Pub Date : 2023-05-29DOI: 10.3389/frmbi.2023.1067019
J. Galeeva, E. Starikova, Dmitry E. Fedorov, A. Manolov, A. Pavlenko, D. Konanov, D.V. Krivonos, V. Babenko, K. Klimina, V. Veselovsky, Maxim D. Morozov, I. Gafurov, R. Gaifullina, V. Govorun, E. Ilina
The microbiota of the respiratory tract remains a relatively poorly studied subject. At the same time, it is involved in modulating the immune response to infectious agents in the host organism, just like the intestinal microbiota. A relationship between the composition of the respiratory microbiota and the likelihood of development and the severity of COVID-19 may be assumed. In this study, we applied the 16S rRNA metagenomic sequencing to analyze the oropharyngeal swabs from 120 COVID-19 patients collected during the first and the second waves of the COVID-19 epidemic in Russia. Differential abundance analysis with respect to comorbidities suggested association of Neisseria oralis, Neisseria mucosa, unidentified Veillonella spp., Lautropia mirabilis species with more severe lung damage, and Streptococcus salivarius, Capnocytophaga sputigena and Haemophilus parahaemolyticus with a milder course of the disease. We hypothesize that the latter bacteria (or some of them) might be beneficial for the respiratory tract and might be able to alleviate the course of the COVID-19 disease.
{"title":"Microbial communities of the upper respiratory tract in mild and severe COVID-19 patients: a possible link with the disease course","authors":"J. Galeeva, E. Starikova, Dmitry E. Fedorov, A. Manolov, A. Pavlenko, D. Konanov, D.V. Krivonos, V. Babenko, K. Klimina, V. Veselovsky, Maxim D. Morozov, I. Gafurov, R. Gaifullina, V. Govorun, E. Ilina","doi":"10.3389/frmbi.2023.1067019","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1067019","url":null,"abstract":"The microbiota of the respiratory tract remains a relatively poorly studied subject. At the same time, it is involved in modulating the immune response to infectious agents in the host organism, just like the intestinal microbiota. A relationship between the composition of the respiratory microbiota and the likelihood of development and the severity of COVID-19 may be assumed. In this study, we applied the 16S rRNA metagenomic sequencing to analyze the oropharyngeal swabs from 120 COVID-19 patients collected during the first and the second waves of the COVID-19 epidemic in Russia. Differential abundance analysis with respect to comorbidities suggested association of Neisseria oralis, Neisseria mucosa, unidentified Veillonella spp., Lautropia mirabilis species with more severe lung damage, and Streptococcus salivarius, Capnocytophaga sputigena and Haemophilus parahaemolyticus with a milder course of the disease. We hypothesize that the latter bacteria (or some of them) might be beneficial for the respiratory tract and might be able to alleviate the course of the COVID-19 disease.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"19 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90928864","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-05-26DOI: 10.3389/frmbi.2023.1072059
J. Song, Joung Ouk Ryan Kim, S. Yoon, M. Kwon, C. Ki
Introduction Several animal and clinical studies have reported that the state of the human gut microbiome is associated with hypertension. In this study, we investigated the association between the gut microbiome and hypertension in a Korean population from an enterotypic perspective. Methods A total of 623 participants were enrolled from a healthcare center and classified into four enterotypes, Bacteroides1- (Bac1), Bacteroides2- (Bac2), Prevotella- (Pre), and Ruminococcus enterotype-like-composition (Rum). Results When comparing the four enterotypes, clinical characteristics related to obesity, metabolic syndrome, and blood pressure were significantly associated with th e enterotypes, showing unfavorable associations with the Bac2 group and the opposite for the Rum group. Similarly, the prevalence of hypertension was highest in the Bac2 group and lowest in the Rum group. When analyzing the association between gut microbiota and blood pressure for each enterotype, gut microbial features of lower diversity, depletion of important short chain fatty acid-producing taxa, such as Faecalibacterium, Blautia, Anaerostipes, and enrichment of lipopolysaccharide -producing taxa, such as Megamonas, were found only in the dysbiotic Bac2 group. Discussion From an enterotype perspective, this study on a large Korean cohort shows that low-diversity Bacteroides2-enterotype-like composition is associated with hypertension, while the reverse is true for high-diversity Ruminococcus-enterotype-like composition and, to a limited degree, Bacteroides1-enterotype-like composition. In addition, we suggest that the effect of gut microbiota-mediated risk of hypertension could be modulated by altering the gut microbiome via diet. Dietary intervention trials promoting a balanced Korean diet instead of a more Western alternative may provide more definitive evidence for the involvement and role of the gut microbiome in relation to blood pressure.
{"title":"The association between gut microbiome and hypertension varies according to enterotypes: a Korean study","authors":"J. Song, Joung Ouk Ryan Kim, S. Yoon, M. Kwon, C. Ki","doi":"10.3389/frmbi.2023.1072059","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1072059","url":null,"abstract":"Introduction Several animal and clinical studies have reported that the state of the human gut microbiome is associated with hypertension. In this study, we investigated the association between the gut microbiome and hypertension in a Korean population from an enterotypic perspective. Methods A total of 623 participants were enrolled from a healthcare center and classified into four enterotypes, Bacteroides1- (Bac1), Bacteroides2- (Bac2), Prevotella- (Pre), and Ruminococcus enterotype-like-composition (Rum). Results When comparing the four enterotypes, clinical characteristics related to obesity, metabolic syndrome, and blood pressure were significantly associated with th e enterotypes, showing unfavorable associations with the Bac2 group and the opposite for the Rum group. Similarly, the prevalence of hypertension was highest in the Bac2 group and lowest in the Rum group. When analyzing the association between gut microbiota and blood pressure for each enterotype, gut microbial features of lower diversity, depletion of important short chain fatty acid-producing taxa, such as Faecalibacterium, Blautia, Anaerostipes, and enrichment of lipopolysaccharide -producing taxa, such as Megamonas, were found only in the dysbiotic Bac2 group. Discussion From an enterotype perspective, this study on a large Korean cohort shows that low-diversity Bacteroides2-enterotype-like composition is associated with hypertension, while the reverse is true for high-diversity Ruminococcus-enterotype-like composition and, to a limited degree, Bacteroides1-enterotype-like composition. In addition, we suggest that the effect of gut microbiota-mediated risk of hypertension could be modulated by altering the gut microbiome via diet. Dietary intervention trials promoting a balanced Korean diet instead of a more Western alternative may provide more definitive evidence for the involvement and role of the gut microbiome in relation to blood pressure.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"92 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73405421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-05-18DOI: 10.3389/frmbi.2023.1174034
B. Walusimbi, Melissa A. E. Lawson, J. Nassuuna, D. Kateete, E. Webb, R. Grencis, A. Elliott
The gut microbiome is important in shaping human health. One key factor that has been proposed to affect the gut microbiome is helminth infection. Unravelling the association and/or interaction between helminth infections and the gut microbiome may reveal new insights into the mechanisms through which parasitic worms impact the prognosis of infections and diseases. While considerable work has gone into reviewing data on the effect of helminth infection on gut microbiome in animal studies, less attention has been given to this area of research in human studies. This study set out to address this through an exhaustive systematic review of literature. Articles were identified through EMBASE, MEDLINE, Web of Science and Science Direct following a registered protocol (PROSPERO). After assessing methodological quality (ICROMS) and publication bias, a random effects meta-analysis was performed to investigate the overall effect that intestinal parasites can have on the human gut microbiome using alpha- and beta-diversity metrics and adjusting for age, sex and antihelminthic treatment taken by individuals. A total of 19 out of 3466 articles were included in the final meta-analysis. Our results show that helminth infection increases the host bacterial diversity, as well as microbial richness. This work further contributes to the understanding of how the gut microbiome structure changes depends on whether one is infected with helminths or not. It also lays the foundation for future research aimed at establishing how these interactions could explain the disparity in phenotypes such as infection, disease and vaccine responses reported in different regions worldwide. Systematic review registration https://www.crd.york.ac.uk/prospero/, identifier CRD42020192182.
肠道微生物群在塑造人类健康方面很重要。已经提出的影响肠道微生物组的一个关键因素是寄生虫感染。揭示寄生虫感染与肠道微生物组之间的关联和/或相互作用可能为寄生虫影响感染和疾病预后的机制提供新的见解。虽然在动物研究中对蠕虫感染对肠道微生物组的影响进行了大量的研究，但在人类研究中对这一领域的研究却很少得到关注。本研究旨在通过对文献的详尽系统回顾来解决这一问题。文章通过EMBASE、MEDLINE、Web of Science和Science Direct按照注册协议(PROSPERO)进行识别。在评估方法学质量(ICROMS)和发表偏倚后，进行随机效应荟萃分析，使用α和β多样性指标，并根据年龄、性别和个体接受的抗寄生虫治疗进行调整，调查肠道寄生虫对人类肠道微生物群的总体影响。3466篇文章中有19篇被纳入最终的meta分析。我们的研究结果表明，蠕虫感染增加了宿主细菌的多样性，以及微生物的丰富度。这项工作进一步有助于理解肠道微生物群结构的变化如何取决于是否感染了蠕虫。它还为未来的研究奠定了基础，旨在确定这些相互作用如何解释世界不同地区报告的感染、疾病和疫苗反应等表型的差异。系统评审注册https://www.crd.york.ac.uk/prospero/，标识符CRD42020192182。
{"title":"The effects of helminth infections on the human gut microbiome: a systematic review and meta-analysis","authors":"B. Walusimbi, Melissa A. E. Lawson, J. Nassuuna, D. Kateete, E. Webb, R. Grencis, A. Elliott","doi":"10.3389/frmbi.2023.1174034","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1174034","url":null,"abstract":"The gut microbiome is important in shaping human health. One key factor that has been proposed to affect the gut microbiome is helminth infection. Unravelling the association and/or interaction between helminth infections and the gut microbiome may reveal new insights into the mechanisms through which parasitic worms impact the prognosis of infections and diseases. While considerable work has gone into reviewing data on the effect of helminth infection on gut microbiome in animal studies, less attention has been given to this area of research in human studies. This study set out to address this through an exhaustive systematic review of literature. Articles were identified through EMBASE, MEDLINE, Web of Science and Science Direct following a registered protocol (PROSPERO). After assessing methodological quality (ICROMS) and publication bias, a random effects meta-analysis was performed to investigate the overall effect that intestinal parasites can have on the human gut microbiome using alpha- and beta-diversity metrics and adjusting for age, sex and antihelminthic treatment taken by individuals. A total of 19 out of 3466 articles were included in the final meta-analysis. Our results show that helminth infection increases the host bacterial diversity, as well as microbial richness. This work further contributes to the understanding of how the gut microbiome structure changes depends on whether one is infected with helminths or not. It also lays the foundation for future research aimed at establishing how these interactions could explain the disparity in phenotypes such as infection, disease and vaccine responses reported in different regions worldwide. Systematic review registration https://www.crd.york.ac.uk/prospero/, identifier CRD42020192182.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"16 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86674854","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-05-17DOI: 10.3389/frmbi.2023.1157681
Alonso Favela, M. Bohn, A. Kent
Plants have a surprising capacity to alter their environmental conditions to create adequate niches for survival and stress tolerance. This process of environmental transformation, commonly referred to as “extended phenotypes” or “niche construction”, has historically been studied in the domain of ecology, but this is a process that is pervasive across the plant kingdom. Furthermore, research is beginning to show that plants’ extended phenotypes shape the assembly and function of closely associated microbial communities. Incorporation and understanding the role that plant-extended phenotypes play in agriculture may offer novel, bioinspired methods to manage our arable soil microbiomes. Here, we review the challenges agriculture faces, the plant extended phenotypes we know to shape the microbiome, and the potential utilization of this knowledge to improve the environmental impact of agriculture. Understanding how plant extended phenotypes shape microbial communities could be a key to creating a sustainable future with both plants and microbiomes in consideration.
{"title":"Application of plant extended phenotypes to manage the agricultural microbiome belowground","authors":"Alonso Favela, M. Bohn, A. Kent","doi":"10.3389/frmbi.2023.1157681","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1157681","url":null,"abstract":"Plants have a surprising capacity to alter their environmental conditions to create adequate niches for survival and stress tolerance. This process of environmental transformation, commonly referred to as “extended phenotypes” or “niche construction”, has historically been studied in the domain of ecology, but this is a process that is pervasive across the plant kingdom. Furthermore, research is beginning to show that plants’ extended phenotypes shape the assembly and function of closely associated microbial communities. Incorporation and understanding the role that plant-extended phenotypes play in agriculture may offer novel, bioinspired methods to manage our arable soil microbiomes. Here, we review the challenges agriculture faces, the plant extended phenotypes we know to shape the microbiome, and the potential utilization of this knowledge to improve the environmental impact of agriculture. Understanding how plant extended phenotypes shape microbial communities could be a key to creating a sustainable future with both plants and microbiomes in consideration.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"116 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75031086","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-04-25DOI: 10.3389/frmbi.2023.1102694
Linzehao Li, Yan Yan, Xiaolei Wang, Y. Hou, Lina Ding, Zhi-bin Wang, Qinghe Song, Wenyu Ding, Xian-Dang Zhang
Introduction Allicin is a wide spectrum prebiotic for human health, but whether it can attenuate blood in diabetes patients is rarely reported. In this study, we built a rat model and investigated the effect of allicin on diabetes mellitus type 2 (T2DM). We found that allicin could effectively reduce blood glucose levels, regulate intestinal microbiota, reduce lipid and body weight accumulation, and systemic inflammation in T2DM rats. Methods The rat model of type 2 diabetes was made by streptozotocin, and different doses of allicin were given orally by gavage. The intestinal contents of diabetes rats were sequenced and analyzed by 16S technology, and the clinical indicators of rats were detected for joint analysis. Results Allicin can improve the intestinal flora of type 2 diabetes rats, enrich beneficial metabolites, reduce blood glucose, improve blood lipids, reduce systemic inflammation, and improve type 2 diabetes. Discussion Intestinal microbiome analysis showed that allicin gavage significantly regulated the structure and main components of the intestinal microbiota in T2DM rats. Allicin increased the abundance of probiotic microbes, such as Lactobacillus, Clostridium and Akkermansia, while it reduced pathogenic microbes, such as Enterobacter, Erysipelatoclostridium and Colidextribacter. Allicin gavage increased the abundance of intestinal short-chain fatty acids, such as acetic acid and propionic acid. Correlation analysis showed that the increased gut microbes by allicin gavage were significantly associated with health physiological parameters but negatively related to serum inflammatory factors such as interleukin-6 (IL-6), tumor necrosis factor alpha (TNF-a), and hypersensitive C-reactive protein (hs-CRP). In addition, our study also suggests that allicin may have prebiotic effects on chronic liver injury. This study shows that allicin can regulate various clinical symptoms of T2DM and is a potential therapeutic drug for T2DM.
{"title":"Allicin modulates the intestinal microbiota to attenuate blood glucose and systemic inflammation in type 2 diabetic rats","authors":"Linzehao Li, Yan Yan, Xiaolei Wang, Y. Hou, Lina Ding, Zhi-bin Wang, Qinghe Song, Wenyu Ding, Xian-Dang Zhang","doi":"10.3389/frmbi.2023.1102694","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1102694","url":null,"abstract":"Introduction Allicin is a wide spectrum prebiotic for human health, but whether it can attenuate blood in diabetes patients is rarely reported. In this study, we built a rat model and investigated the effect of allicin on diabetes mellitus type 2 (T2DM). We found that allicin could effectively reduce blood glucose levels, regulate intestinal microbiota, reduce lipid and body weight accumulation, and systemic inflammation in T2DM rats. Methods The rat model of type 2 diabetes was made by streptozotocin, and different doses of allicin were given orally by gavage. The intestinal contents of diabetes rats were sequenced and analyzed by 16S technology, and the clinical indicators of rats were detected for joint analysis. Results Allicin can improve the intestinal flora of type 2 diabetes rats, enrich beneficial metabolites, reduce blood glucose, improve blood lipids, reduce systemic inflammation, and improve type 2 diabetes. Discussion Intestinal microbiome analysis showed that allicin gavage significantly regulated the structure and main components of the intestinal microbiota in T2DM rats. Allicin increased the abundance of probiotic microbes, such as Lactobacillus, Clostridium and Akkermansia, while it reduced pathogenic microbes, such as Enterobacter, Erysipelatoclostridium and Colidextribacter. Allicin gavage increased the abundance of intestinal short-chain fatty acids, such as acetic acid and propionic acid. Correlation analysis showed that the increased gut microbes by allicin gavage were significantly associated with health physiological parameters but negatively related to serum inflammatory factors such as interleukin-6 (IL-6), tumor necrosis factor alpha (TNF-a), and hypersensitive C-reactive protein (hs-CRP). In addition, our study also suggests that allicin may have prebiotic effects on chronic liver injury. This study shows that allicin can regulate various clinical symptoms of T2DM and is a potential therapeutic drug for T2DM.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"17 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91271495","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Consuming resistant maltodextrin (RMD) decreases food intake and increase appetite-related gut hormones, but the underlying mechanisms have remained unknown. Therefore, we aimed to elucidate the mechanisms underlying the effects of RMD feeding on food intake (appetite) using Institute of Cancer Research male mice fed with a high-fat diet (HFD-cellulose group) or HFD in which cellulose was replaced with RMD (HFD-RMD group). Feeding mice with an HFD-RMD for approximately 8 weeks inhibited excessive calorie intake and altered the gut microbiota composition. Excessive calorie intake was inhibited for several days in mice fed only with an HFD-cellulose and transplanted with fecal microbiota from the HFD-RMD group (FMT-HFD-RMD group). Moreover, in the HFD-RMD and FMT-HFD-RMD groups, serum active glucagon-like peptide (GLP)-1 and peptide tyrosine tyrosine (PYY) levels were significantly higher, and appetite-related neuropeptide gene transcription in the hypothalamus were significantly altered, compared with the HFD-cellulose and FMT-HFD-cellulose groups. These results suggested that the long-term RMD intake changed the gut microbiota composition, increased the GLP-1 and PYY secretion, and altered the appetite-related neuropeptide gene transcription in the hypothalamus, leading to suppressed excessive calorie intake in an HFD.
{"title":"Feeding with resistant maltodextrin suppresses excessive calorie intake in a high-fat diet, mediated by changes in mouse gut microbiota composition, appetite-related gut hormone secretion, and neuropeptide transcriptional levels","authors":"Kaede Ito, Atsushi Haraguchi, Shuhei Sato, Masataka Sekiguchi, Hiroyuki Sasaki, Conn Ryan, Yijin Lyu, S. Shibata","doi":"10.3389/frmbi.2023.1149808","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1149808","url":null,"abstract":"Consuming resistant maltodextrin (RMD) decreases food intake and increase appetite-related gut hormones, but the underlying mechanisms have remained unknown. Therefore, we aimed to elucidate the mechanisms underlying the effects of RMD feeding on food intake (appetite) using Institute of Cancer Research male mice fed with a high-fat diet (HFD-cellulose group) or HFD in which cellulose was replaced with RMD (HFD-RMD group). Feeding mice with an HFD-RMD for approximately 8 weeks inhibited excessive calorie intake and altered the gut microbiota composition. Excessive calorie intake was inhibited for several days in mice fed only with an HFD-cellulose and transplanted with fecal microbiota from the HFD-RMD group (FMT-HFD-RMD group). Moreover, in the HFD-RMD and FMT-HFD-RMD groups, serum active glucagon-like peptide (GLP)-1 and peptide tyrosine tyrosine (PYY) levels were significantly higher, and appetite-related neuropeptide gene transcription in the hypothalamus were significantly altered, compared with the HFD-cellulose and FMT-HFD-cellulose groups. These results suggested that the long-term RMD intake changed the gut microbiota composition, increased the GLP-1 and PYY secretion, and altered the appetite-related neuropeptide gene transcription in the hypothalamus, leading to suppressed excessive calorie intake in an HFD.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"117 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79272330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-30DOI: 10.3389/frmbi.2023.1071186
Mary K. English, C. Langdon, Carla B. Schubiger, Ryan S. Mueller
Oyster aquaculture is a growing industry that depends on production of fast-growing, healthy larvae and juveniles (spat) to be sold to farmers. Despite nearly identical genetics and environmental conditions in the early life stages of oysters, larvae and spat sizes can vary drastically. As the microbiome can influence the health and size of marine invertebrates, we analyzed the microbiomes of differently-sized juvenile Pacific oyster (Crassostrea gigas) spat of the same age to examine the relationship of their microbiomes with size variation. We used 16S sequencing of 128 animals (n = 60 large, n = 68 small) to characterize the microbiomes of each size class, comparing alpha diversity, beta diversity, and differentially abundant taxa between size classes. We observed that small spat had higher alpha diversity using measures that considered only richness, but there was no difference in alpha diversity between the two size classes using measures that incorporate compositional metrics. Additionally, large and small spat had distinct microbiomes, the separation of which was driven by more dominant bacterial taxa. Taxa that were differentially abundant in large oysters were also more abundant overall, and many appear to have roles in nutrient absorption and energy acquisition. The results of this study provide insight into how the microbiome of C. gigas may affect the early development of the animal, which can inform hatchery and nursery practices.
{"title":"Dominant bacterial taxa drive microbiome differences of juvenile Pacific oysters of the same age and variable sizes","authors":"Mary K. English, C. Langdon, Carla B. Schubiger, Ryan S. Mueller","doi":"10.3389/frmbi.2023.1071186","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1071186","url":null,"abstract":"Oyster aquaculture is a growing industry that depends on production of fast-growing, healthy larvae and juveniles (spat) to be sold to farmers. Despite nearly identical genetics and environmental conditions in the early life stages of oysters, larvae and spat sizes can vary drastically. As the microbiome can influence the health and size of marine invertebrates, we analyzed the microbiomes of differently-sized juvenile Pacific oyster (Crassostrea gigas) spat of the same age to examine the relationship of their microbiomes with size variation. We used 16S sequencing of 128 animals (n = 60 large, n = 68 small) to characterize the microbiomes of each size class, comparing alpha diversity, beta diversity, and differentially abundant taxa between size classes. We observed that small spat had higher alpha diversity using measures that considered only richness, but there was no difference in alpha diversity between the two size classes using measures that incorporate compositional metrics. Additionally, large and small spat had distinct microbiomes, the separation of which was driven by more dominant bacterial taxa. Taxa that were differentially abundant in large oysters were also more abundant overall, and many appear to have roles in nutrient absorption and energy acquisition. The results of this study provide insight into how the microbiome of C. gigas may affect the early development of the animal, which can inform hatchery and nursery practices.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"89 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83857071","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-23DOI: 10.3389/frmbi.2023.1029839
K. Jannat, Md Abdul Kader, S. Parvez, Russell Thomson, Md. Mahbubur Rahman, M. Kabir, K. Agho, R. Haque, D. Merom
Introduction We evaluated the effects of yogurt supplementation and nutrition education to low educated mothers on infant-gut health at an early age. Methods We designed a three-arm pilot randomized controlled trial with 162 infants aged 5-6 months and at risk of stunting (LAZ ≤-1 SD and >-2 SD at enrollment) living in slum areas in Dhaka, Bangladesh. Eligible children were randomized to receive, 1) nutrition education, 2) yogurt supplementation plus nutrition education or 3) usual care. Three faecal inflammatory biomarkers alpha-1 antitrypsin (AAT), myeloperoxidase (MPO), and neopterin (NEO) were measured before and after three months of yogurt feeding. Results At the end of three months, there were no significant differences in the biomarker concentrations between the yogurt plus group and control. Compared to control, the adjusted mean faecal NEO concentration decreased by 21% (NEO: RR 0.79, 95% CI: 0.60, 1.04) and the adjusted mean faecal AAT concentration decreased by 8% (AAT: RR 0.92, 95% CI: 0.69, 1.22); whereas, the adjusted mean faecal MPO concentration increased by 14% (MPO: RR 1.14, 95% CI: 0.62, 2.09). Such changes were not apparent in the education only group. Discussion After a three-month trial of daily yogurt feeding to children at risk of stunting and infant feeding education to their mothers, reduction in one inflammatory biomarker reached close to statistical significance, but not all of the measured biomarkers. The study did not finish its endline measurements at 6-month as designed due to COVID 19 pandemic. This has greatly impacted the interpretation of the results as we could not establish a decreasing trend in biomarker concentration with continued yogurt feeding.
{"title":"Faecal markers of intestinal inflammation in slum infants following yogurt intervention: A pilot randomized controlled trial in Bangladesh","authors":"K. Jannat, Md Abdul Kader, S. Parvez, Russell Thomson, Md. Mahbubur Rahman, M. Kabir, K. Agho, R. Haque, D. Merom","doi":"10.3389/frmbi.2023.1029839","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1029839","url":null,"abstract":"Introduction We evaluated the effects of yogurt supplementation and nutrition education to low educated mothers on infant-gut health at an early age. Methods We designed a three-arm pilot randomized controlled trial with 162 infants aged 5-6 months and at risk of stunting (LAZ ≤-1 SD and >-2 SD at enrollment) living in slum areas in Dhaka, Bangladesh. Eligible children were randomized to receive, 1) nutrition education, 2) yogurt supplementation plus nutrition education or 3) usual care. Three faecal inflammatory biomarkers alpha-1 antitrypsin (AAT), myeloperoxidase (MPO), and neopterin (NEO) were measured before and after three months of yogurt feeding. Results At the end of three months, there were no significant differences in the biomarker concentrations between the yogurt plus group and control. Compared to control, the adjusted mean faecal NEO concentration decreased by 21% (NEO: RR 0.79, 95% CI: 0.60, 1.04) and the adjusted mean faecal AAT concentration decreased by 8% (AAT: RR 0.92, 95% CI: 0.69, 1.22); whereas, the adjusted mean faecal MPO concentration increased by 14% (MPO: RR 1.14, 95% CI: 0.62, 2.09). Such changes were not apparent in the education only group. Discussion After a three-month trial of daily yogurt feeding to children at risk of stunting and infant feeding education to their mothers, reduction in one inflammatory biomarker reached close to statistical significance, but not all of the measured biomarkers. The study did not finish its endline measurements at 6-month as designed due to COVID 19 pandemic. This has greatly impacted the interpretation of the results as we could not establish a decreasing trend in biomarker concentration with continued yogurt feeding.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84152141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-20DOI: 10.3389/frmbi.2023.1113635
K. Peng, Jianqiang Qiu, Chaozheng Li, Huijie Lu, Z. Liu, Ding Liu, Wen-bo Huang
Soybean meal is considered as one of the major components of Litopenaeus vannamei diets. However, most previous studies have focused on evaluating the effects of soybean meal on L. vannamei from the perspective of growth, physiology, and feed utilization; information regarding the analysis of serum metabolites, antioxidant and immune response, and intestinal microbiota is limited. Five diets were prepared, comprising 20% (T20), 28% (T28), 35% (T35), 42% (T42), and 50% (T50) soybean meal. A total of 600 shrimp were randomly distributed into 20 tanks (i.e., 30 shrimp per tank), with four tanks assigned to each dietary group. Shrimp were fed to apparent satiation during the 42-day feeding trial. The results showed that levels of serum globulin, alanine aminotransferase, and aspartate aminotransferase linearly increased (p < 0.01), but levels of high-density lipoprotein cholesterol linearly decreased (p < 0.001) as the proportion of soybean meal in the diet increased. Supplementation of shrimp diets with soybean meal linearly and quadratically increased (p < 0.05) serum total antioxidant capacity, levels of malondialdehyde, and activities of catalase, nitric oxide synthase and phenoloxidase. Hepatocytes in T35, T42, and T50 were shown to have different degrees of vacuolar degeneration, hepatic corpuscle atrophy, and star-like lumen loss. Dietary inclusion of soybean meal altered the composition of intestinal bacterial microbiota at phylum level, especially increasing the abundance of on other bacterial genera, whereas it had minimal impact on other bacterial genera and had no significant influence on the bacterial diversity. This study suggests that dietary supplementation of L. vannamei diets with soybean meal at concentrations exceeding 28% induces inflammation and oxidant damage of the hepatopancreas, and increases the risk of intestinal disease.
{"title":"A multi-angle analysis of injury induced by supplementation of soybean meal in Litopenaeus vannamei diets","authors":"K. Peng, Jianqiang Qiu, Chaozheng Li, Huijie Lu, Z. Liu, Ding Liu, Wen-bo Huang","doi":"10.3389/frmbi.2023.1113635","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1113635","url":null,"abstract":"Soybean meal is considered as one of the major components of Litopenaeus vannamei diets. However, most previous studies have focused on evaluating the effects of soybean meal on L. vannamei from the perspective of growth, physiology, and feed utilization; information regarding the analysis of serum metabolites, antioxidant and immune response, and intestinal microbiota is limited. Five diets were prepared, comprising 20% (T20), 28% (T28), 35% (T35), 42% (T42), and 50% (T50) soybean meal. A total of 600 shrimp were randomly distributed into 20 tanks (i.e., 30 shrimp per tank), with four tanks assigned to each dietary group. Shrimp were fed to apparent satiation during the 42-day feeding trial. The results showed that levels of serum globulin, alanine aminotransferase, and aspartate aminotransferase linearly increased (p < 0.01), but levels of high-density lipoprotein cholesterol linearly decreased (p < 0.001) as the proportion of soybean meal in the diet increased. Supplementation of shrimp diets with soybean meal linearly and quadratically increased (p < 0.05) serum total antioxidant capacity, levels of malondialdehyde, and activities of catalase, nitric oxide synthase and phenoloxidase. Hepatocytes in T35, T42, and T50 were shown to have different degrees of vacuolar degeneration, hepatic corpuscle atrophy, and star-like lumen loss. Dietary inclusion of soybean meal altered the composition of intestinal bacterial microbiota at phylum level, especially increasing the abundance of on other bacterial genera, whereas it had minimal impact on other bacterial genera and had no significant influence on the bacterial diversity. This study suggests that dietary supplementation of L. vannamei diets with soybean meal at concentrations exceeding 28% induces inflammation and oxidant damage of the hepatopancreas, and increases the risk of intestinal disease.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89605304","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-16DOI: 10.3389/frmbi.2023.1147082
Stefano Leo, O. F. Cetiner, Laure F. Pittet, N. Messina, W. Jakob, L. Falquet, N. Curtis, P. Zimmermann
Introduction The early-life intestinal microbiome plays a crucial role in the development and regulation of the immune system. Perturbations in its composition during this critical period have been linked to the development of allergic diseases. Objective This study aimed to investigate the association between the composition of the early-life intestinal microbiome and the presence of eczema in the first year of life using shotgun metagenomic sequencing and functional analyses (metabolic pathways). Methods Stool samples from 393 healthy term infants collected at 1 week of age were analyzed with shotgun metagenomic sequencing. Environmental and clinical data were prospectively collected using 3-monthly validated questionnaires. Participants were clinically assessed during study visits at 12 months of age. Eczema was diagnosed by the UK diagnostic tool and by a research nurse. Data analysis was stratified by delivery mode. Results Eczema was diagnosed in 16.4% (60/366) of participants by nurse diagnosis. Infants born by cesarean section (CS) with nurse-diagnosed eczema had a higher relative abundance of Escherichia, Shigella, Enterobacter, and Citrobacter and a lower relative abundance of Veillonella than CS-born infants without eczema. In addition, CS-born infants without eczema had a higher abundance of genes involved in lactic fermentation. Vaginally born infants with eczema had a higher relative abundance of Bacteroides and a lower abundance of Streptococcus. Conclusion There is an association between the bacterial composition of the intestinal microbiome at 1 week of age and the presence of eczema in the first 12 months of life. Graphical Abstract
{"title":"The association between the composition of the early-life intestinal microbiome and eczema in the first year of life","authors":"Stefano Leo, O. F. Cetiner, Laure F. Pittet, N. Messina, W. Jakob, L. Falquet, N. Curtis, P. Zimmermann","doi":"10.3389/frmbi.2023.1147082","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1147082","url":null,"abstract":"Introduction The early-life intestinal microbiome plays a crucial role in the development and regulation of the immune system. Perturbations in its composition during this critical period have been linked to the development of allergic diseases. Objective This study aimed to investigate the association between the composition of the early-life intestinal microbiome and the presence of eczema in the first year of life using shotgun metagenomic sequencing and functional analyses (metabolic pathways). Methods Stool samples from 393 healthy term infants collected at 1 week of age were analyzed with shotgun metagenomic sequencing. Environmental and clinical data were prospectively collected using 3-monthly validated questionnaires. Participants were clinically assessed during study visits at 12 months of age. Eczema was diagnosed by the UK diagnostic tool and by a research nurse. Data analysis was stratified by delivery mode. Results Eczema was diagnosed in 16.4% (60/366) of participants by nurse diagnosis. Infants born by cesarean section (CS) with nurse-diagnosed eczema had a higher relative abundance of Escherichia, Shigella, Enterobacter, and Citrobacter and a lower relative abundance of Veillonella than CS-born infants without eczema. In addition, CS-born infants without eczema had a higher abundance of genes involved in lactic fermentation. Vaginally born infants with eczema had a higher relative abundance of Bacteroides and a lower abundance of Streptococcus. Conclusion There is an association between the bacterial composition of the intestinal microbiome at 1 week of age and the presence of eczema in the first 12 months of life. Graphical Abstract","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"34 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81649994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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