequent nutrient-limited environments. Yeast grown in a calorie-restricted environment took longer to emerge from the lag phase, had an extended doubling time and had a lower percentage of culturability. Cells grown under moderate calorie restriction were able to withstand a gradual heat stress in a similar manner to cells grown without calorie restriction but fared less well with a sudden heat shock. Yeast grown under extreme calorie restriction were less fit when exposed to gradual heating or heat shock. Using RNAseq analysis, we provide novel insight into the mechanisms underlying this response, showing that in the absence of calorie restriction, genes whose products are involved in energy metabolism (glycolysis/gluconeogenesis and the citrate cycle) are predominantly overexpressed when yeasts were exposed to gradual heating, whereas this was not the case when they were exposed to shock. We show that both the culture history and the current environment must be considered when assaying physiological responses, and this has wider implications when developing strategies for the propagation, preservation or destruction of microbial cells.
{"title":"Calorie Restriction Decreases Competitive Fitness in Saccharomyces cerevisiae Following Heat Stress","authors":"Lucy Hill, Stéphane Guyot, Lucie Bertheau, Hazel Davey","doi":"10.3390/microorganisms12091838","DOIUrl":"https://doi.org/10.3390/microorganisms12091838","url":null,"abstract":"Experiments exposing Saccharomyces cerevisiae to glucose limitation (calorie restriction) are widely used to determine impacts on cell health as a model for aging. Using growth on plates and in liquid culture, we demonstrated that calorie restriction reduces fitness in subsequent nutrient-limited environments. Yeast grown in a calorie-restricted environment took longer to emerge from the lag phase, had an extended doubling time and had a lower percentage of culturability. Cells grown under moderate calorie restriction were able to withstand a gradual heat stress in a similar manner to cells grown without calorie restriction but fared less well with a sudden heat shock. Yeast grown under extreme calorie restriction were less fit when exposed to gradual heating or heat shock. Using RNAseq analysis, we provide novel insight into the mechanisms underlying this response, showing that in the absence of calorie restriction, genes whose products are involved in energy metabolism (glycolysis/gluconeogenesis and the citrate cycle) are predominantly overexpressed when yeasts were exposed to gradual heating, whereas this was not the case when they were exposed to shock. We show that both the culture history and the current environment must be considered when assaying physiological responses, and this has wider implications when developing strategies for the propagation, preservation or destruction of microbial cells.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-04DOI: 10.3390/microorganisms12091830
Robert Whitfield, Craig D. Tipton, Niccole Diaz, Jacob Ancira, Kyle S. Landry
The incidence of breast implant illness (BII) and BII-related explant procedures has not decreased with current surgical and treatment techniques. It is speculated the main underlying cause of BII complications is the result of chronic, sub-clinical infections residing on and around the implant. The infection, and subsequent biofilm, produce antagonistic compounds that drive chronic inflammation and immune responses. In this study, the microbial communities in over 600 consecutive samples of infected explant capsules and tissues were identified via next-generation sequencing to identify any commonality between samples. The majority of the bacteria identified were Gram-positive, with Cutibacterium acnes and Staphylococcus epidermidis being the dominant organisms. No correlation between sample richness and implant filling was found. However, there was a significant correlation between sample richness and patient age. Due to the complex nature, breast augmentation failures may be better addressed from a holistic approach than one of limited scope.
{"title":"Clinical Evaluation of Microbial Communities and Associated Biofilms with Breast Augmentation Failure","authors":"Robert Whitfield, Craig D. Tipton, Niccole Diaz, Jacob Ancira, Kyle S. Landry","doi":"10.3390/microorganisms12091830","DOIUrl":"https://doi.org/10.3390/microorganisms12091830","url":null,"abstract":"The incidence of breast implant illness (BII) and BII-related explant procedures has not decreased with current surgical and treatment techniques. It is speculated the main underlying cause of BII complications is the result of chronic, sub-clinical infections residing on and around the implant. The infection, and subsequent biofilm, produce antagonistic compounds that drive chronic inflammation and immune responses. In this study, the microbial communities in over 600 consecutive samples of infected explant capsules and tissues were identified via next-generation sequencing to identify any commonality between samples. The majority of the bacteria identified were Gram-positive, with Cutibacterium acnes and Staphylococcus epidermidis being the dominant organisms. No correlation between sample richness and implant filling was found. However, there was a significant correlation between sample richness and patient age. Due to the complex nature, breast augmentation failures may be better addressed from a holistic approach than one of limited scope.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142226053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-04DOI: 10.3390/microorganisms12091827
Lei Liu, Chongzheng Wen, Xiaoying Cai, Weimin Gong
Nutrients are absorbed by special transport proteins on the cell membrane; however, there is less information regarding transporters across the mycobacterial outer envelope, which comprises dense and intricate structures. In this study, we focus on the model organism Mycolicibacterium smegmatis, which has a cell envelope similar to that of Mycobacterium tuberculosis, as well as on the TiME protein secretion tube across the mycobacterial outer envelope. We present transcriptome results and analyze the protein compositions of a mycobacterial surface envelope, determining that more transporters and porins are induced to complement the deletion of the time gene in Mycolicibacterium smegmatis. The TiME protein is essential for nutrient utilization, as demonstrated in the uptake experiments and growth on various monosaccharides or with amino acids as the sole carbon source. Its deletion caused bacteria to be more sensitive to anti-TB drugs and to show a growth defect at an acid pH level, indicating that TiME promotes the survival of M. smegmatis in antibiotic-containing and acidic environments. These results suggest that TiME tubes facilitate bi-directional processes for both protein secretion and nutrient uptake across the mycobacterial outer envelope.
营养物质是通过细胞膜上的特殊转运蛋白吸收的；然而，有关分枝杆菌外包膜上转运体的信息却较少，因为分枝杆菌的外包膜由密集而复杂的结构组成。在本研究中，我们重点研究了具有与结核分枝杆菌相似细胞包膜的模式生物烟曲霉，以及跨分枝杆菌外包膜的 TiME 蛋白分泌管。我们展示了转录组结果，并分析了分枝杆菌表面包膜的蛋白质组成，确定在烟曲霉中，诱导了更多的转运体和孔蛋白来补充时间基因的缺失。正如吸收实验和在各种单糖或以氨基酸为唯一碳源的条件下生长所证明的那样，TiME 蛋白对营养物质的利用至关重要。它的缺失会导致细菌对抗结核药物更加敏感，并在酸性 pH 水平下表现出生长缺陷，这表明 TiME 促进了烟曲霉菌在含抗生素和酸性环境中的生存。这些结果表明，TiME管促进了分枝杆菌外包膜蛋白质分泌和营养吸收的双向过程。
{"title":"A Novel Bi-Directional Channel for Nutrient Uptake across Mycobacterial Outer Envelope","authors":"Lei Liu, Chongzheng Wen, Xiaoying Cai, Weimin Gong","doi":"10.3390/microorganisms12091827","DOIUrl":"https://doi.org/10.3390/microorganisms12091827","url":null,"abstract":"Nutrients are absorbed by special transport proteins on the cell membrane; however, there is less information regarding transporters across the mycobacterial outer envelope, which comprises dense and intricate structures. In this study, we focus on the model organism Mycolicibacterium smegmatis, which has a cell envelope similar to that of Mycobacterium tuberculosis, as well as on the TiME protein secretion tube across the mycobacterial outer envelope. We present transcriptome results and analyze the protein compositions of a mycobacterial surface envelope, determining that more transporters and porins are induced to complement the deletion of the time gene in Mycolicibacterium smegmatis. The TiME protein is essential for nutrient utilization, as demonstrated in the uptake experiments and growth on various monosaccharides or with amino acids as the sole carbon source. Its deletion caused bacteria to be more sensitive to anti-TB drugs and to show a growth defect at an acid pH level, indicating that TiME promotes the survival of M. smegmatis in antibiotic-containing and acidic environments. These results suggest that TiME tubes facilitate bi-directional processes for both protein secretion and nutrient uptake across the mycobacterial outer envelope.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203472","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
As one of the most important fertilizers in agriculture, the fate of urea-derived nitrogen (urea-N) in agricultural ecosystems has been well documented. However, little is known about the function of urea-derived carbon (urea-C) in soil ecosystems, especially which soil microorganisms benefit most from the supply of urea-C and whether the utilization of urea-C by the rhizosphere and bulk soil microorganisms is affected by irrigation regimes. To address this, a soil pot experiment was conducted using 13C-labeled urea to investigate changes in the composition of the rhizosphere and bulk soil microbial communities and differences in the incorporation of urea-derived C into the rhizosphere and bulk soil phospholipid fatty acids (PLFA) pool under flooded irrigation (FI) and water-saving irrigation (CI). Our results suggest that the size and structure of the rhizosphere and bulk soil microbial communities were strongly influenced by the irrigation regime. The CI treatment significantly increased the total amount of PLFA in both the rhizosphere and bulk soil compared to the FI treatment, but it only significantly affected the abundance of Gram-positive bacteria (G+) in the bulk soil. In contrast, shifts in the microbial community structure induced by irrigation regimes were more pronounced in the rhizosphere soil than in the bulk soil. Compared to the FI treatment, the CI treatment significantly increased the relative abundances of the G+ and Actinobacteria in the rhizosphere soil (p < 0.05). According to the PLFA-SIP, most of the labeled urea-derived C was incorporated into 16:1ω7c, 16:0 and 18:1ω7c under both treatments. Despite these general trends, the pattern of 13C incorporation into the PLFA pool differed between the treatments. The factor loadings of individual PLFAs suggested that 18:1ω7c, 16:1ω7c and 16:1ω5c were relatively enriched in urea-C in the bulk soil, while 17:1ω8c, i16:0 and 16:0 were relatively enriched in urea-C in the rhizosphere soil under different irrigation regimes. The loadings also confirmed that 10-me16:0, cy17:0 and cy19:0 were relatively enriched in urea-C under the CI treatment, whereas 14:0, a15:0 and 15:0 were relatively enriched in urea-C under the FI treatment. These results are helpful not only in revealing the interception mechanism of urea-C in soil but also in understanding the functions of key microbes in element cycles.
作为农业中最重要的肥料之一，尿素衍生氮（urea-N）在农业生态系统中的去向已被详细记录。然而，人们对尿素衍生碳（urea-C）在土壤生态系统中的功能却知之甚少，尤其是哪些土壤微生物从尿素衍生碳的供应中获益最多，以及根瘤菌层和大体积土壤微生物对尿素衍生碳的利用是否会受到灌溉制度的影响。为此，我们使用 13C 标记的尿素进行了土壤盆栽实验，研究在大水漫灌（FI）和节水灌溉（CI）条件下，根圈和大体积土壤微生物群落组成的变化，以及尿素衍生的 C 被根圈和大体积土壤磷脂脂肪酸（PLFA）池吸收的差异。我们的研究结果表明，根圈和大体积土壤微生物群落的大小和结构受灌溉制度的影响很大。与 FI 处理相比，CI 处理明显增加了根圈和大体积土壤中 PLFA 的总量，但只对大体积土壤中革兰氏阳性菌（G+）的丰度有明显影响。相比之下，灌溉制度引起的微生物群落结构变化在根圈土壤中比在块状土壤中更为明显。与 FI 处理相比，CI 处理显著增加了根圈土壤中 G+ 和放线菌的相对丰度（p < 0.05）。根据 PLFA-SIP 的结果，在两种处理中，大部分标记的尿素衍生 C 被结合到 16:1ω7c、16:0 和 18:1ω7c 中。尽管存在这些总体趋势，但不同处理下 13C 在 PLFA 池中的掺入模式有所不同。单个 PLFA 的因子载荷表明，在不同灌溉制度下，18:1ω7c、16:1ω7c 和 16:1ω5c 相对富含块根土壤中的尿素-C，而 17:1ω8c、i16:0 和 16:0 相对富含根瘤土壤中的尿素-C。载荷还证实，在 CI 处理下，10-me16:0、cy17:0 和 cy19:0 的尿素-C 相对富集，而在 FI 处理下，14:0、a15:0 和 15:0 的尿素-C 相对富集。这些结果不仅有助于揭示土壤中尿素-C的截留机制，而且有助于了解关键微生物在元素循环中的功能。
{"title":"Water Management-Mediated Changes in the Rhizosphere and Bulk Soil Microbial Communities Alter Their Utilization of Urea-Derived Carbon","authors":"Peng Chen, Yawei Li, Yuping Lv, Junzeng Xu, Zhongxue Zhang, Xiaoyin Liu, Yajun Luan, Qi Wei, Ennan Zheng, Kechun Wang","doi":"10.3390/microorganisms12091829","DOIUrl":"https://doi.org/10.3390/microorganisms12091829","url":null,"abstract":"As one of the most important fertilizers in agriculture, the fate of urea-derived nitrogen (urea-N) in agricultural ecosystems has been well documented. However, little is known about the function of urea-derived carbon (urea-C) in soil ecosystems, especially which soil microorganisms benefit most from the supply of urea-C and whether the utilization of urea-C by the rhizosphere and bulk soil microorganisms is affected by irrigation regimes. To address this, a soil pot experiment was conducted using 13C-labeled urea to investigate changes in the composition of the rhizosphere and bulk soil microbial communities and differences in the incorporation of urea-derived C into the rhizosphere and bulk soil phospholipid fatty acids (PLFA) pool under flooded irrigation (FI) and water-saving irrigation (CI). Our results suggest that the size and structure of the rhizosphere and bulk soil microbial communities were strongly influenced by the irrigation regime. The CI treatment significantly increased the total amount of PLFA in both the rhizosphere and bulk soil compared to the FI treatment, but it only significantly affected the abundance of Gram-positive bacteria (G+) in the bulk soil. In contrast, shifts in the microbial community structure induced by irrigation regimes were more pronounced in the rhizosphere soil than in the bulk soil. Compared to the FI treatment, the CI treatment significantly increased the relative abundances of the G+ and Actinobacteria in the rhizosphere soil (p < 0.05). According to the PLFA-SIP, most of the labeled urea-derived C was incorporated into 16:1ω7c, 16:0 and 18:1ω7c under both treatments. Despite these general trends, the pattern of 13C incorporation into the PLFA pool differed between the treatments. The factor loadings of individual PLFAs suggested that 18:1ω7c, 16:1ω7c and 16:1ω5c were relatively enriched in urea-C in the bulk soil, while 17:1ω8c, i16:0 and 16:0 were relatively enriched in urea-C in the rhizosphere soil under different irrigation regimes. The loadings also confirmed that 10-me16:0, cy17:0 and cy19:0 were relatively enriched in urea-C under the CI treatment, whereas 14:0, a15:0 and 15:0 were relatively enriched in urea-C under the FI treatment. These results are helpful not only in revealing the interception mechanism of urea-C in soil but also in understanding the functions of key microbes in element cycles.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203503","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-04DOI: 10.3390/microorganisms12091831
Harsh Shah, Mithil Trivedi, Tejas Gurjar, Dipak Kumar Sahoo, Albert E. Jergens, Virendra Kumar Yadav, Ashish Patel, Parth Pandya
The changing notion of “companion animals” and their increasing global status as family members underscores the dynamic interaction between gut microbiota and host health. This review provides a comprehensive understanding of the intricate microbial ecology within companion animals required to maintain overall health and prevent disease. Exploration of specific diseases and syndromes linked to gut microbiome alterations (dysbiosis), such as inflammatory bowel disease, obesity, and neurological conditions like epilepsy, are highlighted. In addition, this review provides an analysis of the various factors that impact the abundance of the gut microbiome like age, breed, habitual diet, and microbe-targeted interventions, such as probiotics. Detection methods including PCR-based algorithms, fluorescence in situ hybridisation, and 16S rRNA gene sequencing are reviewed, along with their limitations and the need for future advancements. Prospects for longitudinal investigations, functional dynamics exploration, and accurate identification of microbial signatures associated with specific health problems offer promising directions for future research. In summary, it is an attempt to provide a deeper insight into the orchestration of multiple microbial species shaping the health of companion animals and possible species-specific differences.
{"title":"Decoding the Gut Microbiome in Companion Animals: Impacts and Innovations","authors":"Harsh Shah, Mithil Trivedi, Tejas Gurjar, Dipak Kumar Sahoo, Albert E. Jergens, Virendra Kumar Yadav, Ashish Patel, Parth Pandya","doi":"10.3390/microorganisms12091831","DOIUrl":"https://doi.org/10.3390/microorganisms12091831","url":null,"abstract":"The changing notion of “companion animals” and their increasing global status as family members underscores the dynamic interaction between gut microbiota and host health. This review provides a comprehensive understanding of the intricate microbial ecology within companion animals required to maintain overall health and prevent disease. Exploration of specific diseases and syndromes linked to gut microbiome alterations (dysbiosis), such as inflammatory bowel disease, obesity, and neurological conditions like epilepsy, are highlighted. In addition, this review provides an analysis of the various factors that impact the abundance of the gut microbiome like age, breed, habitual diet, and microbe-targeted interventions, such as probiotics. Detection methods including PCR-based algorithms, fluorescence in situ hybridisation, and 16S rRNA gene sequencing are reviewed, along with their limitations and the need for future advancements. Prospects for longitudinal investigations, functional dynamics exploration, and accurate identification of microbial signatures associated with specific health problems offer promising directions for future research. In summary, it is an attempt to provide a deeper insight into the orchestration of multiple microbial species shaping the health of companion animals and possible species-specific differences.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203504","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-04DOI: 10.3390/microorganisms12091828
Sara Bertorello, Francesco Cei, Dorian Fink, Elena Niccolai, Amedeo Amedei
Investigating the complex interactions between microbiota and immunity is crucial for a fruitful understanding progress of human health and disease. This review assesses animal models, next-generation in vitro models, and in silico approaches that are used to decipher the microbiome-immunity axis, evaluating their strengths and limitations. While animal models provide a comprehensive biological context, they also raise ethical and practical concerns. Conversely, modern in vitro models reduce animal involvement but require specific costs and materials. When considering the environmental impact of these models, in silico approaches emerge as promising for resource reduction, but they require robust experimental validation and ongoing refinement. Their potential is significant, paving the way for a more sustainable and ethical future in microbiome-immunity research.
{"title":"The Future Exploring of Gut Microbiome-Immunity Interactions: From In Vivo/Vitro Models to In Silico Innovations","authors":"Sara Bertorello, Francesco Cei, Dorian Fink, Elena Niccolai, Amedeo Amedei","doi":"10.3390/microorganisms12091828","DOIUrl":"https://doi.org/10.3390/microorganisms12091828","url":null,"abstract":"Investigating the complex interactions between microbiota and immunity is crucial for a fruitful understanding progress of human health and disease. This review assesses animal models, next-generation in vitro models, and in silico approaches that are used to decipher the microbiome-immunity axis, evaluating their strengths and limitations. While animal models provide a comprehensive biological context, they also raise ethical and practical concerns. Conversely, modern in vitro models reduce animal involvement but require specific costs and materials. When considering the environmental impact of these models, in silico approaches emerge as promising for resource reduction, but they require robust experimental validation and ongoing refinement. Their potential is significant, paving the way for a more sustainable and ethical future in microbiome-immunity research.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203501","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Due to its low dietary impact and bioactive compounds, such as polyphenols and flavonoids, white kidney bean extract is an attractive raw material for fermented drinks. It can be utilized either on its own or blended with cow’s milk, offering a promising solution to help meet dairy product demand during mid-season shortages. Therefore, this study aimed to explore the physicochemical characteristics, sensory properties, and microbiological profile of fermented milk-like drinks made from white kidney bean extract, cow’s milk and their blends during 28 days of storage at 4 °C. Three blends of fermented milk-like drinks (FMLDs) were prepared from different ratios of cow’s milk (CM) and kidney bean extract (BE): FMLD1 (CM 30%:BE 70%); FMLD2 (CM 50%:BE 50%), FMLD3 (CM 70%:BE 30%), along with plain fermented kidney been extract (FBE; CM 0%:BE 100%), and plain fermented cow’s milk (FCM; CM 100%:BE 0%). The mixtures were pasteurized at 92 °C for 25 min and fermented with a probiotic-type starter culture (S. thermophilus, B. bifidum, L. acidophilus) at 43 °C. FBE exhibited the lowest levels of carbohydrates (2.14%), fat (0.11%), and protein (1.45%) compared to fermented cow’s milk and blends. The FBE and the fermented blends with a higher ratio of bean extract had lower viscosity and lactic acid contents, greener hue, more pronounced aftertaste and off-flavors, and received lower overall acceptability scores. Although the FCM had higher counts of S. thermophilus and L. acidophilus, the FBE displayed significantly higher counts of B. bifidum. This study demonstrated the potential of using white kidney bean extract and its blends with cow’s milk to create unique fermented products with a lower dietary impact, highlighting the importance of further optimizing the formulations to enhance sensory qualities and reduce the beany off-flavors in the products with added kidney bean extract.
{"title":"Physicochemical, Sensory, and Microbiological Analysis of Fermented Drinks Made from White Kidney Bean Extract and Cow’s Milk Blends during Refrigerated Storage","authors":"Ibaratkan Kurbanova, Lina Lauciene, Kristina Kondrotiene, Gintare Zakariene, Vitalijs Radenkovs, Sandra Kiselioviene, Alvija Salaseviciene, Agne Vasiliauskaite, Mindaugas Malakauskas, Mukarama Musulmanova, Loreta Serniene","doi":"10.3390/microorganisms12091832","DOIUrl":"https://doi.org/10.3390/microorganisms12091832","url":null,"abstract":"Due to its low dietary impact and bioactive compounds, such as polyphenols and flavonoids, white kidney bean extract is an attractive raw material for fermented drinks. It can be utilized either on its own or blended with cow’s milk, offering a promising solution to help meet dairy product demand during mid-season shortages. Therefore, this study aimed to explore the physicochemical characteristics, sensory properties, and microbiological profile of fermented milk-like drinks made from white kidney bean extract, cow’s milk and their blends during 28 days of storage at 4 °C. Three blends of fermented milk-like drinks (FMLDs) were prepared from different ratios of cow’s milk (CM) and kidney bean extract (BE): FMLD1 (CM 30%:BE 70%); FMLD2 (CM 50%:BE 50%), FMLD3 (CM 70%:BE 30%), along with plain fermented kidney been extract (FBE; CM 0%:BE 100%), and plain fermented cow’s milk (FCM; CM 100%:BE 0%). The mixtures were pasteurized at 92 °C for 25 min and fermented with a probiotic-type starter culture (S. thermophilus, B. bifidum, L. acidophilus) at 43 °C. FBE exhibited the lowest levels of carbohydrates (2.14%), fat (0.11%), and protein (1.45%) compared to fermented cow’s milk and blends. The FBE and the fermented blends with a higher ratio of bean extract had lower viscosity and lactic acid contents, greener hue, more pronounced aftertaste and off-flavors, and received lower overall acceptability scores. Although the FCM had higher counts of S. thermophilus and L. acidophilus, the FBE displayed significantly higher counts of B. bifidum. This study demonstrated the potential of using white kidney bean extract and its blends with cow’s milk to create unique fermented products with a lower dietary impact, highlighting the importance of further optimizing the formulations to enhance sensory qualities and reduce the beany off-flavors in the products with added kidney bean extract.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-03DOI: 10.3390/microorganisms12091821
Elena Y. Enioutina, R. James Keddington, Kurtis G. Hauck, Amarina Chavez, Jeffrey J. Clifford, Thy (April) Cao, Bryce Smith, Kathleen M. Job, Alfred Balch
Persistent malodor affects many people worldwide and is usually associated with poor dental hygiene. This pilot trial aimed to determine whether proper dental hygiene (DH) and a probiotic dietary supplement support oral health in volunteers with persistent malodor. Volunteers (n = 35) were randomly assigned to the probiotic or placebo cohort. The probiotic cohort (n = 20) brushed and flossed their teeth twice daily and used probiotics for 30 days; the placebo cohort (n = 15) followed the same hygiene practices and used the placebo. The intervention phase was followed by a 30-day follow-up period. Measured outcomes were malodor and tongue-coating scores, probiotic DNA levels, salivary cytokines, and salivary pH. DH and probiotics significantly decreased malodor (~50% during intervention) and tongue coating scores (~45% during intervention). These changes remained through the course of the trial. The probiotic DNA levels increased in the probiotic cohort and dropped in the placebo cohort after the intervention started. The malodor moderately correlated with the tongue coating P. acidilactici level. The addition of probiotics increased IL-10 levels during the intervention and decreased IL-8, TNF-α, and IL-6 by the end of the study. People with malodor may benefit from using DH and probiotics. Additional trials are needed to definitively establish the benefits of probiotic dietary supplements.
{"title":"Results of a Pilot Trial Assessing the Effects of Proper Oral Hygiene and a Probiotic Dietary Supplement on Oral Health in Volunteers with Oral Malodor","authors":"Elena Y. Enioutina, R. James Keddington, Kurtis G. Hauck, Amarina Chavez, Jeffrey J. Clifford, Thy (April) Cao, Bryce Smith, Kathleen M. Job, Alfred Balch","doi":"10.3390/microorganisms12091821","DOIUrl":"https://doi.org/10.3390/microorganisms12091821","url":null,"abstract":"Persistent malodor affects many people worldwide and is usually associated with poor dental hygiene. This pilot trial aimed to determine whether proper dental hygiene (DH) and a probiotic dietary supplement support oral health in volunteers with persistent malodor. Volunteers (n = 35) were randomly assigned to the probiotic or placebo cohort. The probiotic cohort (n = 20) brushed and flossed their teeth twice daily and used probiotics for 30 days; the placebo cohort (n = 15) followed the same hygiene practices and used the placebo. The intervention phase was followed by a 30-day follow-up period. Measured outcomes were malodor and tongue-coating scores, probiotic DNA levels, salivary cytokines, and salivary pH. DH and probiotics significantly decreased malodor (~50% during intervention) and tongue coating scores (~45% during intervention). These changes remained through the course of the trial. The probiotic DNA levels increased in the probiotic cohort and dropped in the placebo cohort after the intervention started. The malodor moderately correlated with the tongue coating P. acidilactici level. The addition of probiotics increased IL-10 levels during the intervention and decreased IL-8, TNF-α, and IL-6 by the end of the study. People with malodor may benefit from using DH and probiotics. Additional trials are needed to definitively establish the benefits of probiotic dietary supplements.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mine-tailing dumps are one of the leading sources of environmental degradation, often with public health and ecological consequences. Due to the complex ecosystems generated, they are ideal sites for exploring the bacterial diversity of specially adapted microorganisms. We investigated the concentrations of trace metals in solid copper (Cu) mine tailings from the Ovejería Tailings Dam of the National Copper Corporation of Chile and used high-throughput sequencing techniques to determine the microbial community diversity of the tailings using 16S rRNA gene-based amplicon sequence analysis. The concentrations of the detected metals were highest in the following order: iron (Fe) > Cu > manganese (Mn) > molybdenum (Mo) > lead (Pb) > chromium (Cr) > cadmium (Cd). Furthermore, 16S rRNA gene-based sequence analysis identified 12 phyla, 18 classes, 43 orders, 82 families, and 154 genera at the three sampling points. The phylum Proteobacteria was the most dominant, followed by Chlamydiota, Bacteroidetes, Actinobacteria, and Firmicutes. Genera, such as Bradyrhizobium, Aquabacterium, Paracoccus, Caulobacter, Azospira, and Neochlamydia, showed high relative abundance. These genera are known to possess adaptation mechanisms in high concentrations of metals, such as Cd, Cu, and Pb, along with nitrogen-fixation capacity. In addition to their tolerance to various metals, some of these genera may represent pathogens of amoeba or humans, which contributes to the complexity and resilience of bacterial communities in the studied Cu mining tailings. This study highlights the unique microbial diversity in the Ovejería Tailings Dam, including the discovery of the genus Neochlamydia, reported for the first time for heavy metal resistance. This underscores the importance of characterizing mining sites, particularly in Chile, to uncover novel bacterial mechanisms for potential biotechnological applications.
{"title":"Profile of Bacterial Communities in Copper Mine Tailings Revealed through High-Throughput Sequencing","authors":"Joseline Jiménez-Venegas, Leonardo Zamora-Leiva, Luciano Univaso, Jorge Soto, Yasna Tapia, Manuel Paneque","doi":"10.3390/microorganisms12091820","DOIUrl":"https://doi.org/10.3390/microorganisms12091820","url":null,"abstract":"Mine-tailing dumps are one of the leading sources of environmental degradation, often with public health and ecological consequences. Due to the complex ecosystems generated, they are ideal sites for exploring the bacterial diversity of specially adapted microorganisms. We investigated the concentrations of trace metals in solid copper (Cu) mine tailings from the Ovejería Tailings Dam of the National Copper Corporation of Chile and used high-throughput sequencing techniques to determine the microbial community diversity of the tailings using 16S rRNA gene-based amplicon sequence analysis. The concentrations of the detected metals were highest in the following order: iron (Fe) > Cu > manganese (Mn) > molybdenum (Mo) > lead (Pb) > chromium (Cr) > cadmium (Cd). Furthermore, 16S rRNA gene-based sequence analysis identified 12 phyla, 18 classes, 43 orders, 82 families, and 154 genera at the three sampling points. The phylum Proteobacteria was the most dominant, followed by Chlamydiota, Bacteroidetes, Actinobacteria, and Firmicutes. Genera, such as Bradyrhizobium, Aquabacterium, Paracoccus, Caulobacter, Azospira, and Neochlamydia, showed high relative abundance. These genera are known to possess adaptation mechanisms in high concentrations of metals, such as Cd, Cu, and Pb, along with nitrogen-fixation capacity. In addition to their tolerance to various metals, some of these genera may represent pathogens of amoeba or humans, which contributes to the complexity and resilience of bacterial communities in the studied Cu mining tailings. This study highlights the unique microbial diversity in the Ovejería Tailings Dam, including the discovery of the genus Neochlamydia, reported for the first time for heavy metal resistance. This underscores the importance of characterizing mining sites, particularly in Chile, to uncover novel bacterial mechanisms for potential biotechnological applications.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-03DOI: 10.3390/microorganisms12091822
Manon Denux, Maickel Armenteros, Laura Weber, Carolyn A. Miller, Kinga Sántha, Amy Apprill
Globally, coral reef ecosystems are undergoing significant change related to climate change and anthropogenic activities. Yet, the Cuban archipelago of Jardines de la Reina (JR) has experienced fewer stressors due to its geographical remoteness and high level of conservation. This study examines the surface and benthic reef water microbial communities associated with 32 reef sites along the JR archipelago and explores the relationship between the community composition of reef microorganisms examined using bacterial and archaeal small subunit ribosomal RNA gene (16S rRNA gene) sequencing compared to geographic, conservation/protection level, environmental, physicochemical, and reef benthic and pelagic community features. Reef nutrient concentrations were low and microbial communities dominated by picocyanobacteria and SAR11 and SAR86 clade bacteria, characteristic of an oligotrophic system. Reef water microbial community alpha and beta diversity both varied throughout the archipelago and were strongly related to geography. Three sites in the western archipelago showed unique microbial communities, which may be related to the hydrogeography and influences of the channels linking the Ana Maria gulf with the Caribbean Sea. Overall, this work provides the first extensive description of the reef microbial ecology of the Caribbean’s ‘Crown Jewel’ reef system and a framework to evaluate the influence of ongoing stressors on the reef microorganisms.
在全球范围内，珊瑚礁生态系统正经历着与气候变化和人为活动有关的重大变化。然而，古巴的 Jardines de la Reina（JR）群岛由于地理位置偏远和保护水平较高，受到的压力较小。本研究考察了 JR 群岛沿岸 32 个珊瑚礁地点的表层和底层珊瑚礁水微生物群落，并利用细菌和古细 胞小亚基核糖体 RNA 基因（16S rRNA 基因）测序法，探讨了珊瑚礁微生物群落组成与地理、保护/防护等级、环境、物理化学以及珊瑚礁底层和水层群落特征之间的关系。礁石营养浓度低，微生物群落以微囊藻类、SAR11 和 SAR86 支系细菌为主，是寡营养系统的特征。整个群岛的礁水微生物群落α和β多样性各不相同，并且与地理环境密切相关。群岛西部的三个地点显示出独特的微生物群落，这可能与水文地质和连接安娜玛丽亚海湾与加勒比海的通道的影响有关。总之，这项研究首次对加勒比海 "皇冠上的明珠 "珊瑚礁系统的珊瑚礁微生物生态进行了广泛的描述，并为评估当前压力因素对珊瑚礁微生物的影响提供了一个框架。
{"title":"Coral Reef Water Microbial Communities of Jardines de la Reina, Cuba","authors":"Manon Denux, Maickel Armenteros, Laura Weber, Carolyn A. Miller, Kinga Sántha, Amy Apprill","doi":"10.3390/microorganisms12091822","DOIUrl":"https://doi.org/10.3390/microorganisms12091822","url":null,"abstract":"Globally, coral reef ecosystems are undergoing significant change related to climate change and anthropogenic activities. Yet, the Cuban archipelago of Jardines de la Reina (JR) has experienced fewer stressors due to its geographical remoteness and high level of conservation. This study examines the surface and benthic reef water microbial communities associated with 32 reef sites along the JR archipelago and explores the relationship between the community composition of reef microorganisms examined using bacterial and archaeal small subunit ribosomal RNA gene (16S rRNA gene) sequencing compared to geographic, conservation/protection level, environmental, physicochemical, and reef benthic and pelagic community features. Reef nutrient concentrations were low and microbial communities dominated by picocyanobacteria and SAR11 and SAR86 clade bacteria, characteristic of an oligotrophic system. Reef water microbial community alpha and beta diversity both varied throughout the archipelago and were strongly related to geography. Three sites in the western archipelago showed unique microbial communities, which may be related to the hydrogeography and influences of the channels linking the Ana Maria gulf with the Caribbean Sea. Overall, this work provides the first extensive description of the reef microbial ecology of the Caribbean’s ‘Crown Jewel’ reef system and a framework to evaluate the influence of ongoing stressors on the reef microorganisms.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203507","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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