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Sui Y, Li X, Gao Y, Kong B, Jiang Y, Chen Q. Effect of Yeast Inoculation on the Bacterial Community Structure in Reduced-Salt Harbin Dry Sausages: A Perspective of Fungi-Bacteria Interactions. Foods 2024; 13:307. [PMID: 38254608 PMCID: PMC10815184 DOI: 10.3390/foods13020307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/05/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Yeast strains are promising starters to compensate for the flavor deficiencies of reduced-salt dry sausages, but their influence on the bacterial community's structure has not yet been clarified. In this study, the effect of separately inoculating Pichia kudriavzevii MDJ1 (Pk) and Debaryomyces hansenii HRB3 (Dh) on the bacterial community structure in reduced-salt dry sausage was investigated. The results demonstrated that the inoculation of two yeast strains significantly reduced the pH, and enhanced the total acid content, lactic acid bacteria (LAB) counts, and total bacterial counts of reduced-salt sausages after a 12-day fermentation (p < 0.05). Furthermore, high-throughput sequencing results elucidated that the inoculation of yeast strains significantly affected the bacterial composition of the dry sausages. Especially, the relative abundance of bacteria at the firmicute level in the Pk and Dh treatments exhibited a significant increase of 83.22% and 82.19%, respectively, compared to the noninoculated reduced-salt dry sausage treatment (Cr). The relative abundance of Latilactobacillus, especially L. sakei (0.46%, 2.80%, 65.88%, and 33.41% for the traditional dry sausage (Ct), Cr, Pk, and Dh treatments, respectively), increased significantly in the reduced-salt sausages inoculated with two yeast strains. Our work demonstrates the dynamic changes in the bacterial composition of reduced-salt sausages inoculated with different yeast strains, which could provide the foundation for the in-depth study of fungi-bacteria interactions in fermented foods.
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Affiliation(s)
- Yumeng Sui
- College of Food Science, Northeast Agricultural University, Harbin 150030, China; (Y.S.); (X.L.); (Y.G.); (B.K.)
| | - Xiangao Li
- College of Food Science, Northeast Agricultural University, Harbin 150030, China; (Y.S.); (X.L.); (Y.G.); (B.K.)
| | - Yuan Gao
- College of Food Science, Northeast Agricultural University, Harbin 150030, China; (Y.S.); (X.L.); (Y.G.); (B.K.)
| | - Baohua Kong
- College of Food Science, Northeast Agricultural University, Harbin 150030, China; (Y.S.); (X.L.); (Y.G.); (B.K.)
| | - Yitong Jiang
- Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Qian Chen
- College of Food Science, Northeast Agricultural University, Harbin 150030, China; (Y.S.); (X.L.); (Y.G.); (B.K.)
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Palmnäs-Bédard M, de Santa Izabel A, Dicksved J, Landberg R. Characterization of the Bacterial Composition of 47 Fermented Foods in Sweden. Foods 2023; 12:3827. [PMID: 37893721 PMCID: PMC10606000 DOI: 10.3390/foods12203827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Fermentation has long been utilized to preserve and enhance the flavor and nutritional value of foods. Recently, fermented foods have gained popularity, reaching new consumer groups due to perceived health benefits. However, the microbial composition of many fermented foods re-mains unknown. Here, we characterized the bacterial composition, diversity, and richness of 47 fermented foods available in Sweden, including kombucha, water kefir, milk kefir, yogurt, plant-based yogurt alternatives, kimchi, sauerkraut, and fermented vegetables. Via 16S rRNA gene sequencing, we identified 2497 bacteria (amplicon sequence variants). The bacterial composition was strongly associated with the type of fermented food, and lactic acid bacteria and/or acetic acid bacteria dominated most samples. However, each fermented food had a unique composition, with kombucha and water kefir having the highest diversity across and within samples. Few bacteria were abundant in multiple foods and food groups. These were Streptococcus thermophilus in yogurts and plant-based yoghurts; Lactococcus lactis in milk kefirs and one water kefir; and Lactiplantibacillus plantarum in kimchi, sauerkraut, and fermented cucumber. The broad range of fermented foods included in this study and their diverse bacterial communities warrant further investigation into the implications of microbial compositions for product traits and potential impact on human health.
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Affiliation(s)
- Marie Palmnäs-Bédard
- Department of Life Sciences, Division of Food and Nutrition Science, Chalmers University of Technology, 412 96 Gothenburg, Sweden;
| | | | - Johan Dicksved
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden;
| | - Rikard Landberg
- Department of Life Sciences, Division of Food and Nutrition Science, Chalmers University of Technology, 412 96 Gothenburg, Sweden;
- Department of Public Health and Clinical Medicine, Umeå University, 901 87 Umeå, Sweden
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Bai F, Guo W, Li P, Qiao D, Du Z, Qi X. Different responses of abundant and rare bacterial composition to groundwater depth and reduced nitrogen application in summer maize field. Front Microbiol 2023; 14:1220731. [PMID: 37901810 PMCID: PMC10613034 DOI: 10.3389/fmicb.2023.1220731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 09/18/2023] [Indexed: 10/31/2023] Open
Abstract
Introduction It is well known that reduced nitrogen application and groundwater depth can change soil microbial communities, but the associated difference in the response of abundant and rare bacterial composition to these local environmental changes remains unclear. Methods In this study a lysimeter experiment was carried out to examine the impact of reduced nitrogen and groundwater depth on the composition of abundant and rare bacteria. Results and discussion Our results demonstrated that the summer maize field soil species composition of rare bacterial sub-communities was significantly regulated by reduced nitrogen application, groundwater depth change and their interactions. However, only reduced nitrogen application had a significant influence on the species composition of abundant bacterial sub-communities. The structural equation model (SEM) indicated that reduced nitrogen application and groundwater depth change also could indirectly regulate the species composition of abundant and rare bacteria by altering soil attributes. The changes in soil pH and TSN had the most significant effects on the community composition of abundant and rare bacteria, respectively. More importantly, rare bacterial sub-communities were more sensitive to the changes in nitrogen input, groundwater depth and soil factors. Collectively, our study first demonstrated that abundant and rare microbial sub-communities responded differently to reduced nitrogen application and groundwater depth change. This study highlights that summer maize farmland production management should take nitrogen input and groundwater depth into consideration to maintain the compositional stability of soil rare microbial sub-communities.
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Affiliation(s)
- Fangfang Bai
- Institute of Farmland Irrigation, Chinese Academy of Agricultural Sciences, Xinxiang, China
| | - Wei Guo
- Institute of Farmland Irrigation, Chinese Academy of Agricultural Sciences, Xinxiang, China
- Water Environment Factor Risk Assessment Laboratory of Agricultural Products Quality and Safety, Ministry of Agriculture and Rural Affairs, Xinxiang, China
| | - Ping Li
- Institute of Farmland Irrigation, Chinese Academy of Agricultural Sciences, Xinxiang, China
- Agricultural Water Soil Environmental Field Research Station of Xinxiang, Chinese Academy of Agricultural Sciences, Xinxiang, China
| | - Dongmei Qiao
- Institute of Farmland Irrigation, Chinese Academy of Agricultural Sciences, Xinxiang, China
| | - Zhenjie Du
- Institute of Farmland Irrigation, Chinese Academy of Agricultural Sciences, Xinxiang, China
- Water Environment Factor Risk Assessment Laboratory of Agricultural Products Quality and Safety, Ministry of Agriculture and Rural Affairs, Xinxiang, China
| | - Xuebin Qi
- Institute of Farmland Irrigation, Chinese Academy of Agricultural Sciences, Xinxiang, China
- Water Environment Factor Risk Assessment Laboratory of Agricultural Products Quality and Safety, Ministry of Agriculture and Rural Affairs, Xinxiang, China
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Halfen J, Carpinelli NA, Lasso-Ramirez S, Michelotti TC, Fowler EC, St-Pierre B, Trevisi E, Osorio JS. Physiological Conditions Leading to Maternal Subclinical Ketosis in Holstein Dairy Cows Can Impair the Offspring's Postnatal Growth and Gut Microbiome Development. Microorganisms 2023; 11:1839. [PMID: 37513011 PMCID: PMC10383123 DOI: 10.3390/microorganisms11071839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Maternal metabolic disruptions, such as ketosis, can have adverse effects on fetal development and influence postnatal factors. Twelve Holstein calves were randomly enrolled in this study at birth and monitored until 8 weeks of age. The study was conducted from fall 2018 until spring 2019. After completing the data collection period, calves were classified according to their respective dams ketotic condition after parturition. This classification was based on dam blood β-hydroxybutyrate < 1.4 mmol/L nonketotic (NONKET; n = 6 calves) or ≥1.4 mmol/L subclinical-ketotic (SK; n = 6 calves). SK calves had greater birth body weight (p = 0.05) but exhibited a slower growth rate compared to NONKET calves from 1 to 8 weeks (p = 0.02). At birth, SK calves had lower (p < 0.01) levels of non-esterified fatty acids and bilirubin compared to NONKET calves. Analysis of feces alpha diversity indicates that by 3 weeks, NONKET calves had greater diversity, richness, and evenness. Butyricicoccus pullicaecorum and Gallibacterium anatis were more abundant in SK calves (p < 0.05) at 3 weeks. In contrast, NONKET calves had a greater (p < 0.05) abundance of Sharpae azabuensis at 3 weeks. These findings suggest that subclinical ketosis in cows can impact the in-utero development, postnatal growth, and maturing gut microbiome of their offspring.
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Affiliation(s)
- Jessica Halfen
- School of Animal Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Nathaly Ana Carpinelli
- Department of Dairy and Food Science, South Dakota State University, Brookings, SD 57007, USA
| | - Sergio Lasso-Ramirez
- Department of Dairy and Food Science, South Dakota State University, Brookings, SD 57007, USA
- Deparment of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Tainara Cristina Michelotti
- Department of Dairy and Food Science, South Dakota State University, Brookings, SD 57007, USA
- Unité Mixte de Recherche sur les Herbivores, INRAE, F-63122 Saint-Genès-Champanelle, France
| | - Emily C Fowler
- Department of Animal Science, South Dakota State University, Brookings, SD 57007, USA
| | - Benoit St-Pierre
- Department of Animal Science, South Dakota State University, Brookings, SD 57007, USA
| | - Erminio Trevisi
- Department of Animal Sciences, Food and Nutrition (DIANA), Faculty of Agriculture, Food and Environmental Science, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - Johan S Osorio
- School of Animal Science, Virginia Tech, Blacksburg, VA 24061, USA
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Fresno Rueda A, Griffith JE, Kruse C, St-Pierre B. Effects of grain-based diets on the rumen and fecal bacterial communities of the North American bison ( Bison bison). Front Microbiol 2023; 14:1163423. [PMID: 37485522 PMCID: PMC10359189 DOI: 10.3389/fmicb.2023.1163423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/09/2023] [Indexed: 07/25/2023] Open
Abstract
To overcome the challenges of pasture-finishing of bison, producers commonly feed them with higher energy, grain-based diets to reach the desired market weight. However, decades of research on domesticated ruminants have shown that such diets can have profound effects on the composition of gut microbial communities. To gain further insight, the 16S rRNA gene-based study described in this report aimed to compare the composition of ruminal and fecal bacterial communities from two herds of bison heifers (n = 20/herd) raised on different ranches that were both transitioned from native pasture to a grain-based, free-choice diet for ~100 days prior to slaughter. Comparative analyses of operational taxonomic unit (OTU) composition, either by alpha diversity indices, principal coordinate analysis (PCoA), or on the most abundant individual OTUs, showed the dramatic effect of a diet on the composition of both rumen and fecal bacterial communities in bison. Indeed, feeding a grain-based diet resulted in a lower number of rumen and fecal bacterial OTUs, respectively, compared to grazing on pasture (p < 0.05). PCoA revealed that the composition of the rumen and fecal bacterial communities from the two herds was more similar when they were grazing on native pastures compared to when they were fed a grain-based, free-choice diet. Finally, a comparative analysis of the 20 most abundant OTUs from the rumen and fecal communities further showed that the representation of all these species-level bacterial groups differed (p < 0.05) between the two dietary treatments. Together, these results provide further insights into the rumen and fecal microbiomes of grazing bison and their response to grain-based diet regimens commonly used in intensive ruminant production systems.
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Affiliation(s)
- Anlly Fresno Rueda
- Department of Animal Science, South Dakota State University, Brookings, SD, United States
| | - Jason Eric Griffith
- Department of Animal Science, South Dakota State University, Brookings, SD, United States
| | - Carter Kruse
- Department of Animal Science, South Dakota State University, Brookings, SD, United States
- Turner Institute of Ecoagriculture, Bozeman, MT, United States
| | - Benoit St-Pierre
- Department of Animal Science, South Dakota State University, Brookings, SD, United States
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Su Q, Yang C, Chen L, She Y, Xu Q, Zhao J, Liu C, Sun H. Inference of drowning sites using bacterial composition and random forest algorithm. Front Microbiol 2023; 14:1213271. [PMID: 37440892 PMCID: PMC10335767 DOI: 10.3389/fmicb.2023.1213271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 05/26/2023] [Indexed: 07/15/2023] Open
Abstract
Diagnosing the drowning site is a major challenge in forensic practice, particularly when corpses are recovered from flowing rivers. Recently, forensic experts have focused on aquatic microorganisms, including bacteria, which can enter the bloodstream during drowning and may proliferate in corpses. The emergence of 16S ribosomal RNA gene (16S rDNA) amplicon sequencing has provided a new method for analyzing bacterial composition and has facilitated the development of forensic microbiology. We propose that 16S rDNA amplicon sequencing could be a useful tool for inferring drowning sites. Our study found significant differences in bacterial composition in different regions of the Guangzhou section of the Pearl River, which led to differences in bacteria of drowned rabbit lungs at different drowning sites. Using the genus level of bacteria in the lung tissue of drowned rabbits, we constructed a random forest model that accurately predicted the drowning site in a test set with 100% accuracy. Furthermore, we discovered that bacterial species endemic to the water were not always present in the corresponding drowned lung tissue. Our findings demonstrate the potential of a random forest model based on bacterial genus and composition in drowned lung tissues for inferring drowning sites.
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Affiliation(s)
- Qin Su
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Guangzhou Forensic Science Institute, Guangzhou, China
| | - Chengliang Yang
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Ling Chen
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Yiqing She
- Guangzhou Municipal Public Security Bureau, Guangzhou, China
| | - Quyi Xu
- Guangzhou Forensic Science Institute, Guangzhou, China
| | - Jian Zhao
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Guangzhou Forensic Science Institute, Guangzhou, China
| | - Chao Liu
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
- National Anti-Drug Laboratory Guangdong Regional Center, Guangzhou, China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, China
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Guo Y, Wang H, Liu Z, Chang Z. Comprehensive analysis of the microbiome and metabolome in pus from pyogenic liver abscess patients with and without diabetes mellitus. Front Microbiol 2023; 14:1211835. [PMID: 37426007 PMCID: PMC10328747 DOI: 10.3389/fmicb.2023.1211835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 05/31/2023] [Indexed: 07/11/2023] Open
Abstract
Introduction Pyogenic liver abscess (PLA) patients combined with diabetes mellitus (DM) tend to have more severe clinical manifestations than without DM. The mechanism responsible for this phenomenon is not entirely clear. The current study therefore aimed to comprehensively analyze the microbiome composition and metabolome in pus from PLA patients with and without DM, to determine the potential reasons for these differences. Methods Clinical data from 290 PLA patients were collected retrospectively. We analyzed the pus microbiota using 16S rDNA sequencing in 62 PLA patients. In addition, the pus metabolomes of 38 pus samples were characterized by untargeted metabolomics analysis. Correlation analyses of microbiota, metabolites and laboratory findings were performed to identify significant associations. Results PLA patients with DM had more severe clinical manifestations than PLA patients without DM. There were 17 discriminating genera between the two groups at the genus level, among which Klebsiella was the most discriminating taxa. The ABC transporters was the most significant differential metabolic pathway predicted by PICRUSt2. Untargeted metabolomics analysis showed that concentrations of various metabolites were significantly different between the two groups and seven metabolites were enriched in the ABC transporters pathway. Phosphoric acid, taurine, and orthophosphate in the ABC transporters pathway were negatively correlated with the relative abundance of Klebsiella and the blood glucose level. Discussion The results showed that the relative abundance of Klebsiella in the pus cavity of PLA patients with DM was higher than those without DM, accompanied by changes of various metabolites and metabolic pathways, which may be associated with more severe clinical manifestations.
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Fowler EC, Samuel RS, St-Pierre B. A Comparative Analysis of the Fecal Bacterial Communities of Light and Heavy Finishing Barrows Raised in a Commercial Swine Production Environment. Pathogens 2023; 12:pathogens12050738. [PMID: 37242408 DOI: 10.3390/pathogens12050738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
For commercial swine producers, the natural variation in body weight amongst pigs in a herd presents a challenge in meeting the standards of meat processors who incentivize target carcass weights by offering more favorable purchase prices. Body weight variation in a swine herd is evident as early as birth, and it is typically maintained throughout the entire production cycle. Amongst the various factors that can affect growth performance, the gut microbiome has emerged as an important factor that can affect efficiency, as it contributes to vital functions such as providing assimilable nutrients from feed ingredients that are inedible to the host, as well as resistance to infection by a pathogen. In this context, the objective of the study described in this report was to compare the fecal microbiomes of light and heavy barrows (castrated male finishing pigs) that were part of the same research herd that was raised under commercial conditions. Using high-throughput sequencing of amplicons generated from the V1-V3 regions of the 16S rRNA gene, two abundant candidate bacterial species identified as operational taxonomic units (OTUs), Ssd-1085 and Ssd-1144, were found to be in higher abundance in the light barrows group. Ssd-1085 was predicted to be a potential strain of Clostridium jeddahitimonense, a bacterial species capable of utilizing tagatose, a monosaccharide known to act as a prebiotic that can enhance the proliferation of beneficial microorganisms while inhibiting the growth of bacterial pathogens. OTU Ssd-1144 was identified as a candidate strain of C. beijerinckii, which would be expected to function as a starch utilizing symbiont in the swine gut. While it remains to be determined why putative strains of these beneficial bacterial species would be in higher abundance in lower weight pigs, their overall high levels in finishing pigs could be the result of including ingredients such as corn and soybean-based products in swine diets. Another contribution from this study was the determination that these two OTUs, along with five others that were also abundant in the fecal bacterial communities of the barrows that were analyzed, had been previously identified in weaned pigs, suggesting that these OTUs can become established as early as the nursery phase.
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Affiliation(s)
- Emily C Fowler
- Department of Animal Science, South Dakota State University, Animal Science Complex, Box 2170, Brookings, SD 57007, USA
| | - Ryan S Samuel
- Department of Animal Science, South Dakota State University, Animal Science Complex, Box 2170, Brookings, SD 57007, USA
| | - Benoit St-Pierre
- Department of Animal Science, South Dakota State University, Animal Science Complex, Box 2170, Brookings, SD 57007, USA
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Díaz-Regañón D, García-Sancho M, Villaescusa A, Sainz Á, Agulla B, Reyes-Prieto M, Rodríguez-Bertos A, Rodríguez-Franco F. Characterization of the Fecal and Mucosa-Associated Microbiota in Dogs with Chronic Inflammatory Enteropathy. Animals (Basel) 2023; 13. [PMID: 36766216 DOI: 10.3390/ani13030326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 01/18/2023] Open
Abstract
Canine chronic inflammatory enteropathy implicates multifactorial pathogenesis where immunological dysregulation and gut microbiota changes have a central role. Most sequencing-based taxonomic studies have been focused on the fecal microbiota. However, the analysis of these samples does not provide complete information regarding the composition of the small intestine affected by this canine disease. Therefore, in this study, we aimed to characterize the intestinal bacterial microbiota in dogs with inflammatory bowel disease (IBD) (n = 34) by means of duodenal biopsies and fecal samples collected at the time of the diagnosis and to compare those to a group of healthy dogs (n = 12) using the 16S ribosomal RNA (16S rRNA) gene-targeted sequencing (Illumina MiSeq platform). Our study showed that IBD dogs presented differences in the fecal bacterial communities when compared with healthy dogs, with a lower relative abundance of Prevotellaceae (p = 0.005), Prevotella (p = 0.002), and Prevotellaceae Ga6A1 group (0.006); Erysipelotrichales (p = 0.019), Candidatus Stoquefichus (p < 0.001), Erysipelotrichaceae (p = 0.011), and Allobaculum (p = 0.003); Lachnospiraceae NK4A136 group (p = 0.015), Sellimonas (p = 0.042), Oscillospirales (p = 0.037), Oscillospiraceae UCG-005 (p < 0.001), Faecalibacterium (p = 0.028), and Fournierella (p = 0.034); Acidaminococcales, Acidaminococcaceae, and Phascolarctobacterium (p = 0.001); Aeromonadales (p = 0.026), Succinivibrionaceae (p = 0.037), and Succinivibrio (p = 0.031). On the other hand, a higher relative abundance of Enterococcaceae (Enterococcus; p = 0.003), Streptococcaceae (Streptococcus, p = 0.021), Enterobacterales (p = 0.027), Enterobacteriaceae (p = 0.008), and Escherichia-Shigella (p = 0.011) was detected. Moreover, when evaluating α-diversity, the dogs with IBD showed lower diversity in terms of richness and abundance of species (observed species [p = 0.031] and Shannon index [p = 0.039]). Furthermore, fecal microbiota in dogs with IBD was significantly different from healthy dogs (p = 0.006). However, only a few taxa relative abundance shifts (lower Rubrobacteria, Rubrobacterales, Rubrobacteriaceae, and Rubrobacter [p = 0.002]; Cyanobacteria [p = 0.010], Vampirivibrionia, Obscuribacterales, and Obscuribacteraceae [p = 0.005]; Neisseriaceae [p = 0.004] and Conchiformibius [p = 0.003]) were observed when assessing duodenal-associated microbiota of dogs with IBD. Thus, even if the bowel inflammation mainly affects the small intestine in the IBD-affected dogs of the study, fecal specimens may constitute a better sample due not only to their easy availability but also in terms of searching for bacterial taxa as biomarkers for canine IBD. The use of different diets in the study can also have a partial influence on the microbiota composition. Future studies encompassing multi-omics approaches should evaluate the functionality in both levels to unravel the pathophysiology of canine IBD.
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Qin LG, Li XA, Huang YX, Li YJ, Chen Q. Flavour Profile of Traditional Dry Sausage Prepared with Partial Substitution of NaCl with KCl. Foods 2023; 12:foods12020388. [PMID: 36673479 PMCID: PMC9858023 DOI: 10.3390/foods12020388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 01/18/2023] Open
Abstract
The effects of partial substitution of NaCl with 0%, 20%, 30% and 40% KCl on the physical characteristics, bacterial community and flavour profile of traditional dry sausage were investigated in this study. With the increase in KCl substitution ratio, the moisture content, astringency, bitterness and umami increased significantly, and the saltiness gradually decreased (p < 0.05). The high-throughput sequencing results showed that the dry sausages with KCl substitution had relatively high abundances of Staphylococcus. For volatile compounds, increasing the KCl substitution ratio reduced the formation of aldehydes, ketones and some alcohols, but promoted the formation of acids and esters (p < 0.05). Sensory evaluation and partial least square regression analysis showed that the dry sausages with 20% and 30% KCl were similar in overall physical and microbial properties, flavour profiles and sensory attributes, and the sausages with 40% KCl were characterized by taste defects. Overall, partial substitution of NaCl with 30% KCl could ensure the acceptable flavour and sensory attributes of dry sausages.
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Affiliation(s)
- Li-Gang Qin
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Xiang-Ao Li
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Yu-Xiang Huang
- Branch of Animal Husbandry and Veterinary of Heilongjiang Academy of Agricultural Sciences, Qiqihar 161005, China
| | - Yong-Jie Li
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Qian Chen
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
- Correspondence: ; Tel.: +86-451-55191794
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Xia Y, Eerdun B, Wang J, Li Y, Shuang Q, Chen Y. Variation and Correlation Analysis of Flavour and Bacterial Diversity of Low-Salt Hotpot Sauce during Storage. Foods 2023; 12:foods12020333. [PMID: 36673425 PMCID: PMC9857581 DOI: 10.3390/foods12020333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/01/2023] [Accepted: 01/05/2023] [Indexed: 01/13/2023] Open
Abstract
Culinary circles have experienced a recent trend towards low-salt hotpot sauces. Here, changes in the physicochemical quality, flavour, and bacterial diversity of hotpot sauces with different salt concentrations were studied during storage. The results indicated that the peroxide and acid values of hotpot sauce increased gradually and that the quality began to deteriorate with storage. A storage temperature of 4 °C and salt concentration above 4.4% significantly reduced spoilage. The salt concentration had no significant effect on the flavour but extended storage resulted in significant differences in flavour reflected in the changes of sweet, sour, bitter, umami, aftertaste-A, abundance, organic sulphide, and alkanes. Significant differences were found in the bacterial composition between samples stored at different temperatures. Norank-f-o-Chloroplast was the main bacterium in the samples stored at low temperatures, which was beneficial for preservation. Bacillus was detected in 4.1% NaCl samples stored at 25 °C, directly promoting sauce spoilage and an unpleasant flavour. This bacterium signalled the spoilage of low-salt hotpot sauce stored at room temperature.
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Affiliation(s)
- Yanan Xia
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Ministry of Education, Hohhot 010018, China
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Bayaer Eerdun
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Junlin Wang
- Inner Mongolia Red Sun Food Co., Ltd., Hohhot 010020, China
| | - Yankai Li
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Quan Shuang
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Yongfu Chen
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Ministry of Education, Hohhot 010018, China
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
- Correspondence: ; Tel.: +86-180-4712-4962
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Kim J, Kim E, Kim B, Kim J, Lee HJ, Park JS, Hwang S, Rho M, Pai H. Different maturation of gut microbiome in Korean children. Front Microbiol 2022; 13:1036533. [PMID: 36504822 PMCID: PMC9726757 DOI: 10.3389/fmicb.2022.1036533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 11/04/2022] [Indexed: 11/24/2022] Open
Abstract
Introduction Gut microbiome plays a crucial role in maintaining human health and is influenced by food intake, age, and other factors. Methods In this study based in Korea, we examined the bacterial taxonomic composition of the gut microbiota in infants (≤ 1 year), toddlers (1-<4 years), and school-aged children (4-13 years) and compared them with those of healthy adults to investigate the microbiota changes in early life and their association with the resistome. We used whole metagenome sequences obtained by Illumina HiSeq sequencing and clinical information of 53 healthy children, and sequence data of 61 adults from our previous study. Results Our results indicate that the bacterial proportion of the gut in the population ranging from infants to adults forms three clusters: the Ruminococcus-Eubacterium (G1), Bifidobacterium-Escherichia (G2), and Bacteroides-Faecalibacterium (G3) groups. The gut microbiota of infants and toddlers (100% of infants and 85% of toddlers) constituted mostly of G2 and G3 groups, whereas 90% of adults showed G1-type gut microbiota. School-aged children showed a transitional gut microbiota composition of both infants and adults (31%, 38%, and 31% in G1, G2, and G3, respectively). Notably, the three clusters of microbiota showed significantly different patterns of bacterial diversity (p < 0.001): G2 showed the lowest Shannon index, followed by G3 and G1 (1.41, 2.08, and 2.48, respectively; median Shannon index). When combined with the adult group, alpha diversity showed a positive correlation with age (R2 = 0.3). Furthermore, clustering the composition of antibiotic resistance genes (ARG) identified two clusters (A1 and A2), and most of G1 (95%) and G3 (80%) belonged to A1. However, G2 showed the least diversity and the highest abundance of ARGs. Nine ARG families showed a significant difference among age groups; three tetracycline resistance genes, tet32, tetO, and tetW, showed a positive correlation, and six other genes, ampC, TEM, ileS, bacA, pmr transferase, and cepA, showed a negative correlation with age. Discussion In conclusion, our results highlighted that a delayed persistence of the Bifidobacterium-dominant enterotype with a lower bacterial diversity was observed in Korean children up to 13 years of age, which suggests a different maturation process with a delayed maturation time.
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Affiliation(s)
- Jieun Kim
- Department of Internal Medicine, College of Medicine, Hanyang University, Seoul, South Korea
| | - Erin Kim
- Department of Computer Science and Engineering, Hanyang University, Seoul, South Korea
| | - Bongyoung Kim
- Department of Internal Medicine, College of Medicine, Hanyang University, Seoul, South Korea
| | - Jinsup Kim
- Department of Clinical Development, Novel Pharma Inc., Seoul, South Korea
| | - Hyun Ju Lee
- Department of Pediatrics, College of Medicine, Hanyang University, Seoul, South Korea
| | - Jun-Sun Park
- Translational Research Center, Research Institute of Public Health, National Medical Center, Seoul, Republic of Korea
| | - Sehee Hwang
- Cancer Information Center, Yonsei University Health System, Yonsei Cancer Center, Seoul, South Korea,Sehee Hwang,
| | - Mina Rho
- Department of Computer Science and Engineering, Hanyang University, Seoul, South Korea,Department of Biomedical Informatics, Hanyang University, Seoul, South Korea,Mina Rho,
| | - Hyunjoo Pai
- Department of Internal Medicine, College of Medicine, Hanyang University, Seoul, South Korea,*Correspondence: Hyunjoo Pai,
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Kinga H, Kengne-Ouafo JA, King SA, Egyirifa RK, Aboagye-Antwi F, Akorli J. Water Physicochemical Parameters and Microbial Composition Distinguish Anopheles and Culex Mosquito Breeding Sites: Potential as Ecological Markers for Larval Source Surveillance. J Med Entomol 2022; 59:1817-1826. [PMID: 35920087 DOI: 10.1093/jme/tjac115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Indexed: 05/19/2023]
Abstract
The presence of mosquitoes in an area is dependent on the availability of suitable breeding sites that are influenced by several environmental factors. Identification of breeding habitats for vector surveillance and larval source management is key to disease control programs. We investigated water quality parameters and microbial composition in selected mosquito breeding sites in urban Accra, Ghana and associated these with abundance of Anopheles (Diptera: Culicidae) and Culex (Diptera: Culicidae) larvae. Physicochemical parameters and microbial composition explained up to 72% variance among the breeding sites and separated Anopheles and Culex habitats (P < 0.05). Anopheles and Culex abundances were commonly influenced by water temperature, pH, nitrate, and total hardness with contrasting impacts on the two mosquito species. In addition, total dissolved solids, biochemical oxygen demand, and alkalinity uniquely influenced Anopheles abundance, while total suspended solids, phosphate, sulphate, ammonium, and salinity were significant determinants for Culex. The correlation of these multiple parameters with the occurrence of each mosquito species was high (R2 = 0.99, P < 0.0001). Bacterial content assessment of the breeding ponds revealed that the most abundant bacterial phyla were Patescibacteria, Cyanobacteria, and Proteobacteria, constituting >70% of the total bacterial richness. The oligotrophic Patescibacteria was strongly associated with Anopheles suggestive of the mosquito's adaptation to environments with less nutrients, while predominance of Cyanobacteria, indicative of rich nutritional source was associated with Culex larval ponds. We propose further evaluation of these significant abiotic and biotic parameters in field identification of larval sources and how knowledge of these can be harnessed effectively to reduce conducive breeding sites for mosquitoes.
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Affiliation(s)
- Harriet Kinga
- African Regional Postgraduate Program in Insect Science, University of Ghana, Legon, Ghana
| | - Jonas A Kengne-Ouafo
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana
- Medical Entomology Department, Centre of Research in Infectious Diseases (CRID), Yaounde, Cameroon
| | - Sandra A King
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Richardson K Egyirifa
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Fred Aboagye-Antwi
- African Regional Postgraduate Program in Insect Science, University of Ghana, Legon, Ghana
- Department of Animal Biology and Conservation Sciences, University of Ghana, Legon, Ghana
| | - Jewelna Akorli
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
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Marcondes MA, Nascimento A, Pessôa R, Victor JR, Duarte AJDS, Clissa PB, Sanabani SS. Characterization of Bacterial Communities from the Surface and Adjacent Bottom Layers of Water in the Billings Reservoir. Life (Basel) 2022; 12:1280. [PMID: 36013459 DOI: 10.3390/life12081280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/04/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022]
Abstract
Here, we describe the bacterial diversity and physicochemical properties in freshwater samples from the surface and bottom layers of the Billings Reservoir, the largest open-air storage ecosystem in the São Paulo (Brazil) metropolitan area. Forty-four samples (22 from the surface and 22 from the bottom layers) were characterized based on 16S rRNA gene analysis using Illumina MiSeq. Taxonomical composition revealed an abundance of the Cyanobacteria phylum, followed by Proteobacteria, which were grouped into 1903 and 2689 different genera in the surface and the deep-water layers, respectively. Chroobacteria, Actinobacteria, Betaproteobacteria, and Alphaproteobacteria were the most dominant classes. The Shannon diversity index was in the range of 2.3–5.39 and 4.04–6.86 in the surface and bottom layers, respectively. Flavobacterium was the most predominant pathogenic genus. Temperature and phosphorus concentrations were among the most influential factors in shaping the microbial communities of both layers. Predictive functional analysis suggests that the reservoir is enriched in motility genes involved in flagellar assembly. The overall results provide new information on the diversity composition, ecological function, and health risks of the bacterial community detected in the Billings freshwater reservoir. The broad bacterial diversity indicates that the bacterioplankton communities in the reservoir were involved in multiple essential environmental processes.
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15
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Kursa O, Tomczyk G, Adamska K, Chrzanowska J, Sawicka-Durkalec A. The Microbial Community of the Respiratory Tract of Commercial Chickens and Turkeys. Microorganisms 2022; 10:987. [PMID: 35630431 PMCID: PMC9147466 DOI: 10.3390/microorganisms10050987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/28/2022] [Accepted: 05/05/2022] [Indexed: 12/10/2022] Open
Abstract
Respiratory tract health critically affects the performance of commercial poultry. This report presents data on the microbial community in these organs from a comprehensive study of laying chickens and turkey breeders. The main objective was to characterize and compare the compositions of the respiratory system bacteria isolated from birds of different ages and geographical locations in Poland. Using samples from 28 turkey and 26 chicken flocks, the microbial community was determined by 16S ribosomal RNA sequencing. There was great variability between flocks. The diversity and abundance of upper respiratory tract (URT) bacteria was greater in chickens than in turkeys. At the phyla level, the URT of the chickens was heavily colonized by Proteobacteria, which represented 66.4% of the total microbiota, while in turkeys, this phylum constituted 42.6% of all bacteria. Firmicutes bacteria were more abundant in turkeys (43.2%) than in chickens (24.1%). The comparison of the respiratory tracts at the family and genus levels showed the diversity and abundance of amplicon sequence variants (ASV) differing markedly between the species. Potentially pathogenic bacteria ASV were identified in the respiratory tract, which are not always associated with clinical signs, but may affect bird productivity and performance. The data obtained, including characterization of the bacterial composition found in the respiratory system, may be useful for developing effective interventions strategies to improve production performance and prevent and control disease in commercial laying chickens and turkeys.
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Affiliation(s)
- Olimpia Kursa
- Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantów 57, 24-100 Puławy, Poland; (G.T.); (K.A.); (A.S.-D.)
| | - Grzegorz Tomczyk
- Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantów 57, 24-100 Puławy, Poland; (G.T.); (K.A.); (A.S.-D.)
| | - Karolina Adamska
- Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantów 57, 24-100 Puławy, Poland; (G.T.); (K.A.); (A.S.-D.)
| | | | - Anna Sawicka-Durkalec
- Department of Poultry Diseases, National Veterinary Research Institute, Al. Partyzantów 57, 24-100 Puławy, Poland; (G.T.); (K.A.); (A.S.-D.)
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Wang F, Li Z, Fu B, Lü Y, Liu G, Wang D, Wu X. Short-Term Grazing Exclusion Alters Soil Bacterial Co-occurrence Patterns Rather Than Community Diversity or Composition in Temperate Grasslands. Front Microbiol 2022; 13:824192. [PMID: 35422777 PMCID: PMC9005194 DOI: 10.3389/fmicb.2022.824192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/31/2022] [Indexed: 11/30/2022] Open
Abstract
Grazing exclusion is one of the most common practices for degraded grassland restoration worldwide. Soil microorganisms are critical components in soil and play important roles in maintaining grassland ecosystem functions. However, the changes of soil bacterial community characteristics during grazing exclusion for different types of grassland remain unclear. In this study, the soil bacterial community diversity and composition as well as the co-occurrence patterns were investigated and compared between grazing exclusion (4 years) and the paired adjacent grazing sites for three types of temperate grasslands (desert steppe, typical steppe, and meadow steppe) in the Hulunbuir grassland of Inner Mongolia. Our results showed that short-term grazing exclusion decreased the complexity and connectivity of bacterial co-occurrence patterns while increasing the network modules in three types of temperate grasslands. The effects of grazing exclusion on soil bacterial α-diversity and composition were not significant in typical steppe and meadow steppe. However, short-term grazing exclusion significantly altered the community composition in desert steppe, indicating that the soil bacteria communities in desert steppe could respond faster than those in other two types of steppes. In addition, the composition of bacterial community is predominantly affected by soil chemical properties, such as soil total carbon and pH, instead of spatial distance. These results indicated that short-term grazing exclusion altered the soil bacterial co-occurrence patterns rather than community diversity or composition in three types of temperate grasslands. Moreover, our study suggested that soil bacterial co-occurrence patterns were more sensitive to grazing exclusion, and the restoration of soil bacterial community might need a long term (>4 years) in our study area.
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Affiliation(s)
- Fangfang Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Zongming Li
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Agro-Ecological Processes in Subtropical Region and Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Bojie Fu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Yihe Lü
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Guoping Liu
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Dongbo Wang
- Hulunbuir Eco-environmental Monitoring Center of Inner Mongolia, Hulunbuir, China
| | - Xing Wu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
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Kong F, Liu Y, Wang S, Zhang Y, Wang W, Yang H, Lu N, Li S. Nutrient Digestibility, Microbial Fermentation, and Response in Bacterial Composition to Methionine Dipeptide: An In Vitro Study. Biology (Basel) 2022; 11:biology11010093. [PMID: 35053091 PMCID: PMC8772947 DOI: 10.3390/biology11010093] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 11/20/2022]
Abstract
Simple Summary The rumen microbiota plays an important role in maintaining microbiota homeostasis and promoting milk production synthesis through utilizing amino acids and non-protein nitrogen. Furthermore, various nitrogen sources have shown distinct effects on microbial growth rates. The methionine dipeptide (MD) is a bioactive peptide consisting of two methionine (Met) residues linked by a peptide bond. Although the role of MD in milk protein synthesis is established, little is known about its role in bacterial fermentation. The present study demonstrates that the various nitrogen sources could reshape microbiota differently, and MD could be more efficient than free Met in the rumen to support acetate producer growth. Our study provides some new insights into the relationship between ruminal microbiota of dairy cows and small peptides and points to potential strategies to effectively enhance the health condition and digestion ability of dairy cows. Abstract It is well known that the methionine dipeptide (MD) could enhance the dairy cows milking performance. However, there is still a knowledge gap of the effects of MD on the rumen fermentation characteristics, microbiota composition, and digestibility. This experiment was conducted to determine the effect of different nitrogen sources with a total mixed ration on in vitro nutrient digestibility, fermentation characteristics, and bacterial composition. The treatments included 5 mg urea (UR), 25.08 mg methionine (Met), 23.57 mg MD, and no additive (CON) in fermentation culture medium composed of buffer solution, filtrated Holstein dairy cow rumen fluid, and substrate (1 g total mixed ration). Nutrient digestibility was measured after 24 h and 48 h fermentation, and fermentation parameters and microbial composition were measured after 48 h fermentation. Digestibility of dry matter, crude protein, neutral detergent fiber (NDF), and acid detergent fiber (ADF) in the MD group at 48 h were significantly higher than in the CON and UR groups. The total volatile fatty acid concentration was higher in the MD group than in the other groups. In addition, 16S rRNA microbial sequencing results showed MD significantly improved the relative abundances of Succinivibrio, Anaerotruncus, and Treponema_2, whereas there was no significant difference between Met and UR groups. Spearman’s correlation analysis showed the relative abundance of Succinivibrio and Anaerotruncus were positively correlated with gas production, NDF digestibility, ADF digestibility, and acetate, propionate, butyrate, and total volatile fatty acid concentrations. Overall, our results suggested that the microbiota in the fermentation system could be affected by additional nitrogen supplementation and MD could effectively enhance the nutrient utilization in dairy cows.
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Affiliation(s)
- Fanlin Kong
- The State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (F.K.); (S.W.); (W.W.); (H.Y.)
| | - Yanfang Liu
- Beijing Jingwa Agricultural Science & Technology Innovation Center, Beijing 100193, China;
| | - Shuo Wang
- The State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (F.K.); (S.W.); (W.W.); (H.Y.)
| | - Yijia Zhang
- Laboratory of Anatomy of Domestic Animals, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China;
| | - Wei Wang
- The State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (F.K.); (S.W.); (W.W.); (H.Y.)
| | - Hongjian Yang
- The State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (F.K.); (S.W.); (W.W.); (H.Y.)
| | - Na Lu
- Beijing Jingwa Agricultural Science & Technology Innovation Center, Beijing 100193, China;
- Correspondence: (N.L.); (S.L.); Tel.: +86-10-62731254 (S.L.)
| | - Shengli Li
- The State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (F.K.); (S.W.); (W.W.); (H.Y.)
- Correspondence: (N.L.); (S.L.); Tel.: +86-10-62731254 (S.L.)
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Laviad-Shitrit S, Sela R, Sharaby Y, Thorat L, Nath BB, Halpern M. Comparative Microbiota Composition Across Developmental Stages of Natural and Laboratory-Reared Chironomus circumdatus Populations From India. Front Microbiol 2021; 12:746830. [PMID: 34899634 PMCID: PMC8661057 DOI: 10.3389/fmicb.2021.746830] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/26/2021] [Indexed: 01/04/2023] Open
Abstract
Chironomids are aquatic insects that undergo a complete metamorphosis of four life stages. Here we studied, for the first time, the microbiota composition of Chironomus circumdatus, a tropical midge species, both from the Mula and Mutha Rivers in Pune, India and as a laboratory-reared culture. We generated a comparative microbial profile of the eggs, larvae and pupae, the three aquatic life stages of C. circumdatus. Non-metric multidimensional scaling analysis (NMDS) demonstrated that the developmental stage had a more prominent effect on the microbiota composition compared to the sampling location. Notably, the microbiota composition of the egg masses from the different sampling points clustered together and differed from laboratory culture larvae. Proteobacteria was the dominant phylum in all the environmental and laboratory-reared egg masses and pupal samples, and in the laboratory-reared larvae, while Fusobacteria was the dominant phylum in the larvae collected from the field environment. The most abundant genera were Cetobacterium, Aeromonas, Dysgonomonas, Vibrio, and Flavobacterium. The ten amplicon sequence variants (ASVs) that most significantly contributed to differences in microbiota composition between the three sampled locations were: Burkholderiaceae (ASVs 04 and 37), C39 (Rhodocyclaceae, ASV 14), Vibrio (ASV 07), Arcobacter (ASV 21), Sphaerotilus (ASV 22), Bacteroidia (ASVs 12 and 28), Flavobacterium (ASV 29), and Gottschalkia (ASV 10). No significant differences were found in the microbial richness (Chao1) or diversity (Shannon H’) of the three sampled locations. In contrast, significant differences were found between the microbial richness of the three life stages. Studying the microbiota of this Chironomus species may contribute to a better understanding of the association of C. circumdatus and its microbial inhabitants.
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Affiliation(s)
- Sivan Laviad-Shitrit
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
| | - Rotem Sela
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
| | - Yehonatan Sharaby
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
| | - Leena Thorat
- Department of Zoology, Savitribai Phule Pune University, Pune, India.,Department of Biology, York University, Toronto, ON, Canada
| | - Bimalendu B Nath
- Department of Zoology, Savitribai Phule Pune University, Pune, India
| | - Malka Halpern
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel.,Department of Biology and Environment, University of Haifa, Haifa, Israel
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Chen B, Tang G, Guo W, Lei J, Yao J, Xu X. Detection of the Core Bacteria in Colostrum and Their Association with the Rectal Microbiota and with Milk Composition in Two Dairy Cow Farms. Animals (Basel) 2021; 11:3363. [PMID: 34944139 DOI: 10.3390/ani11123363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/27/2021] [Accepted: 11/09/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary In order to provide information on developing probiotics for newborn calves, this research detected the bacterial composition in colostrum and rectal feces of healthy Holstein cows from two dairy farms. Our results found several core bacterial species and some core genus and families in colostrum. About half of the OTUs detected in colostrum were found in the rectal content including some strictly anaerobic bacteria. In addition, some well-known intestinal beneficial bacteria including Lactobacillus plantarum and Bacillus subtilis were present in cow colostrum. Our results confirm that colostrum provides intestinal probiotics for calves. Furthermore, we might be able to develop new probiotics for calves according to the core symbiotic genus or families in colostrum. Abstract As one of the pioneer bacterial sources of intestinal microbiota, the information of bacterial composition in colostrum might provide a reference for developing specific probiotics for newborn calves, especially calves fed with pasteurized milk. The present study aimed to detect the core bacteria at different taxonomic levels and the common beneficial ones in colostrum by analyzing the bacterial composition in 34 colostrum samples of healthy cows selected from two dairy farms. The results of the further analysis showed that the bacterial composition in the colostrum of the two dairy farms was different, but their four most dominant phyla were the same including Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. The microbiome of all colostrum samples shared ten core operational taxonomic units (OTUs), 21 core genera, and 34 core families, and most of them had no difference in relative abundance between the two farms. The ten core OTUs did not belong to the identified commensal bacteria and have not been detected by previous study. However, several core genera found in our study were also identified as core genus in a previous study. Some well-known beneficial and pathogenic bacteria including Lactobacillus plantarum, Bacillus subtilis, Acinetobacter lwoffii, and Streptococcus pneumoniae were present in the colostrum of healthy cows. However, none had a correlation with the number of somatic cell count (SCC), but the core genera Nubella and Brevundinimas and the core families Methylobacteriaceae and Caulobacteraceae positively correlated with the number of SCC. The genus Staphylococcus, Pseudomonas, and Chryseobacterium in colostrum had a positive correlation with each other, while the probiotics unidentified-Bacteroidales-S24-7-group had a negative correlation with Pseudomonas and Chryseobacterium. In addition, more than 50% bacterial OTUs in colostrum were detected in the rectal content including some strictly anaerobic bacteria that are generally present in the intestine and rumen. However, of the top 30 commonly shared bacterial genera in the colostrum and rectal feces, no genus in colostrum was positively correlated with that same genus in rectal feces. In conclusion, the bacterial composition of colostrum microbiota is greatly influenced by external factors and individuals. There were several core OTUs, and some core genus and families in the colostrum samples. Colostrum from healthy cows contained both beneficial and pathogenic bacteria and shared many common bacteria with rectal content including some gastrointestinal anaerobes.
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20
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Oost MJ, Velkers FC, Kraneveld AD, Venema K. Development of the in vitro Cecal Chicken ALIMEntary tRact mOdel-2 to Study Microbiota Composition and Function. Front Microbiol 2021; 12:726447. [PMID: 34707583 PMCID: PMC8542841 DOI: 10.3389/fmicb.2021.726447] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/16/2021] [Indexed: 01/04/2023] Open
Abstract
The digestive system of the chicken plays an important role in metabolism, immunity, and chicken health and production performance. The chicken ceca harbor a diverse microbial community and play a crucial role in the microbial fermentation and production of energy-rich short-chain fatty acids (SCFA). For humans, dogs, and piglets in vitro digestive system models have been developed and are used to study the microbiota composition and metabolism after intervention studies. For chickens, most research on the cecal microbiota has been performed in in vivo experiments or in static in vitro models that may not accurately resemble the in vivo situations. This paper introduces an optimized digestive system model that simulates the conditions in the ceca of the chicken, i.e., the Chicken ALIMEntary tRact mOdel-2 (CALIMERO-2). The system is based on the well-validated TNO in vitro model of the colon-2 (TIM-2) and is the first dynamic in vitro digestion model for chickens species. To validate this model, the pH, temperature, and different types of microbial feeding were compared and analyzed, to best mimic the conditions in the chicken ceca. The bacterial composition, as well as the metabolite production at 72 h, showed no significant difference between the different microbial feedings. Moreover, we compared the CALIMERO-2 digestive samples to the original inoculum and found some significant shifts in bacterial composition after the fermentation started. Over time the bacterial diversity increased and became more similar to the original inoculum. We can conclude that CALIMERO-2 is reproducible and can be used as a digestive system model for the chicken ceca, in which the microbial composition and activity can be maintained and shows similar results to the in vivo cecum. CALIMERO-2 can be used to study effects on composition and activity of the chicken cecum microbiota in response to in-feed interventions.
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Affiliation(s)
- Miriam J Oost
- Centre for Healthy Eating and Food Innovation, Faculty of Science and Engineering, Maastricht University-Campus Venlo, Venlo, Netherlands.,Division Farm Animal Health, Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Francisca C Velkers
- Division Farm Animal Health, Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Aletta D Kraneveld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Koen Venema
- Centre for Healthy Eating and Food Innovation, Department of Human Biology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Venlo, Netherlands
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21
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Huang T, Liu W, Long XE, Jia Y, Wang X, Chen Y. Different Responses of Soil Bacterial Communities to Nitrogen Addition in Moss Crust. Front Microbiol 2021; 12:665975. [PMID: 34566900 PMCID: PMC8460773 DOI: 10.3389/fmicb.2021.665975] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 08/16/2021] [Indexed: 11/21/2022] Open
Abstract
Bacterial communities in soil serve an important role in controlling terrestrial biogeochemical cycles and ecosystem processes. Increased nitrogen (N) deposition in Northwest China is generating quantifiable changes in many elements of the desert environment, but the impacts of N deposition, as well as seasonal variations, on soil bacterial community composition and structure are poorly understood. We used high-throughput sequencing of bacterial 16S rRNA genes from Gurbantünggüt Desert moss crust soils to study the impacts of N addition on soil bacterial communities in March, May, and November. In November, we discovered that the OTU richness and diversity of soil bacterial community dropped linearly with increasing N input. In November and March, the diversity of the soil bacterial community decreased significantly in the medium-N and high-N treatments. In May, N addition caused a substantial change in the makeup of the soil bacterial composition, while the impacts were far less apparent in November and March. Furthermore, the relative abundance of major bacterial phyla reacted non-linearly to N addition, with high-N additions decreasing the relative richness of Proteobacteria, Bacteroidetes, and Acidobacteria while increasing the relative abundance of Actinobacteria and Chloroflexi. We also discovered that seasonality, as characterized by changes in soil moisture, pH, SOC, and AK content, had a significant impact on soil bacterial communities. Significant variations in the makeup of the community were discovered at the phylum and genus levels throughout the various months. In May, the variety of soil bacterial community was at its peak. Further investigation showed that the decrease in soil bacterial diversity was mostly attributed to a drop in soil pH. These results indicated that the impact of N deposition on the soil bacterial community was seasonally dependent, suggesting that future research should evaluate more than one sample season at the same time.
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Affiliation(s)
- Tingwen Huang
- Ministry of Education, Key Laboratory of Oasis Ecology, College of Resources and Environment Science, Xinjiang University, Urumqi, China
| | - Weiguo Liu
- Ministry of Education, Key Laboratory of Oasis Ecology, College of Resources and Environment Science, Xinjiang University, Urumqi, China
| | - Xi-En Long
- School of Geographic Sciences, Nantong University, Nantong, China
| | - Yangyang Jia
- Ministry of Education, Key Laboratory of Oasis Ecology, College of Resources and Environment Science, Xinjiang University, Urumqi, China
| | - Xiyuan Wang
- Ministry of Education, Key Laboratory of Oasis Ecology, College of Resources and Environment Science, Xinjiang University, Urumqi, China
| | - Yinguang Chen
- College of Environmental Science and Engineering, Tongji University, Shanghai, China
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22
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Shiba T, Watanabe T, Komatsu K, Koyanagi T, Nemoto T, Ohsugi Y, Michi Y, Katagiri S, Takeuchi Y, Ishihara K, Iwata T. Non-surgical treatment for periodontitis and peri-implantitis: longitudinal clinical and bacteriological findings-A case report with a 7-year follow-up evaluation. SAGE Open Med Case Rep 2021; 9:2050313X211029154. [PMID: 34285805 PMCID: PMC8261847 DOI: 10.1177/2050313x211029154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 06/11/2021] [Indexed: 12/12/2022] Open
Abstract
The aim of this report is to show that periodontitis and peri-implantitis with horizontal bone resorption in a 68-year-old male patient were successfully treated by non-surgical treatment. Scaling with an ultrasonic device was performed for moderate periodontitis around the mandibular left first premolar and moderate peri-implantitis around the maxillary right molar implants. Root planing with a metal curette was performed for the periodontal site, and debridement with a plastic curette was performed for the peri-implant site. A month after treatment, probing depth decreased from 5 to 2 mm at the periodontal site and 8 to 3 mm at the peri-implant site. The investigation of bacterial composition by sequencing the 16S rRNA gene amplicons showed that the composition similarly changed at both sites, 5 years after treatment; the change reflected the typical recovery of periodontitis. The clinical condition was maintained for 7 years after treatment at both sites. This was a successful case of non-surgical treatment for peri-implantitis with horizontal bone resorption, promoting recovery of the microbiota from dysbiotic shift.
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Affiliation(s)
- Takahiko Shiba
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takayasu Watanabe
- Department of Chemistry, Nihon University School of Dentistry, Tokyo, Japan
| | - Keiji Komatsu
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tatsuro Koyanagi
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takashi Nemoto
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yujin Ohsugi
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yasuyuki Michi
- Department of Oral and Maxillofacial Surgery, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Sayaka Katagiri
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yasuo Takeuchi
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Takanori Iwata
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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23
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Shimogishi M, Watanabe T, Shibasaki M, Shiba T, Komatsu K, Nemoto T, Ishihara K, Nakano Y, Iwata T, Kasugai S, Nakagawa I. Patient-specific establishment of bacterial composition within the peri-implant microbiota during the earliest weeks after implant uncovering. J Periodontal Res 2021; 56:964-971. [PMID: 34057208 DOI: 10.1111/jre.12898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/15/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND OBJECTIVE Dysbiosis, a loss of balance in the microbiota, is a potential factor of peri-implantitis. However, compositional change of the peri-implant microbiota soon after implant uncovering is still unknown. In this study, bacterial composition in the peri-implant sulcus was examined to understand the establishment of bacterial composition within the peri-implant microbiota during the earliest weeks after implant uncovering. METHODS Microbiota samples were collected at weeks 1, 2, 4, and 6 after stage-two surgery. Bacterial DNA was isolated from the samples, and a 16S rRNA gene library was constructed. Sequence reads were obtained using a high-throughput sequencing platform and were taxonomically assigned at the phylum and genus levels. RESULTS Alpha diversity indices, which did not include taxonomic information, were at similar levels throughout the four time points. At 1 and 2 weeks, the bacterial composition was similar among patients with the predominance of Firmicutes and Proteobacteria. However, the composition was diverse at 4 and 6 weeks and significantly dissimilar to the composition at 1 week. CONCLUSIONS At 1 week, the peri-implant microbiota was already formed with alpha diversity as high as that at the later time points. However, the bacterial composition was not highly dissimilar among patients at 1 week. The composition changed over the passage of several weeks and was specific for each patient.
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Affiliation(s)
- Masahiro Shimogishi
- Department of Oral Implantology and Regenerative Dental Medicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takayasu Watanabe
- Department of Chemistry, Nihon University School of Dentistry, Tokyo, Japan
| | - Masaki Shibasaki
- Department of Oral Implantology and Regenerative Dental Medicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takahiko Shiba
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Keiji Komatsu
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takashi Nemoto
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Yoshio Nakano
- Department of Chemistry, Nihon University School of Dentistry, Tokyo, Japan
| | - Takanori Iwata
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shohei Kasugai
- Department of Oral Implantology and Regenerative Dental Medicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ichiro Nakagawa
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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24
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Toro F, Alarcón J, Márquez S, Capella J, Bahamonde P, Esperón F, Moreno-Switt A, Castro-Nallar E. Composition and structure of the skin microbiota of rorquals off the Eastern South Pacific. FEMS Microbiol Ecol 2021; 97:6179854. [PMID: 33749784 DOI: 10.1093/femsec/fiab050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 03/18/2021] [Indexed: 01/04/2023] Open
Abstract
Recent advances in high-throughput sequencing have enabled the large-scale interrogation of microbiota in the most diverse environments, including host-associated microbiota. This has led to the recognition that the skin microbiota of rorquals is specific and structurally different from that of the ocean. This study reveals the skin microbiome of 85 wild individuals along the Chilean coast belonging to Megaptera novaeangliae, Balaenoptera musculus and Balaenoptera physalus. Alpha diversity analysis revealed significant differences in richness and phylogenetic diversity, particularly among humpback whales from different locations and between blue and humpback whales. Beta diversity was partially explained by host and location but only accounting for up to 17% of microbiota variability (adjusted VPA). Overall, we found that microbiota composition was dominated by bacterial genera such as Cardiobacter, Moraxella, Tenacibaculum, Stenotrophomonas, Flavobacteria and Pseudomonas. We also found that no ASVs were associated with the three rorqual species. Up to four ASVs were specific of a location, indicating a great variability in the microbiota. To the best of our knowledge, this is the first report on the composition and structure of the skin microbiota of whales off the coast of Chile, providing a foundational dataset to understand the microbiota's role in rorquals.
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Affiliation(s)
- Frederick Toro
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Center for Bioinformatics and Integrative Biology, Avenida Republica 330, Santiago 8370186, Chile.,Doctorate in Conservation Medicine, Facultad de Ciencias de la Vida, Universidad Andres Bello, Departamento de Ecologia y Recursos Naturales, Avenida Republica 330, Santiago 8370186, Chile.,Panthalassa, Red de Estudios de Vertebrados Marinos de Chile Toesca 2002 P6, Santiago, Chile.,Facultad de Medicina Veterinaria y Recursos Naturales, Universidad Santo Tomás, Escuela de Medicina Veterinaria, Avenida Limonares 190, Viña del Mar, Chile
| | - Jaime Alarcón
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Center for Bioinformatics and Integrative Biology, Avenida Republica 330, Santiago 8370186, Chile
| | - Sebastián Márquez
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Center for Bioinformatics and Integrative Biology, Avenida Republica 330, Santiago 8370186, Chile
| | - Juan Capella
- Whalesound Ltda., Lautaro Navarro 1163, 2do piso. Punta Arenas, Chile.,Fundación Yubarta, Apartado Aéreo 33141, Cali, Colombia
| | - Paulina Bahamonde
- Melimoyu Ecosystem Research Institute, Avenida Kennedy 5682, Vitacura, Chile.,Universidad de Playa Ancha, HUB AMBIENTAL UPLA - Centro de Estudios Avanzados, Playa Ancha 850, Valparaíso, Chile
| | - Fernando Esperón
- Animal Health Research Center, INIA-CISA, Valdeolmos, Carretera Algete-El Casar de Talamanca, Km. 8,1, 28130 Valdeolmos, Madrid, Spain
| | - Andrea Moreno-Switt
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Avenida Las Condes 12.461, torre 3, oficina 205. Las Condes, Chile.,Facultad de Medicina Veterinaria, Pontificia Universidad Católica de Chile
| | - Eduardo Castro-Nallar
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Center for Bioinformatics and Integrative Biology, Avenida Republica 330, Santiago 8370186, Chile
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25
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Zhang B, Zhou J, Li X, Ye L, Jia D, Gan B, Tan W. Temperature affects substrate-associated bacterial composition during Ganoderma lucidum hyphal growth. Can J Microbiol 2021; 67:281-289. [PMID: 33591216 DOI: 10.1139/cjm-2020-0070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The growth of the well-known fungus Ganoderma lucidum is influenced by temperature, which has an impact on the associated microbial structure in the substrate. In this study, we analyzed the bacterial diversity of the substrate at different temperatures using next-generation sequencing technology. A total of 513 733 sequences from 15 samples were assigned to 19 bacterial phyla. The samples were dominated by Proteobacteria, followed by Firmicutes; the 2 phyla exhibited opposite changes with elevated temperature. Bacterial genera showed different abundances at different temperatures, in which Sediminibacterium maintained a stable abundance below 40 °C, while Ochrobactrum and Rhodococcus were enriched with elevated temperature and both showed their highest abundances at 40 °C. Functional prediction uncovered 39 identified KEGG pathways, and bacterial genes involved in the membrane transport pathway exhibited the highest abundance subject to heat (40 °C) during the growth of G. lucidum. In general, our findings illustrated the influence of temperatures on G. lucidum mycelial morphology and the bacterial community in the substrate, and the results will facilitate cultivation of this fungus.
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Affiliation(s)
- Bo Zhang
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China.,Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Jie Zhou
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China.,Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Xiaolin Li
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China.,Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Lei Ye
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China.,Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Dinghong Jia
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China.,Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Bingcheng Gan
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China.,Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Wei Tan
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China.,Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
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26
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Aguayo P, Campos VL, Henríquez C, Olivares F, De Ia Iglesia R, Ulloa O, Vargas CA. The Influence of pCO 2-Driven Ocean Acidification on Open Ocean Bacterial Communities during A Short-Term Microcosm Experiment in the Eastern Tropical South Pacific (ETSP) off Northern Chile. Microorganisms 2020; 8:E1924. [PMID: 33291533 DOI: 10.3390/microorganisms8121924] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/27/2020] [Accepted: 11/28/2020] [Indexed: 11/23/2022] Open
Abstract
Due to the increasing anthropogenic CO2 emissions, Ocean Acidification (OA) is progressing rapidly around the world. Despite the major role that microorganisms play on the marine biogeochemical cycling and ecosystem functioning, the response of bacterial communities upon OA scenarios is still not well understood. Here, we have conducted a detailed characterization of the composition and relative abundance of bacterial communities in the water column of an open-ocean station in the Eastern Tropical South Pacific (ETSP) off northern Chile and their interactions with environmental factors. In addition, through a short-term microcosm experiment, we have assessed the effect of low pH/high pCO2 conditions over the abundance and genetic diversity of bacterial communities. Our results evidence a clear partitioning of community composition that could be attributed mostly to dissolved oxygen. However, our experimental approach demonstrated that low pH/high pCO2 conditions might modify the structure of the bacterial community, evidencing that small changes in pH may impact significantly the abundance and diversity of key microorganisms. This study constitutes a first step aiming to provide insight about the influence of changing carbonate chemistry conditions on natural bacterial communities and to shed light on the potential impact of OA in biogeochemical cycles on the ETSP region.
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27
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Kim D, Chae N, Kim M, Nam S, Kim E, Lee H. Soil water content as a critical factor for stable bacterial community structure and degradative activity in maritime Antarctic soil. J Microbiol 2020; 58:1010-1017. [PMID: 33263894 DOI: 10.1007/s12275-020-0490-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/26/2020] [Accepted: 10/29/2020] [Indexed: 12/26/2022]
Abstract
Recent increases in air temperature across the Antarctic Peninsula may prolong the thawing period and directly affect the soil temperature (Ts) and volumetric soil water content (SWC) in maritime tundra. Under an 8°C soil warming scenario, two customized microcosm systems with maritime Antarctic soils were incubated to investigate the differential influence of SWC on the bacterial community and degradation activity of humic substances (HS), the largest constituent of soil organic carbon and a key component of the terrestrial ecosystem. When the microcosm soil (KS1-4Feb) was incubated for 90 days (T = 90) at a constant SWC of ~32%, the initial HS content (167.0 mg/g of dried soil) decreased to 156.0 mg (approximately 6.6% loss, p < 0.05). However, when another microcosm soil (KS1-4Apr) was incubated with SWCs that gradually decreased from 37% to 9% for T = 90, HS degradation was undetected. The low HS degradative activity persisted, even after the SWC was restored to 30% with water supply for an additional T = 30. Overall bacterial community structure remained relatively stable at a constant SWC setting (KS1-4Feb). In contrast, we saw marked shifts in the bacterial community structure with the changing SWC regimen (KS1-4Apr), suggesting that the soil bacterial communities are vulnerable to drying and re-wetting conditions. These microcosm experiments provide new information regarding the effects of constant SWC and higher Ts on bacterial communities for HS degradation in maritime Antarctic tundra soil.
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Affiliation(s)
- Dockyu Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea.
| | - Namyi Chae
- Institutes of Life Sciences and Natural Resources, Korea University, Seoul, 02841, Republic of Korea
| | - Mincheol Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Sungjin Nam
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Eungbin Kim
- Department of Systems Biology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Hyoungseok Lee
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
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28
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Illescas M, Rubio MB, Hernández-Ruiz V, Morán-Diez ME, Martínez de Alba AE, Nicolás C, Monte E, Hermosa R. Effect of Inorganic N Top Dressing and Trichoderma harzianum Seed-Inoculation on Crop Yield and the Shaping of Root Microbial Communities of Wheat Plants Cultivated Under High Basal N Fertilization. Front Plant Sci 2020; 11:575861. [PMID: 33193517 PMCID: PMC7644891 DOI: 10.3389/fpls.2020.575861] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
Wheat crop production needs nitrogen (N) for ensuring yield and quality. High doses of inorganic N fertilizer are applied to soil before sowing (basal dressing), with additional doses supplied along the cultivation (top dressing). Here, a long-term wheat field trial (12 plots), including four conditions (control, N top dressing, Trichoderma harzianum T34 seed-inoculation, and top dressing plus T34) in triplicate, was performed to assess, under high basal N fertilization, the influence of these treatments on crop yield and root microbial community shaping. Crop yield was not affected by top dressing and T. harzianum T34, but top dressing significantly increased grain protein and gluten contents. Twenty-seven-week old wheat plants were collected at 12 days after top dressing application and sampled as bulk soil, rhizosphere and root endosphere compartments in order to analyze their bacterial and fungal assemblies by 16S rDNA and ITS2 high-throughput sequencing, respectively. Significant differences for bacterial and fungal richness and diversity were detected among the three compartments with a microbial decline from bulk soil to root endosphere. The most abundant wheat root phyla were Proteobacteria and Actinobacteria for bacteria, and Ascomycota and Basidiomycota for fungi. An enrichment of genera commonly associated with soils subjected to chemical N fertilization was observed: Kaistobacter, Mortierella, and Solicoccozyma in bulk soil, Olpidium in rhizosphere, and Janthinobacterium and Pedobacter in root endosphere. Taxa whose abundance significantly differed among conditions within each compartment were identified. Results show that: (i) single or strain T34-combined application of N top dressing affected to a greater extent the bulk soil bacterial levels than the use of T34 alone; (ii) when N top dressing and T34 were applied in combination, the N fertilizer played a more decisive role in the bacterial microbiome than T34; (iii) many genera of plant beneficial bacteria, negatively affected by N top dressing, were increased by the application of T34 alone; (iv) bulk soil and rhizosphere fungal microbiomes were affected by any of the three treatments assayed; and (v) all treatments reduced Claroideoglomus in bulk soil but the single application of T34 raised the rhizosphere levels of this mycorrhizal fungus.
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Affiliation(s)
- María Illescas
- Spanish-Portuguese Institute for Agricultural Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - M. Belén Rubio
- Spanish-Portuguese Institute for Agricultural Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Víctor Hernández-Ruiz
- Spanish-Portuguese Institute for Agricultural Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - María E. Morán-Diez
- Spanish-Portuguese Institute for Agricultural Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - A. Emilio Martínez de Alba
- Spanish-Portuguese Institute for Agricultural Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Carlos Nicolás
- Spanish-Portuguese Institute for Agricultural Research (CIALE), Department of Botany and Plant Physiology, University of Salamanca, Salamanca, Spain
| | - Enrique Monte
- Spanish-Portuguese Institute for Agricultural Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Rosa Hermosa
- Spanish-Portuguese Institute for Agricultural Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
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29
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Cao N, Wu H, Zhang XZ, Meng QX, Zhou ZM. Calcium propionate supplementation alters the ruminal bacterial and archaeal communities in pre- and postweaning calves. J Dairy Sci 2020; 103:3204-3218. [PMID: 32113756 DOI: 10.3168/jds.2019-16964] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 12/01/2019] [Indexed: 01/27/2023]
Abstract
The aim of this study was to determine the effect of calcium propionate (CaP) on rumen microbiota, fermentation indicators, and weight gain in calves both pre- and postweaning. Twenty-four newborn calves were randomly divided into 4 groups (2 × 2 factorial treatment arrangement): either pre- (90 d) or postweaning (160 d), and either without or with dietary CaP supplementation (5% dry matter). The CaP supplementation increased the body weight and rumen weight of the calves and lowered NH3-N concentration in the rumen. Microbiota composition was characterized by sequencing the amplicons of the bacterial and archaeal 16S rRNA genes. The CaP supplementation decreased the relative abundance of the phylum Bacteroidetes but tended to increase that of Proteobacteria. In addition, CaP supplementation decreased the diversity of bacteria and archaea in the rumen compared with the calves fed the control diet. Linear discriminant analysis of the rumen microbiota revealed that Succinivibrionaceae and Methanobrevibacter were enriched in the CaP group postweaning. A correlation was also present between the acetate to propionate ratio and the species that acted as co-occurrence network hubs, including Succiniclasticum, Treponema, and Megasphaera. In conclusion, CaP supplementation can improve body weight gain and rumen growth and alter the ruminal microbiota in calves both pre- and postweaning.
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Affiliation(s)
- N Cao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - H Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - X Z Zhang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Q X Meng
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Z M Zhou
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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30
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Yamamoto EA, Jørgensen TN. Relationships Between Vitamin D, Gut Microbiome, and Systemic Autoimmunity. Front Immunol 2020; 10:3141. [PMID: 32038645 PMCID: PMC6985452 DOI: 10.3389/fimmu.2019.03141] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/24/2019] [Indexed: 12/12/2022] Open
Abstract
There is increasing recognition of the role the microbiome plays in states of health and disease. Microbiome studies in systemic autoimmune diseases demonstrate unique microbial patterns in Inflammatory Bowel Disease, Rheumatoid Arthritis, and Systemic Lupus Erythematosus to a lesser extent, whereas there is no single bug or pattern that characterizes Multiple Sclerosis. Autoimmune diseases tend to share a predisposition for vitamin D deficiency, which alters the microbiome and integrity of the gut epithelial barrier. In this review, we summarize the influence of intestinal bacteria on the immune system, explore the microbial patterns that have emerged from studies on autoimmune diseases, and discuss how vitamin D deficiency may contribute to autoimmunity via its effects on the intestinal barrier function, microbiome composition, and/or direct effects on immune responses.
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Affiliation(s)
- Erin A Yamamoto
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, United States
| | - Trine N Jørgensen
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
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Zhou R, Wu J, Lang X, Liu L, Casper DP, Wang C, Zhang L, Wei S. Effects of oregano essential oil on in vitro ruminal fermentation, methane production, and ruminal microbial community. J Dairy Sci 2020; 103:2303-2314. [PMID: 31954586 DOI: 10.3168/jds.2019-16611] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 11/07/2019] [Indexed: 12/26/2022]
Abstract
Different inclusion rates of oregano essential oil (OEO) were investigated for their effects on ruminal in vitro fermentation parameters, total gas, methane production, and bacterial communities. Treatments were (1) control, 0 mg/L of OEO (CON); 13 mg/L (OEO1); 52 mg/L (OEO2); 91 mg/L (OEO3); and 130 mg/L (OEO4), each incubated with 150 mL of buffered rumen fluid and 1,200 mg of substrate for 24 h using the Ankom in vitro gas production system (Ankom Technology Corp., Fairport, NY). Treatment responses were statistically analyzed using polynomial contrasts. Digestibility of DM, NDF, and ADF increased quadratically with increasing OEO inclusion rates. Digestibility of DM and NDF were highest for OEO2, whereas ADF digestibility was highest for OEO3, compared with CON, with the remaining treatments being intermediate and similar. Ammonia nitrogen concentrations decreased from CON at a quadratic rate with increasing OEO inclusion rates, and OEO2 had the lowest concentration compared with the other groups. Total VFA, acetate, propionate, butyrate, valerate, and isovalerate concentrations linearly decreased with increasing OEO inclusion rates. Total gas production levels by CON and OEO4 were greater than those of OEO1, OEO2, and OEO3 in a quadratic response, and methane production linearly decreased from CON, compared with OEO4, at a decreasing rate with OEO inclusion rates. As determined by 16S rRNA sequencing, the α biodiversity of ruminal bacteria was similar among OEO inclusion rates. Increasing OEO inclusion rates linearly increased the relative abundance of Prevotella and Dialister bacteria. Several bacteria demonstrated different polynomial responses, whereas several bacteria were similar among increasing OEO inclusion rates. These results suggested that OEO supplementation can modify ruminal fermentation to alter VFA concentrations and reduce methane emissions by extensively altering the ruminal bacterial community, suggesting an optimal feeding rate for future animal studies of approximately 52 mg/L for mature ruminants.
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Affiliation(s)
- Rui Zhou
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmen Village Anning, Lanzhou, Gansu, People's Republic of China, 730070
| | - Jianping Wu
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmen Village Anning, Lanzhou, Gansu, People's Republic of China, 730070.
| | - Xia Lang
- Animal Husbandry, Pasture, and Green Agriculture Institute, Gansu Academy of Agricultural Sciences, No. 1 Nongkeyuan Village Anning, Lanzhou, Gansu, People's Republic of China, 730030
| | - Lishan Liu
- Animal Husbandry, Pasture, and Green Agriculture Institute, Gansu Academy of Agricultural Sciences, No. 1 Nongkeyuan Village Anning, Lanzhou, Gansu, People's Republic of China, 730030
| | - David P Casper
- Casper's Calf Ranch, 4890 West Lily Creek Road, Freeport, IL 61032
| | - Cailian Wang
- Animal Husbandry, Pasture, and Green Agriculture Institute, Gansu Academy of Agricultural Sciences, No. 1 Nongkeyuan Village Anning, Lanzhou, Gansu, People's Republic of China, 730030
| | - Liping Zhang
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmen Village Anning, Lanzhou, Gansu, People's Republic of China, 730070
| | - Sheng Wei
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmen Village Anning, Lanzhou, Gansu, People's Republic of China, 730070
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Espuela-Ortiz A, Lorenzo-Diaz F, Baez-Ortega A, Eng C, Hernandez-Pacheco N, Oh SS, Lenoir M, Burchard EG, Flores C, Pino-Yanes M. Bacterial salivary microbiome associates with asthma among african american children and young adults. Pediatr Pulmonol 2019; 54:1948-1956. [PMID: 31496123 PMCID: PMC6851413 DOI: 10.1002/ppul.24504] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 08/21/2019] [Indexed: 02/01/2023]
Abstract
Several studies have shown that the airways of asthma patients contain higher diversity of bacteria and are enriched in pathogenic species. However, sampling the airways in children is challenging. Here we aimed to identify differences in the salivary bacterial composition between African Americans children with and without asthma. Saliva samples from 57 asthma cases and 57 healthy controls were analyzed by means of 16S ribosomal RNA amplicon profiling. Measurements of bacterial diversity and genus relative abundance were compared between cases and controls using the nonparametric Wilcoxon test and multivariate regression models. A total of five phyla and a mean of 56 genera were identified. Among them, 15 genera had a relative abundance greater than 1%, being Prevotella, Haemophilus, Streptococcus, and Veillonella the most abundant genera. Differences between cases and controls were found in terms of diversity, as well as in relative abundance for Streptococcus genus (13.0% in cases vs 18.3% in controls; P = .003) and Veillonella genus (11.1% in cases vs 8.0% in controls; P = .002). These differences remained significant after correction for multiple comparisons and when potential confounders were taken into account in logistic regression models. In conclusion, we identified changes in the salivary microbiota associated with asthma among African Americans.
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Affiliation(s)
- Antonio Espuela-Ortiz
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Fabian Lorenzo-Diaz
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Adrian Baez-Ortega
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States
| | - Natalia Hernandez-Pacheco
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Sam S. Oh
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States
| | | | - Esteban G. Burchard
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, United States
| | - Carlos Flores
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Maria Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, Santa Cruz de Tenerife, Spain
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Chen J, Li JM, Tang YJ, Xing YM, Qiao P, Li Y, Liu PG, Guo SX. Chinese Black Truffle-Associated Bacterial Communities of Tuber indicum From Different Geographical Regions With Nitrogen Fixing Bioactivity. Front Microbiol 2019; 10:2515. [PMID: 31749786 PMCID: PMC6848067 DOI: 10.3389/fmicb.2019.02515] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/18/2019] [Indexed: 11/13/2022] Open
Abstract
It is well known that the microbes associated with truffle fruiting bodies play a very important role during the truffle lifecycle. Tuber indicum, commonly called Chinese black truffle, is a species endemic to Eastern Asia and in the genus of Tuber. Here, we reported the bacterial communities of T. indicum from different geographical regions and described the bacterial diversity from three compartments (soil, ectomycorrhizae and ascocarps) of T. indicum using high-throughput sequencing combined tissue culture. The results revealed that Bradyrhizobium was the dominant genus in fruiting bodies of T. indicum from nine geographical sites in China, and the microbes in T. indicum ascocarps were influenced by geological locations and soil characteristics. More specific bacterial taxa were enriched in the fruiting bodies than in the ectomycorrhizae and soil. In addition, 60 cultural bacteria were isolated from T. indicum fruiting bodies (4 families, 24 genera), and Pseudomonas, Alcaligenes faecalis, Microbacterium, and Arthrobacter were dominant. One of 13 strains that have potential nitrogen-fixation activities was further verified by an acetylene reduction assay (ARA). Together, this research provides new and important data for better understanding of the interaction between truffle and associated microbe and the biology of truffle itself.
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Affiliation(s)
- Juan Chen
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jia-Mei Li
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yan-Jing Tang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yong-Mei Xing
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Peng Qiao
- Shandong Institute of Sericulture, Shandong Academy of Agricultural Sciences, Yantai, China
| | - Yang Li
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Pei-Gui Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Shun-Xing Guo
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Liu CJ, Zhang YL, Shang Y, Wu B, Yang E, Luo YY, Li XR. Intestinal bacteria detected in cancer and adjacent tissue from patients with colorectal cancer. Oncol Lett 2018; 17:1115-1127. [PMID: 30655873 PMCID: PMC6313076 DOI: 10.3892/ol.2018.9714] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 10/12/2018] [Indexed: 12/18/2022] Open
Abstract
Intestinal bacteria are symbiotic microbiota within the human gut and are implicated in the occurrence and development of colorectal cancer (CRC). The current study investigated the changes in bacterial composition prior to and following surgery, as well as the differences in the bacterial community structure between cancer tissue and adjacent normal tissue. The diversity of the bacterial community and the composition of the bacteria were assessed. In addition, phylogenetic analysis and principle component analysis (PCA) were performed. The results revealed that cancer tissue and adjacent normal tissue exhibited similar bacterial compositions. However, a significant difference was identified in the composition of intestinal bacteria in stool samples collected from patients following surgery compared with stool samples collected prior to surgery. Each patient had their own unique intestinal bacterial community, likely due to a number of factors, including diet, genetic factors and health status. In addition, phylogenetic trees revealed that the most abundant operational taxonomic unit, 0001, was associated with Escherichia coli in all samples. Finally, PCA suggested that the bacterial community structure in all patient stools was similar following surgery. The current study provides information regarding the diversity of the intestinal bacterial community of patients with CRC and provides a basis for postoperative intestinal assessments.
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Affiliation(s)
- Chen-Jian Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Yuan-Lian Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Yun Shang
- Department of General Surgery, First People's Hospital of Yunnan Province, Kunming, Yunnan 650032, P.R. China
| | - Bian Wu
- Department of General Surgery, First People's Hospital of Yunnan Province, Kunming, Yunnan 650032, P.R. China
| | - En Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Yi-Yong Luo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
| | - Xiao-Ran Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, P.R. China
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35
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Klabukova DL, Kolotvina SV, Titov EI, Mashentseva NG. [The study of starter cultures compositions influence on the cholesterol level in fermented meat products]. Vopr Pitan 2017; 86:82-90. [PMID: 30695632 DOI: 10.24411/0042-8833-2017-00080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 09/08/2017] [Indexed: 06/09/2023]
Abstract
The article considers the possibility of using starter cultures compositions to reduce cholesterol in meat fermented products. An analysis of own researches and other scientific data allowed to conclude that the ability to reduce cholesterol by starting cultures in vitro is the strain-specific property. In view of the technological properties and the ability to reduce cholesterol in vitro, six compositions of starter cultures from the MGUPP collection were suggested. The compositions consisted of microorganisms belonging to the three genuses: Lactobacillus, Pediococcus and Staphylococcus. The absence of antagonism between the strains within each composition was determined by perpendicular strokes. Strains of each composition were co-cultured in a medium containing cholesterol. The residual cholesterol amount in the medium was determined after 24 hours by the Zlatkis- Zakmethod. This method is based on the cholesterol reaction with FeCl3 in the presence of concentrated sulfuric acid and glacial acetic acid to form a yellow colored complex. It was found that the compositions showed stronger activity for cholesterol reduction than each strain separately. Synergistic effect of cholesterol reduction was detected in starter cultures strains included into compositions. Reduction of cholesterol observed at 25.0-45.7%of its initial concentration in the medium. In those compositions, which included strains with a high capacity to reduce cholesterol, total cholesterol degradation ability was also higher. It was found that starter cultures reduced cholesterol not only in vitro, but also in the process of meat raw material fermentation in production of dry-smoked sausage. Composition a (Lactobacillus sakei 105, Pediococcus pentosaceus 31, Staphylococcus xylosus 45 at a ratio of 1:1:1) was chosen for the manufacture of drysmoked sausage. Bacterial composition was introduced into the meat raw materials on the mince preparation step in an amount of 109 CFU/g mince. Cholesterol maintenance in minced meat and ready-made dry-smoked sausages was determined by HPLC. In minced meat it was 840±10 mg/kg. In the ready sausages the greatest amount of cholesterol was detected in the control sample and was 971±15 mg/kg. Increasing cholesterol levels apparently due to loss of product weight by drying. Cholesterol level decreased by 21.4% in the test sample with the addition of bacterial composition (763±12 mg/kg).
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Affiliation(s)
| | | | - E I Titov
- Moscow State University of Food Production
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Sha Y, Liu M, Wang B, Jiang K, Qi C, Wang L. Bacterial Population in Intestines of Litopenaeus vannamei Fed Different Probiotics or Probiotic Supernatant. J Microbiol Biotechnol 2017; 26:1736-1745. [PMID: 27381338 DOI: 10.4014/jmb.1603.03078] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
The interactions of microbiota in the gut play an important role in promoting or maintaining the health of hosts. In this study, in order to investigate and compare the effects of dietary supplementation with Lactobacillus pentosus HC-2 (HC-2), Enterococcus faecium NRW-2, or the bacteria-free supernatant of a HC-2 culture on the bacterial composition of Litopenaeus vannamei, Illumina sequencing of the V1-V2 region of the 16S rRNA gene was used. The results showed that unique species exclusively existed in specific dietary groups, and the abundance of Actinobacteria was significantly increased in the intestinal bacterial community of shrimp fed with the bacteria-free supernatant of an HC-2 culture compared with the control. In addition, the histology of intestines of the shrimp from the four dietary groups was also described, but no obvious improvements in the intestinal histology were observed. The findings in this work will help to promote the understanding of the roles of intestinal bacteria in shrimps when fed with probiotics or probiotic supernatant.
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Affiliation(s)
- Yujie Sha
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, P.R. China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Mei Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, P.R. China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, P.R. China
| | - Baojie Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, P.R. China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, P.R. China
| | - Keyong Jiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, P.R. China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, P.R. China
| | - Cancan Qi
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, P.R. China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Lei Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, P.R. China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, P.R. China
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Jung JE, Cai JN, Cho SD, Song KY, Jeon JG. Influence of fluoride on the bacterial composition of a dual-species biofilm composed of Streptococcus mutans and Streptococcus oralis. Biofouling 2016; 32:1079-1087. [PMID: 27643392 DOI: 10.1080/08927014.2016.1230607] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 08/23/2016] [Indexed: 06/06/2023]
Abstract
Despite the widespread use of fluoride for the prevention of dental caries, few studies have demonstrated the effects of fluoride on the bacterial composition of dental biofilms. This study investigated whether fluoride affects the proportion of Streptococcus mutans and S. oralis in mono- and dual-species biofilm models, via microbiological, biochemical, and confocal fluorescence microscope studies. Fluoride did not affect the bacterial count and bio-volume of S. mutans and S. oralis in mono-species biofilms, except for the 24-h-old S. mutans biofilms. However, fluoride reduced the proportion and bio-volume of S. mutans but did not decrease those of S. oralis during both S. oralis and S. mutans dual-species biofilm formation, which may be related to the decrease in extracellular polysaccharide formation by fluoride. These results suggest that fluoride may prevent the shift in the microbial proportion to cariogenic bacteria in dental biofilms, subsequently inhibiting the cariogenic bacteria dominant biofilm formation.
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Affiliation(s)
- Ji-Eun Jung
- a Department of Preventive Dentistry, School of Dentistry, Institute of Oral Bioscience and BK 21 Plus Program , Chonbuk National University , Jeonju , Republic of Korea
| | - Jian-Na Cai
- a Department of Preventive Dentistry, School of Dentistry, Institute of Oral Bioscience and BK 21 Plus Program , Chonbuk National University , Jeonju , Republic of Korea
| | - Sung-Dae Cho
- b Department of Oral Pathology, School of Dentistry, Institute of Oral Bioscience and BK 21 Plus Program , Chonbuk National University , Jeonju , Republic of Korea
| | - Kwang-Yeob Song
- c Department of Prosthodontics, School of Dentistry, Institute of Oral Bioscience and BK 21 Plus Program , Chonbuk National University , Jeonju , Republic of Korea
| | - Jae-Gyu Jeon
- a Department of Preventive Dentistry, School of Dentistry, Institute of Oral Bioscience and BK 21 Plus Program , Chonbuk National University , Jeonju , Republic of Korea
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Metzler-Zebeli BU, Lawlor PG, Magowan E, Zebeli Q. Effect of Freezing Conditions on Fecal Bacterial Composition in Pigs. Animals (Basel) 2016; 6:ani6030018. [PMID: 26927191 PMCID: PMC4810046 DOI: 10.3390/ani6030018] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/10/2016] [Accepted: 02/19/2016] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Storage of gut samples may affect the extractability of intact DNA and analyzed bacterial composition. In this study, we compared the DNA yield and the abundance of total bacteria and eight bacterial taxa when DNA was extracted from fresh fecal samples of pigs or from freeze stored samples with or without prior snap-freezing in liquid nitrogen. Results showed that the greatest differences in DNA yield and bacterial abundances were found when DNA was extracted from fresh feces compared to freeze stored fecal samples. Abstract Sample preservation and recovery of intact DNA from gut samples may affect the inferred gut microbiota composition in pigs. This study aimed to evaluate the effect of the freezing process and storage temperature prior to DNA extraction on DNA recovery and bacterial community composition in pig feces using quantitative PCR. Fresh fecal samples from six growing pigs were collected and five aliquots of each prepared: (1) total DNA extracted immediately; (2) stored at −20 °C; (3) snap frozen and stored at −20 °C; (4) stored at −80 °C; and (5) snap frozen and stored at −80 °C. Results showed that DNA yields from fresh fecal samples were, on average, 25 to 30 ng higher than those from the various stored samples. The DNA extracted from fresh samples had more gene copies of total bacteria and all targeted bacterial groups per gram feces compared to DNA extraction from frozen samples. Data presentation also modified the observed effect of freeze storage; as results for Lactobacillus group, Enterococcus spp., Streptococcus spp., Clostridium cluster IV, Bacteroides-Prevotella-Porphyromonas and Enterobacteriaceae showed the opposite effect when expressed as relative abundance, by being greater in freeze stored feces than in fresh feces. Snap freezing increased the relative proportion of Clostridium cluster IV by 24%. In conclusion, the freezing process affected DNA yield and bacterial abundances, whereas snap freezing and storage temperature had only little influence on abundances of bacterial populations in pig feces.
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Affiliation(s)
- Barbara U Metzler-Zebeli
- Department of Farm Animals and Veterinary Public Health, UniversityClinic for Swine, Vetmeduni Vienna, Veterinaerplatz 1, 1210 Vienna, Austria.
| | - Peadar G Lawlor
- Pig Development Department, Animal and Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy, Co. Cork P61 C996, Ireland.
| | - Elizabeth Magowan
- Agri-Food and and Biosciences Institute, Large Park, Hillsborough, N. Ireland BT26 6DR, UK.
| | - Qendrim Zebeli
- Department of Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, Vetmeduni Vienna, Veterinaerplatz 1, 1210 Vienna, Austria.
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Li Y, Lin Q, Wang S, Li X, Liu W, Luo C, Zhang Z, Zhu X, Jiang L, Li X. Soil bacterial community responses to warming and grazing in a Tibetan alpine meadow. FEMS Microbiol Ecol 2015; 92:fiv152. [PMID: 26635411 DOI: 10.1093/femsec/fiv152] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2015] [Indexed: 02/04/2023] Open
Abstract
Warming and grazing significantly affect the structure and function of an alpine meadow ecosystem. Yet, the responses of soil microbes to these disturbances are not well understood. Controlled asymmetrical warming (+1.2/1.7°C during daytime/nighttime) with grazing experiments were conducted to study microbial response to warming, grazing and their interactions. Significant interactive effects of warming and grazing were observed on soil bacterial α-diversity and composition. Warming only caused significant increase in bacterial α-diversity under no-grazing conditions. Grazing induced no substantial differences in bacterial α-diversity and composition irrespective of warming. Warming, regardless of grazing, caused a significant increase in soil bacterial community similarity across space, but grazing only induced significant increases under no-warming conditions. The positive effects of warming on bacterial α-diversity and grazing on community similarity were weakened by grazing and warming, respectively. Soil and plant variables explained well the variations in microbial communities, indicating that changes in soil and plant properties may primarily regulate soil microbial responses to warming in this alpine meadow. The results suggest that bacterial communities may become more similar across space in a future, warmed climate and moderate grazing may potentially offset, at least partially, the effects of global warming on the soil microbial diversity.
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Affiliation(s)
- Yaoming Li
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiaoyan Lin
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Shiping Wang
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing 100101, China
| | - Xiangzhen Li
- Key Laboratory of Environmental and Applied Microbiology & Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Sichuan 610041, China
| | - Wentso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Caiyun Luo
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Zhenhua Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Xiaoxue Zhu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Lili Jiang
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Xine Li
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
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40
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Masters N, Christie M, Stratton H, Katouli M. Viability and stability of Escherichia coli and enterococci populations in fecal samples upon freezing. Can J Microbiol 2015; 61:495-501. [PMID: 26053765 DOI: 10.1139/cjm-2015-0020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We studied the survival of Escherichia coli and enterococci populations in fecal samples of 7 host species after storage at -20 and -80 °C for 30 days. Composite fecal samples were collected from cows, chickens, horses, pigs, dogs, birds, and humans, and bacteria were enumerated before and after storage. Twenty-eight colonies of each bacterial species were typed before and after storage and the strains were assigned to different biochemical phenotypes (BPTs). A significant reduction in the number of E. coli was observed in all samples stored at -20 °C but in only 3 of those samples stored at -80 °C. However, the numbers of enterococci were similar in most stored samples (except cow and birds). The number and the distribution of E. coli and enterococci BPTs in fresh samples did not vary significantly from those stored at either temperature. Furthermore, the population structure of E. coli and enterococci did not change significantly after storage at -80 °C, this was always the case for those samples stored at -20 °C. We conclude that for those studies investigating E. coli or enterococci population structure, short-term storage (≤ 30 days) of fecal samples in a glycerol broth at -80 °C is a preferable option.
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Affiliation(s)
- N Masters
- a GeneCology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - M Christie
- b School of Biomolecular and Physical Sciences, Griffith University, Nathan, Queensland, Australia
| | - H Stratton
- b School of Biomolecular and Physical Sciences, Griffith University, Nathan, Queensland, Australia.,c Smart Water Research Centre, Griffith University, Gold Coast, Queensland, Australia
| | - M Katouli
- a GeneCology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia.,c Smart Water Research Centre, Griffith University, Gold Coast, Queensland, Australia
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Patra AK, Yu Z. Essential oils affect populations of some rumen bacteria in vitro as revealed by microarray (RumenBactArray) analysis. Front Microbiol 2015; 6:297. [PMID: 25914694 PMCID: PMC4392297 DOI: 10.3389/fmicb.2015.00297] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 03/26/2015] [Indexed: 11/13/2022] Open
Abstract
In a previous study origanum oil (ORO), garlic oil (GAO), and peppermint oil (PEO) were shown to effectively lower methane production, decrease abundance of methanogens, and change abundances of several bacterial populations important to feed digestion in vitro. In this study, the impact of these essential oils (EOs, at 0.50 g/L) on the rumen bacterial community composition and population was further examined using the recently developed RumenBactArray. Species richness (expressed as number of operational taxonomic units, OTUs) in the phylum Firmicutes, especially those in the class Clostridia, was decreased by ORO and GAO, but increased by PEO, while that in the phylum Bacteroidetes was increased by ORO and PEO. Species richness in the genus Butyrivibrio was lowered by all the EOs. Increases of Bacteroidetes OTUs mainly resulted from increases of Prevotella OTUs. Overall, 67 individual OTUs showed significant differences (P ≤ 0.05) in relative abundance across the EO treatments. The predominant OTUs affected by EOs were diverse, including those related to Syntrophococcus sucromutans, Succiniclasticum ruminis, and Lachnobacterium bovis, and those classified to Prevotella, Clostridium, Roseburia, Pseudobutyrivibrio, Lachnospiraceae, Ruminococcaceae, Prevotellaceae, Bacteroidales, and Clostridiales. In total, 60 OTUs were found significantly (P ≤ 0.05) correlated with feed degradability, ammonia concentration, and molar percentage of volatile fatty acids. Taken together, this study demonstrated extensive impact of EOs on rumen bacterial communities in an EO type-dependent manner, especially those in the predominant families Prevotellaceae, Lachnospiraceae, and Ruminococcaceae. The information from this study may aid in understanding the effect of EOs on feed digestion and fermentation by rumen bacteria.
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Affiliation(s)
- Amlan K Patra
- Department of Animal Sciences, The Ohio State University Columbus, OH, USA ; Department of Animal Nutrition, West Bengal University of Animal and Fishery Sciences Kolkata, India
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State University Columbus, OH, USA
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Pérez-Cobas AE, Artacho A, Ott SJ, Moya A, Gosalbes MJ, Latorre A. Structural and functional changes in the gut microbiota associated to Clostridium difficile infection. Front Microbiol 2014; 5:335. [PMID: 25309515 PMCID: PMC4163665 DOI: 10.3389/fmicb.2014.00335] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 06/16/2014] [Indexed: 02/05/2023] Open
Abstract
Antibiotic therapy is a causative agent of severe disturbances in microbial communities. In healthy individuals, the gut microbiota prevents infection by harmful microorganisms through direct inhibition (releasing antimicrobial compounds), competition, or stimulation of the host's immune defenses. However, widespread antibiotic use has resulted in short- and long-term shifts in the gut microbiota structure, leading to a loss in colonization resistance in some cases. Consequently, some patients develop Clostridium difficile infection (CDI) after taking an antibiotic (AB) and, at present, this opportunistic pathogen is one of the main causes of antibiotic-associated diarrhea in hospitalized patients. Here, we analyze the composition and functional differences in the gut microbiota of C. difficile infected (CDI) vs. non-infected patients, both patient groups having been treated with AB therapy. To do so we used 16S rRNA gene and metagenomic 454-based pyrosequencing approaches. Samples were taken before, during and after AB treatment and were checked for the presence of the pathogen. We performed different analyses and comparisons between infected (CD+) vs. non-infected (CD-) samples, allowing proposing putative candidate taxa and functions that might protect against C. difficile colonization. Most of these potentially protective taxa belonged to the Firmicutes phylum, mainly to the order Clostridiales, while some candidate protective functions were related to aromatic amino acid biosynthesis and stress response mechanisms. We also found that CDI patients showed, in general, lower diversity and richness than non-infected, as well as an overrepresentation of members of the families Bacteroidaceae, Enterococcaceae, Lactobacillaceae and Clostridium clusters XI and XIVa. Regarding metabolic functions, we detected higher abundance of genes involved in the transport and binding of carbohydrates, ions, and others compounds as a response to an antibiotic environment.
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Affiliation(s)
- Ana E. Pérez-Cobas
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) y el Instituto Cavanilles de Biodiversidad y Biología Evolutiva de la Universitat de ValènciaValència, Spain
- CIBER en Epidemiología y Salud PúblicaMadrid, Spain
| | - Alejandro Artacho
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) y el Instituto Cavanilles de Biodiversidad y Biología Evolutiva de la Universitat de ValènciaValència, Spain
| | - Stephan J. Ott
- Institute for Clinical Molecular Biology, Christian-Albrechts-UniversityKiel, Germany
- Department for Internal Medicine, University Hospital Schleswig-HolsteinKiel, Germany
| | - Andrés Moya
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) y el Instituto Cavanilles de Biodiversidad y Biología Evolutiva de la Universitat de ValènciaValència, Spain
- CIBER en Epidemiología y Salud PúblicaMadrid, Spain
| | - María J. Gosalbes
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) y el Instituto Cavanilles de Biodiversidad y Biología Evolutiva de la Universitat de ValènciaValència, Spain
- CIBER en Epidemiología y Salud PúblicaMadrid, Spain
| | - Amparo Latorre
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) y el Instituto Cavanilles de Biodiversidad y Biología Evolutiva de la Universitat de ValènciaValència, Spain
- CIBER en Epidemiología y Salud PúblicaMadrid, Spain
- *Correspondence: Amparo Latorre, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, C/ Catedrático José Beltrán 2, 46980 Paterna (València), PO Box 46071, València, Spain e-mail:
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