Jeonghyun Kim, Kotone Niioka, Eijiro Maeda, Takeo Matsumoto
In this study, we developed a hydrostatic pressurizing chamber capable of applying hydrostatic pressure to osteocytic spheroids derived from mouse osteoblastic MC3T3-E1 cells. Our results demonstrate that a 4-h exposure to 200 kPa of hydrostatic pressure did not alter the apparent morphology of the spheroids. However, gene expression analysis revealed a significant up-regulation of Sost, a marker of late-stage osteocyte differentiation.
{"title":"Application of hydrostatic pressure up-regulates Sost gene expression in osteocytic spheroids.","authors":"Jeonghyun Kim, Kotone Niioka, Eijiro Maeda, Takeo Matsumoto","doi":"10.1093/bbb/zbae165","DOIUrl":"10.1093/bbb/zbae165","url":null,"abstract":"<p><p>In this study, we developed a hydrostatic pressurizing chamber capable of applying hydrostatic pressure to osteocytic spheroids derived from mouse osteoblastic MC3T3-E1 cells. Our results demonstrate that a 4-h exposure to 200 kPa of hydrostatic pressure did not alter the apparent morphology of the spheroids. However, gene expression analysis revealed a significant up-regulation of Sost, a marker of late-stage osteocyte differentiation.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":"263-267"},"PeriodicalIF":1.4,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142667078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The results of research on food functionality in Japan have been passed on to society in the form of Foods for Specified Health Uses and Foods with Functional Claims. However, it is also true that there are people who do not experience any health benefits even when they consume these foods. To clarify the factors that cause such individual differences in the health benefits of food, research into the following points is important: (1) Elucidation of the molecular mechanisms behind why food factors exert their functionality. (2) Research into the functional interactions between food factors that exert their functionality in multi-component systems. (3) Research into the functionality of food factors that have not been the subject of research until now. We will introduce the results of our research in these areas. We will also discuss our expectations for the application of food functionality research to pharmaceutical development as an extension of this research.
{"title":"Future outlook for food function research.","authors":"Hirofumi Tachibana","doi":"10.1093/bbb/zbae137","DOIUrl":"10.1093/bbb/zbae137","url":null,"abstract":"<p><p>The results of research on food functionality in Japan have been passed on to society in the form of Foods for Specified Health Uses and Foods with Functional Claims. However, it is also true that there are people who do not experience any health benefits even when they consume these foods. To clarify the factors that cause such individual differences in the health benefits of food, research into the following points is important: (1) Elucidation of the molecular mechanisms behind why food factors exert their functionality. (2) Research into the functional interactions between food factors that exert their functionality in multi-component systems. (3) Research into the functionality of food factors that have not been the subject of research until now. We will introduce the results of our research in these areas. We will also discuss our expectations for the application of food functionality research to pharmaceutical development as an extension of this research.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":"201-204"},"PeriodicalIF":1.4,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142341802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A new xenicane diterpene named 4α-acetoxyisodictyohemiacetal (1) was isolated from the brown alga Dictyota coriacea, along with 11 known diterpenoids. The structure of 1 was established by spectroscopic analyses, and its absolute configuration was determined by comparing the experimental and theoretical electronic circular dichroism spectra. Two dictyodiacetal diastereomers (5 and 6) were isolated, and the full NMR assignments were performed. The anti-inflammatory activities of the isolated compounds were evaluated using the lipopolysaccharide-stimulated mouse macrophage cell line, RAW264. The hemiacetal-containing xenicanes and dictyol-type diterpene inhibited not only the production of nitric oxide but also the expression of inducible nitric oxide synthase, interleukin-6, and cyclooxygenase-2 mRNA in RAW264 cells. This study demonstrated that diterpenes from D. coriacea may be useful as natural anti-inflammatory agents.
{"title":"Anti-inflammatory diterpenoids from the brown alga Dictyota coriacea.","authors":"Nozomi Shiiba, Momochika Kumagai, Hikaru Endo, Tomoki Tsuruta, Keisuke Nishikawa, Yoshiki Morimoto","doi":"10.1093/bbb/zbae163","DOIUrl":"10.1093/bbb/zbae163","url":null,"abstract":"<p><p>A new xenicane diterpene named 4α-acetoxyisodictyohemiacetal (1) was isolated from the brown alga Dictyota coriacea, along with 11 known diterpenoids. The structure of 1 was established by spectroscopic analyses, and its absolute configuration was determined by comparing the experimental and theoretical electronic circular dichroism spectra. Two dictyodiacetal diastereomers (5 and 6) were isolated, and the full NMR assignments were performed. The anti-inflammatory activities of the isolated compounds were evaluated using the lipopolysaccharide-stimulated mouse macrophage cell line, RAW264. The hemiacetal-containing xenicanes and dictyol-type diterpene inhibited not only the production of nitric oxide but also the expression of inducible nitric oxide synthase, interleukin-6, and cyclooxygenase-2 mRNA in RAW264 cells. This study demonstrated that diterpenes from D. coriacea may be useful as natural anti-inflammatory agents.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":"224-231"},"PeriodicalIF":1.4,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142615023","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nano-sized vesicles are ubiquitous in vegetables, fruits, and other edible plants. We have successfully prepared nanovesicles (NVs) from over 150 edible plants. These results suggest that the daily intake of NVs from various foods and their roles in food function are promising novel approaches for explaining the health-promoting properties of edible plants. These vesicles contain RNAs, including miRNAs, similar to extracellular NVs, which play pivotal roles in cell-cell communication. Intriguingly, NVs also contain phytochemicals such as polyphenols and carotenoids that are specific to each edible plant. In conclusion, these dietary NVs have the potential to serve as functional packages to deliver RNAs or phytochemicals to target cells across species from plants to humans.
{"title":"Nanovesicles derived from edible plants: a new player that contributes to the function of foods.","authors":"Masao Yamasaki, Yumi Yamasaki, Tatsuya Oshima","doi":"10.1093/bbb/zbae198","DOIUrl":"10.1093/bbb/zbae198","url":null,"abstract":"<p><p>Nano-sized vesicles are ubiquitous in vegetables, fruits, and other edible plants. We have successfully prepared nanovesicles (NVs) from over 150 edible plants. These results suggest that the daily intake of NVs from various foods and their roles in food function are promising novel approaches for explaining the health-promoting properties of edible plants. These vesicles contain RNAs, including miRNAs, similar to extracellular NVs, which play pivotal roles in cell-cell communication. Intriguingly, NVs also contain phytochemicals such as polyphenols and carotenoids that are specific to each edible plant. In conclusion, these dietary NVs have the potential to serve as functional packages to deliver RNAs or phytochemicals to target cells across species from plants to humans.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":"179-186"},"PeriodicalIF":1.4,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142892212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Seungjoo Baik, Seonghwa Hong, Hyun Joo Kim, Heon Sang Jeong, Hana Lee, Junsoo Lee
This study compared the antihypertensive effects of avenanthramides A, B, and C, with a focus on their antioxidant and anti-inflammatory properties. Treatment with avenanthramides A, B, and C (50 μm) significantly enhanced cell viability and nitric oxide production in H2O2-induced endothelial dysfunction in EA.hy926 cells. Avenanthramides notably increased the levels of antioxidant enzymes and glutathione while reducing malondialdehyde and reactive oxygen species. Moreover, avenanthramides promoted the Nrf2 translocation to nucleus, enhancing the expression of antioxidant enzymes. Furthermore, avenanthramides inhibited the protein levels of iNOS and COX-2, as well as the phosphorylation of IkBα and translocation of p65, thereby mitigating endothelial inflammation. Molecular docking analysis revealed that avenanthramide A exhibited the strongest binding affinity for HO-1 and iNOS, which was correlated with its superior biological activity. Overall, by upregulating Nrf2/HO-1 pathways and downregulating NF-kB pathways, avenanthramides show potential as therapeutic agents for the treatment of endothelial dysfunction.
{"title":"Relative protective activities of avenanthramide A, B, and C against H2O2-induced endothelial dysfunction in EA.hy926 cells.","authors":"Seungjoo Baik, Seonghwa Hong, Hyun Joo Kim, Heon Sang Jeong, Hana Lee, Junsoo Lee","doi":"10.1093/bbb/zbae170","DOIUrl":"10.1093/bbb/zbae170","url":null,"abstract":"<p><p>This study compared the antihypertensive effects of avenanthramides A, B, and C, with a focus on their antioxidant and anti-inflammatory properties. Treatment with avenanthramides A, B, and C (50 μm) significantly enhanced cell viability and nitric oxide production in H2O2-induced endothelial dysfunction in EA.hy926 cells. Avenanthramides notably increased the levels of antioxidant enzymes and glutathione while reducing malondialdehyde and reactive oxygen species. Moreover, avenanthramides promoted the Nrf2 translocation to nucleus, enhancing the expression of antioxidant enzymes. Furthermore, avenanthramides inhibited the protein levels of iNOS and COX-2, as well as the phosphorylation of IkBα and translocation of p65, thereby mitigating endothelial inflammation. Molecular docking analysis revealed that avenanthramide A exhibited the strongest binding affinity for HO-1 and iNOS, which was correlated with its superior biological activity. Overall, by upregulating Nrf2/HO-1 pathways and downregulating NF-kB pathways, avenanthramides show potential as therapeutic agents for the treatment of endothelial dysfunction.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":"268-274"},"PeriodicalIF":1.4,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142667080","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Koji made using Aspergillus oryzae shows potential for application as a cheese adjunct; however, flavor defects resulting from volatile free fatty acid (FFA) accumulation should be avoided. Hence, a modified glucose-containing whey solid medium was used to culture A. oryzae AHU 7139, and the triacylglycerol (TG) lipase activity and lipase gene (tglA and mdlB) expression were compared with those of a culture using a conventional whey solid medium. The results showed that TG lipase activity and the expression of both lipase genes were reduced in the modified medium. Moreover, the expression level of farA, a positive transcription factor of the lipase genes, was also reduced. The cheese adjunct prepared by culturing the AHU 7139 strain in the modified medium lowered the FFA content in the cheese products, resulting in comparable FFA levels with those in the adjunct-free cheese. Thus, adding glucose is recommended to prepare the koji adjunct for cheesemaking.
用米曲霉制作的曲料显示出作为奶酪辅料的潜力;但应避免挥发性游离脂肪酸(FFA)积累引起的风味缺陷。因此,采用改良的含葡萄糖乳清固体培养基培养a . oryzae AHU 7139,并与常规乳清固体培养基培养的三酰甘油(TG)脂肪酶活性和脂肪酶基因(tglA和mdlB)表达进行比较。结果表明,TG脂肪酶活性降低,两种脂肪酶基因的表达量均降低。脂肪酶基因的正转录因子farA的表达水平也降低。在改良培养基中培养AHU 7139菌株制备的奶酪添加剂降低了奶酪产品中的FFA含量,其FFA水平与不含添加剂的奶酪相当。因此,建议添加葡萄糖制备用于奶酪制作的曲剂。
{"title":"Application of glucose to prepare Aspergillus oryzae koji as an adjunct to prevent rancidity in cheese products.","authors":"Napaporn Chintagavongse, Tomohiro Mitani, Koichi Tamano, Toru Hayakawa, Jun-Ichi Wakamatsu, Haruto Kumura","doi":"10.1093/bbb/zbae174","DOIUrl":"10.1093/bbb/zbae174","url":null,"abstract":"<p><p>Koji made using Aspergillus oryzae shows potential for application as a cheese adjunct; however, flavor defects resulting from volatile free fatty acid (FFA) accumulation should be avoided. Hence, a modified glucose-containing whey solid medium was used to culture A. oryzae AHU 7139, and the triacylglycerol (TG) lipase activity and lipase gene (tglA and mdlB) expression were compared with those of a culture using a conventional whey solid medium. The results showed that TG lipase activity and the expression of both lipase genes were reduced in the modified medium. Moreover, the expression level of farA, a positive transcription factor of the lipase genes, was also reduced. The cheese adjunct prepared by culturing the AHU 7139 strain in the modified medium lowered the FFA content in the cheese products, resulting in comparable FFA levels with those in the adjunct-free cheese. Thus, adding glucose is recommended to prepare the koji adjunct for cheesemaking.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":"275-283"},"PeriodicalIF":1.4,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142749957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sphingolipids (SLs), found in all animals, plants, and fungi and in certain prokaryotic organisms, exhibit essential physiological functions that cannot be replicated by other lipids. Although SLs and their related biomolecules behave as lipid mediators, skin barrier systems, and epitopes, their detailed biological functions have not yet been revealed, unlike those of proteins and nucleic acids, because the biosynthesis of SLs is not governed by the central dogma. Recently, SLs have been widely studied in relation to diseases such as obesity, dementia, and neuron agenesis and have attracted attention as molecules related to unmet medical needs. This review presents the recent applications of the SL chemical biology in unmet medical needs.
{"title":"Elucidation of physiological functions of sphingolipid-related molecules by chemical approaches.","authors":"Yuta Murai","doi":"10.1093/bbb/zbae166","DOIUrl":"10.1093/bbb/zbae166","url":null,"abstract":"<p><p>Sphingolipids (SLs), found in all animals, plants, and fungi and in certain prokaryotic organisms, exhibit essential physiological functions that cannot be replicated by other lipids. Although SLs and their related biomolecules behave as lipid mediators, skin barrier systems, and epitopes, their detailed biological functions have not yet been revealed, unlike those of proteins and nucleic acids, because the biosynthesis of SLs is not governed by the central dogma. Recently, SLs have been widely studied in relation to diseases such as obesity, dementia, and neuron agenesis and have attracted attention as molecules related to unmet medical needs. This review presents the recent applications of the SL chemical biology in unmet medical needs.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":"205-214"},"PeriodicalIF":1.4,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845749","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The high heat-producing capacity of brown and beige adipocytes, collectively known as thermogenic adipocytes, contributes to whole-body energy expenditure and is an attractive target for the management of obesity. It has been revealed that the functions of thermogenic adipocytes are important for the regulation of whole-body carbohydrate and lipid metabolism, and the activation of thermogenic adipocytes seems to have beneficial effects for the management of obesity-related metabolic disorders, such as dyslipidemia. Recent studies have showed that specific food ingredients have the potential to activate thermogenic adipocytes via various mechanisms. Some of these are effective not only in rodents, but also in humans, and effective prevention of obesity using these food ingredients is expected. In this review, we introduce the recent findings on the regulatory mechanisms of lipid metabolism by thermogenic adipocytes and food ingredients, demonstrating the potential to activate thermogenic adipocytes and their underlying mechanisms.
{"title":"Lipid metabolism and food ingredients from the perspective of thermogenic adipocytes.","authors":"Mai Takada, Satoko Kawarasaki, Jungin Kwon, Zheng Ni, Haruya Takahashi, Kazuo Inoue, Tsuyoshi Goto","doi":"10.1093/bbb/zbae162","DOIUrl":"10.1093/bbb/zbae162","url":null,"abstract":"<p><p>The high heat-producing capacity of brown and beige adipocytes, collectively known as thermogenic adipocytes, contributes to whole-body energy expenditure and is an attractive target for the management of obesity. It has been revealed that the functions of thermogenic adipocytes are important for the regulation of whole-body carbohydrate and lipid metabolism, and the activation of thermogenic adipocytes seems to have beneficial effects for the management of obesity-related metabolic disorders, such as dyslipidemia. Recent studies have showed that specific food ingredients have the potential to activate thermogenic adipocytes via various mechanisms. Some of these are effective not only in rodents, but also in humans, and effective prevention of obesity using these food ingredients is expected. In this review, we introduce the recent findings on the regulatory mechanisms of lipid metabolism by thermogenic adipocytes and food ingredients, demonstrating the potential to activate thermogenic adipocytes and their underlying mechanisms.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":"193-200"},"PeriodicalIF":1.4,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142615007","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Food factors elicit physiological effects by interfering with the central dogma system, including DNA methylation, replication, transcription, and translation. MicroRNAs (miRNAs) are noncoding short RNAs that are ∼20 nucleotides long and play a crucial role in the regulation of mRNA levels and translation processes. Importantly, miRNAs can be delivered to different locations in nanovesicles. However, little is known about their roles as mediators of the effects of food factors. This review introduces recent findings on the role of miRNAs in the beneficial effects of food factors, including green tea polyphenols and soybean isoflavones, and discusses the importance of miRNAs as mediators of the beneficial effects of food.
食物因子通过干扰中枢神经系统(包括 DNA 甲基化、复制、转录和翻译)引起生理效应。微小RNA(miRNA)是一种非编码短RNA,长约20个核苷酸,在调节mRNA水平和翻译过程中发挥着重要作用。重要的是,miRNA 可被输送到纳米颗粒的不同位置。然而,人们对它们作为食物因子效应介质的作用知之甚少。本综述介绍了 miRNAs 在食物因子(包括绿茶多酚和大豆异黄酮)的有益效应中的作用的最新发现,并讨论了 miRNAs 作为食物有益效应介质的重要性。
{"title":"MicroRNA mediates the effects of food factors.","authors":"Motofumi Kumazoe, Hirofumi Tachibana","doi":"10.1093/bbb/zbae152","DOIUrl":"10.1093/bbb/zbae152","url":null,"abstract":"<p><p>Food factors elicit physiological effects by interfering with the central dogma system, including DNA methylation, replication, transcription, and translation. MicroRNAs (miRNAs) are noncoding short RNAs that are ∼20 nucleotides long and play a crucial role in the regulation of mRNA levels and translation processes. Importantly, miRNAs can be delivered to different locations in nanovesicles. However, little is known about their roles as mediators of the effects of food factors. This review introduces recent findings on the role of miRNAs in the beneficial effects of food factors, including green tea polyphenols and soybean isoflavones, and discusses the importance of miRNAs as mediators of the beneficial effects of food.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":"174-178"},"PeriodicalIF":1.4,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142495171","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lactic acid bacteria (LAB) shape diverse communities in fermented foods. Developing comprehensive quantification methods for community structure will revolutionize our understanding of food LAB microbiome. For this purpose, 16S rRNA gene amplicon-based quantification, using spiked exogenous bacterial cells as an internal standard, shows potential for comprehensiveness and accuracy. We validated cell spike-in amplicon sequencing for quantifying LAB communities in food. Low efficiency of LAB DNA extraction underscores the importance of compensating for DNA loss by spiking internal standard cells. Quantitative equations generated using 15 selected LAB mock species showed positive relationships between the ratio of MiSeq read counts and the expected 16S rRNA gene copy numbers, with coefficients of determination (R2) ≥ 0.6823. The fold differences between observed and expected 16S copy numbers were within the range of 1/3 to 3-fold. Our validation highlights that accurate preparation of the LAB mock community is crucial for cell spike-in amplicon sequencing accuracy.
{"title":"Challenge of validation in whole-cell spike-in amplicon sequencing to comprehensively quantify food lactic acid bacteriota.","authors":"Mugihito Oshiro, Keisuke Nakamura, Yukihiro Tashiro","doi":"10.1093/bbb/zbae173","DOIUrl":"10.1093/bbb/zbae173","url":null,"abstract":"<p><p>Lactic acid bacteria (LAB) shape diverse communities in fermented foods. Developing comprehensive quantification methods for community structure will revolutionize our understanding of food LAB microbiome. For this purpose, 16S rRNA gene amplicon-based quantification, using spiked exogenous bacterial cells as an internal standard, shows potential for comprehensiveness and accuracy. We validated cell spike-in amplicon sequencing for quantifying LAB communities in food. Low efficiency of LAB DNA extraction underscores the importance of compensating for DNA loss by spiking internal standard cells. Quantitative equations generated using 15 selected LAB mock species showed positive relationships between the ratio of MiSeq read counts and the expected 16S rRNA gene copy numbers, with coefficients of determination (R2) ≥ 0.6823. The fold differences between observed and expected 16S copy numbers were within the range of 1/3 to 3-fold. Our validation highlights that accurate preparation of the LAB mock community is crucial for cell spike-in amplicon sequencing accuracy.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":"294-303"},"PeriodicalIF":1.4,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142685990","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}