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Siegl D, Kruchem M, Jansky S, Eichler E, Thies D, Hartwig U, Schuppan D, Bockamp E. A PCR protocol to establish standards for routine mycoplasma testing that by design detects over ninety percent of all known mycoplasma species. iScience 2023; 26:106724. [PMID: 37216121 PMCID: PMC10192841 DOI: 10.1016/j.isci.2023.106724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/07/2023] [Accepted: 04/19/2023] [Indexed: 05/24/2023] Open
Abstract
Mycoplasma infection leads to false and non-reproducible scientific data and poses a risk to human health. Despite strict guidelines calling for regular mycoplasma screening, there is no universal and widely established standard procedure. Here, we describe a reliable and cost-effective PCR method that establishes a universal protocol for mycoplasma testing. The applied strategy utilizes ultra-conserved eukaryotic and mycoplasma sequence primers covering by design 92% of all species in the six orders of the class Mollicutes within the phylum Mycoplasmatota and is applicable to mammalian and many non-mammalian cell types. This method can stratify mycoplasma screening and is suitable as a common standard for routine mycoplasma testing.
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Affiliation(s)
- Dominik Siegl
- Institute of Translational Immunology (TIM), University Medical Center of the Johannes Gutenberg-University, Mainz 55131, Germany
| | - Marie Kruchem
- Institute of Translational Immunology (TIM), University Medical Center of the Johannes Gutenberg-University, Mainz 55131, Germany
| | - Sandrine Jansky
- Institute of Translational Immunology (TIM), University Medical Center of the Johannes Gutenberg-University, Mainz 55131, Germany
| | - Emma Eichler
- Institute of Translational Immunology (TIM), University Medical Center of the Johannes Gutenberg-University, Mainz 55131, Germany
| | - Dorothe Thies
- Institute of Translational Immunology (TIM), University Medical Center of the Johannes Gutenberg-University, Mainz 55131, Germany
| | - Udo Hartwig
- Department of Medicine III Hematology & Medical Oncology, University Medical Center of the Johannes Gutenberg-University, Mainz 55131, Germany
- Research Center for Immunotherapy, University Medical Center of the Johannes Gutenberg-University, Mainz 55131, Germany
| | - Detlef Schuppan
- Institute of Translational Immunology (TIM), University Medical Center of the Johannes Gutenberg-University, Mainz 55131, Germany
- ImmuneNTech GmbH, Wendelsheim 55234, Germany
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Research Center for Immunotherapy, University Medical Center of the Johannes Gutenberg-University, Mainz 55131, Germany
| | - Ernesto Bockamp
- Institute of Translational Immunology (TIM), University Medical Center of the Johannes Gutenberg-University, Mainz 55131, Germany
- ImmuneNTech GmbH, Wendelsheim 55234, Germany
- Research Center for Immunotherapy, University Medical Center of the Johannes Gutenberg-University, Mainz 55131, Germany
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Thie N, Corl A, Turjeman S, Efrat R, Kamath PL, Getz WM, Bowie RCK, Nathan R. Linking migration and microbiota at a major stopover site in a long-distance avian migrant. MOVEMENT ECOLOGY 2022; 10:46. [PMID: 36345043 PMCID: PMC9641824 DOI: 10.1186/s40462-022-00347-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Migration is one of the most physical and energetically demanding periods in an individual bird's life. The composition of the bird's gut or cloacal microbiota can temporarily change during migration, likely due to differences in diets, habitats and other environmental conditions experienced en route. However, how physiological condition, migratory patterns, and other drivers interact to affect microbiota composition of migratory birds is still unclear. We sampled the cloacal bacterial microbiota of a long-distance migrant, the steppe buzzard (Buteo buteo vulpinus), at an important spring stopover bottleneck in Eilat, Israel, after crossing the ca. 1800 km Sahara Desert. We examined whether diversity and composition of the cloacal microbiota varied with body condition, sex, movement patterns (i.e., arrival time and migration distance), and survival. Early arrival to Eilat was associated with better body condition, longer post-Eilat spring migration distance, higher microbial α-diversity, and differences in microbiota composition. Specifically, early arrivals had higher abundance of the phylum Synergistota and five genera, including Jonquetella and Peptococcus, whereas the phylum Proteobacteria and genus Escherichia-Shigella (as well as three other genera) were more abundant in later arrivals. While the differences in α-diversity and Escherichia-Shigella seem to be mainly driven by body condition, other compositional differences associated with arrival date could be indicators of longer migratory journeys (e.g., pre-fueling at wintering grounds or stopover habitats along the way) or migratory performance. No significant differences were found between the microbiota of surviving and non-surviving individuals. Overall, our results indicate that variation in steppe buzzard microbiota is linked to variation in migratory patterns (i.e., capture/arrival date) and body condition, highlighting the importance of sampling the microbiota of GPS-tracked individuals on multiple occasions along their migration routes to gain a more detailed understanding of the links between migration, microbiota, and health in birds.
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Affiliation(s)
- Nikki Thie
- Movement Ecology Lab, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Ammon Corl
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, USA
| | - Sondra Turjeman
- Movement Ecology Lab, The Hebrew University of Jerusalem, Jerusalem, Israel
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Ron Efrat
- Movement Ecology Lab, The Hebrew University of Jerusalem, Jerusalem, Israel
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Pauline L Kamath
- School of Food and Agriculture, University of Maine, Orono, ME, USA
| | - Wayne M Getz
- Department of Environmental Science Policy and Management, University of California, Berkeley, Berkeley, CA, USA
- School of Mathematical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, USA
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ran Nathan
- Movement Ecology Lab, The Hebrew University of Jerusalem, Jerusalem, Israel.
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Effect of Sodium Nitrate and Cysteamine on In Vitro Ruminal Fermentation, Amino Acid Metabolism and Microbiota in Buffalo. Microorganisms 2022; 10:microorganisms10102038. [PMID: 36296314 PMCID: PMC9609660 DOI: 10.3390/microorganisms10102038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/09/2022] [Accepted: 10/10/2022] [Indexed: 11/17/2022] Open
Abstract
Nitrate is used as a methane inhibitor while cysteamine is considered as a growth promoter in ruminants. The present study evaluated the effect of sodium nitrate and cysteamine on methane (CH4) production, rumen fermentation, amino acid (AA) metabolism, and rumen microbiota in a low protein diet. Four treatments containing a 0.5 g of substrate were supplemented with 1 mg/mL sodium nitrate (SN), 100 ppm cysteamine hydrochloride (CS), and a combination of SN 1 mg/mL and CS 100 ppm (CS+SN), and a control (no additive) were applied in a completely randomized design. Each treatment group had five replicates. Two experimental runs using in vitro batch culture technique were performed for two consecutive weeks. Total gas and CH4 production were measured in each fermentation bottle at 3, 6, 9, 12, 24, 48, and 72 h of incubation. The results showed that SN and CS+SN reduced the production of total gas and CH4, increased the rumen pH, acetate, acetate to propionate ratio (A/P), and microbial protein (MCP) contents (p < 0.05), but decreased other volatile fatty acids (VFA) and total VFA (p = 0.001). The CS had no effect on CH4 production and rumen fermentation parameters except for increasing A/P. The CSN increased the populations of total bacteria, fungi, and methanogens but decreased the diversity and richness of rumen microorganisms. In conclusion, CS+SN exhibited a positive effect on rumen fermentation by increasing the number of fiber degrading and hydrogen-utilizing bacteria, with a desirable impact on rumen fermentation while reducing total gas and CH4 production.
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Chen YJ, Hung WC, Chou YH, Lai CH, Peng P, Jhou PS, Tsai MR, Sheu JJC, Yen JH. Subgingival Microbiome in Rheumatoid Arthritis Patients with Periodontitis. Int J Mol Sci 2022; 23:ijms23179883. [PMID: 36077282 PMCID: PMC9456296 DOI: 10.3390/ijms23179883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/22/2022] [Accepted: 08/27/2022] [Indexed: 11/16/2022] Open
Abstract
Rheumatoid arthritis (RA) and periodontitis are suggested to be closely linked based on microbial dysbiosis, but limited subgingival bacteria have been proven in the pathogenesis of RA. We enrolled 30 RA patients and 25 controls and divided them into three groups with matched age, gender, and diabetes statuses: group AM (all of the matched participants), group PD (periodontally diseased), and group PH (periodontally healthy). Their subgingival microbial composition was determined by V3–V4 16S rRNA gene sequencing. Significant differences in subgingival microbial clustering between the RA patients and controls were observed in groups AM and PD. Among the taxa enriched in RA, Aminipila butyrica and Peptococcus simiae were the only two species displaying positive correlation to the level of anti-citrullinated protein antibodies (ACPAs) in both of the groups. Surprisingly, the median of relative abundances of A. butyrica and P. simiae were 0% in the controls of group PD. Furthermore, a gene encoding arginine deiminase with the capability to produce citrulline was addressed in the complete genome sequence of A. butyrica. This is the first study to elucidate the important roles of A. butyrica and P. simiae as periodontal bacteria leading to RA possibly through the induction of ACPA production.
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Affiliation(s)
- Yi-Jing Chen
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
| | - Wei-Chun Hung
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
| | - Yu-Hsiang Chou
- Division of Periodontics, Department of Dentistry, Kaohsiung Medical University Hospital, Kaohsiung 807377, Taiwan
- School of Dentistry, College of Dental Medicine, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
| | - Chern-Hsiung Lai
- School of Dentistry, College of Dental Medicine, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
- Anaerobic and Oral Microbiology Testing Center, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
| | - Po Peng
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
| | - Pei-Syuan Jhou
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
| | - Min-Ru Tsai
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
| | - Jim Jinn-Chyuan Sheu
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
- Correspondence: (J.J.-C.S.); (J.-H.Y.)
| | - Jeng-Hsien Yen
- Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807377, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
- Correspondence: (J.J.-C.S.); (J.-H.Y.)
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Arcos SC, Lira F, Robertson L, González MR, Carballeda-Sangiao N, Sánchez-Alonso I, Zamorano L, Careche M, Jiménez-Ruíz Y, Ramos R, Llorens C, González-Muñoz M, Oliver A, Martínez JL, Navas A. Metagenomics Analysis Reveals an Extraordinary Inner Bacterial Diversity in Anisakids (Nematoda: Anisakidae) L3 Larvae. Microorganisms 2021; 9:1088. [PMID: 34069371 PMCID: PMC8158776 DOI: 10.3390/microorganisms9051088] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/05/2021] [Accepted: 05/10/2021] [Indexed: 11/28/2022] Open
Abstract
L3 larvae of anisakid nematodes are an important problem for the fisheries industry and pose a potential risk for human health by acting as infectious agents causing allergies and as potential vectors of pathogens and microrganisms. In spite of the close bacteria-nematode relationship very little is known of the anisakids microbiota. Fresh fish could be contaminated by bacteria vectored in the cuticle or in the intestine of anisakids when the L3 larvae migrate through the muscles. As a consequence, the bacterial inoculum will be spread, with potential effects on the quality of the fish, and possible clinical effects cannot be discarded. A total of 2,689,113 16S rRNA gene sequences from a total of 113 L3 individuals obtained from fish captured along the FAO 27 fishing area were studied. Bacteria were taxonomically characterized through 1803 representative operational taxonomic units (OTUs) sequences. Fourteen phyla, 31 classes, 52 orders, 129 families and 187 genera were unambiguously identified. We have found as part of microbiome an average of 123 OTUs per L3 individual. Diversity indices (Shannon and Simpson) indicate an extraordinary diversity of bacteria at an OTU level. There are clusters of anisakids individuals (samples) defined by the associated bacteria which, however, are not significantly related to fish hosts or anisakid taxa. This suggests that association or relationship among bacteria in anisakids, exists without the influence of fishes or nematodes. The lack of relationships with hosts of anisakids taxa has to be expressed by the association among bacterial OTUs or other taxonomical levels which range from OTUs to the phylum level. There are significant biological structural associations of microbiota in anisakid nematodes which manifest in clusters of bacteria ranging from phylum to genus level, which could also be an indicator of fish contamination or the geographic zone of fish capture. Actinobacteria, Aquificae, Firmicutes, and Proteobacteria are the phyla whose abundance value discriminate for defining such structures.
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Affiliation(s)
- Susana C. Arcos
- Museo Nacional de Ciencias Naturales, Dpto Biodiversidad y Biología Evolutiva, CSIC, 28006 Madrid, Spain; (S.C.A.); (L.R.); (M.R.G.); (Y.J.-R.)
| | - Felipe Lira
- Centro Nacional de Biotecnología, Departamento de Biotecnología Microbiana, CSIC, 28049 Madrid, Spain; (F.L.); (J.L.M.)
| | - Lee Robertson
- Museo Nacional de Ciencias Naturales, Dpto Biodiversidad y Biología Evolutiva, CSIC, 28006 Madrid, Spain; (S.C.A.); (L.R.); (M.R.G.); (Y.J.-R.)
- Departamento de Protección Vegetal, INIA, 28040 Madrid, Spain
| | - María Rosa González
- Museo Nacional de Ciencias Naturales, Dpto Biodiversidad y Biología Evolutiva, CSIC, 28006 Madrid, Spain; (S.C.A.); (L.R.); (M.R.G.); (Y.J.-R.)
| | | | - Isabel Sánchez-Alonso
- Instituto de Ciencia y Tecnología de Alimentos y Nutrición, CSIC, 28040 Madrid, Spain; (I.S.-A.); (M.C.)
| | - Laura Zamorano
- Servicio de Microbiología y Unidad de Investigación, Hospital Son Espases, (IdISPa), 07120 Palma de Mallorca, Spain; (L.Z.); (A.O.)
| | - Mercedes Careche
- Instituto de Ciencia y Tecnología de Alimentos y Nutrición, CSIC, 28040 Madrid, Spain; (I.S.-A.); (M.C.)
| | - Yolanda Jiménez-Ruíz
- Museo Nacional de Ciencias Naturales, Dpto Biodiversidad y Biología Evolutiva, CSIC, 28006 Madrid, Spain; (S.C.A.); (L.R.); (M.R.G.); (Y.J.-R.)
| | - Ricardo Ramos
- Unidad de Genómica, “Scientific Park of Madrid”, Campus de Cantoblanco, 28049 Madrid, Spain;
| | - Carlos Llorens
- Biotechvana, “Scientific Park”, University of Valencia, 46980 Valencia, Spain;
| | - Miguel González-Muñoz
- Servicio de Immunología, Hospital Universitario La Paz, 28046 Madrid, Spain; (N.C.-S.); (M.G.-M.)
| | - Antonio Oliver
- Servicio de Microbiología y Unidad de Investigación, Hospital Son Espases, (IdISPa), 07120 Palma de Mallorca, Spain; (L.Z.); (A.O.)
| | - José L. Martínez
- Centro Nacional de Biotecnología, Departamento de Biotecnología Microbiana, CSIC, 28049 Madrid, Spain; (F.L.); (J.L.M.)
| | - Alfonso Navas
- Museo Nacional de Ciencias Naturales, Dpto Biodiversidad y Biología Evolutiva, CSIC, 28006 Madrid, Spain; (S.C.A.); (L.R.); (M.R.G.); (Y.J.-R.)
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6
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Kumar S, Khan MA, Beijer E, Liu J, Lowe KK, Young W, Mills DA, Moon CD. Effect of milk replacer allowance on calf faecal bacterial community profiles and fermentation. Anim Microbiome 2021; 3:27. [PMID: 33795026 PMCID: PMC8017768 DOI: 10.1186/s42523-021-00088-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/15/2021] [Indexed: 12/02/2022] Open
Abstract
Background The nutrition of calves from birth until weaning is predominantly from liquid (milk or milk-based) feeds. Liquid feed allowances are often restricted during artificial rearing to accelerate the development of the rumen by promoting solid feed intake. Liquid feeds bypass the rumen and are digested in the lower digestive tract, however, the influence of different types of milk feeds, and their allowances, on the calf hindgut microbiota is not well understood. In this study, faecal samples from 199 calves raised on three different allowances of milk replacer: 10% of initial bodyweight (LA), 20% of initial bodyweight (HA), and ad libitum (ADLIB), were collected just prior to weaning. Bacterial community structures and fermentation products were analysed, and their relationships with calf growth and health parameters were examined to identify potential interactions between diet, gut microbiota and calf performance. Results Differences in the total concentrations of short-chain fatty acids were not observed, but higher milk replacer allowances increased the concentrations of branched short-chain fatty acids and decreased acetate to propionate ratios. The bacterial communities were dominated by Ruminococcaceae, Lachnospiraceae and Bacteroides, and the bacterial diversity of the ADLIB diet group was greater than that of the other diet groups. Faecalibacterium was over three times more abundant in the ADLIB compared to the LA group, and its abundance correlated strongly with girth and body weight gains. Milk replacer intake correlated strongly with Peptococcus and Blautia, which also correlated with body weight gain. Bifidobacterium averaged less than 1% abundance, however its levels, and those of Clostridium sensu stricto 1, correlated strongly with initial serum protein levels, which are an indicator of colostrum intake and passive transfer of immunoglobulins in early life. Conclusions Higher milk replacer intakes in calves increased hindgut bacterial diversity and resulted in bacterial communities and short chain fatty acid profiles associated with greater protein fermentation. Increased abundances of beneficial bacteria such as Faecalibacterium, were also observed, which may contribute to development and growth. Moreover, correlations between microbial taxa and initial serum protein levels suggest that colostrum intake in the first days of life may influence microbiota composition at pre-weaning. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00088-2.
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Affiliation(s)
- Sandeep Kumar
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - M Ajmal Khan
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Emma Beijer
- Animal Nutrition Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Jinxin Liu
- Department of Food Science and Technology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA.,Foods for Health Institute, University of California, Davis, California, One Shields Ave, Davis, CA, 95616, USA
| | - Katherine K Lowe
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Wayne Young
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - David A Mills
- Department of Food Science and Technology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA.,Foods for Health Institute, University of California, Davis, California, One Shields Ave, Davis, CA, 95616, USA.,Department of Viticulture and Enology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, California, One Shields Ave, Davis, CA, 95616, USA
| | - Christina D Moon
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand.
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Wang F, Bao YF, Si JJ, Duan Y, Weng ZB, Shen XC. The Beneficial Effects of a Polysaccharide from Moringa oleifera Leaf on Gut Microecology in Mice. J Med Food 2019; 22:907-918. [PMID: 31390269 DOI: 10.1089/jmf.2018.4382] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Moringa oleifera is a natural plant with high nutritional and pharmacological value. Leaves of M. oleifera contain a variety of active substances. In our previous research, we had obtained a polysaccharide separated from M. oleifera leaf, namely MOs-2-a (1.35 × 104 Da). In this study, this polysaccharide was administrated daily to 6 week-old ICR mice for 4 weeks. Then, the body weight, immunity, intestinal digestion, and intestinal microenvironment of Institute of Cancer Research (ICR) mice were investigated. After 4 weeks of feeding intervention with the polysaccharide, the immune and intestinal digestive ability of the ICR mice were significant as shown by the organ index, digestive enzymes, and reduction of serum tumor necrosis factor-alpha and diamine oxidase levels. The polysaccharide could regulate the microbial composition of the intestinal tract in mice by increasing the bacteria that have been reported for antiobesity effects, short chain fatty acid production, and lactic acid production. These findings indicate that the polysaccharide of M. oleifera leaf might be a promising prebiotic that exhibits health promotion effects.
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Affiliation(s)
- Fang Wang
- Key Laboratory of Grains and Oils Quality Control and Processing, College of Food Science and Engineering, Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing University of Finance and Economics, Nanjing, China
| | - Yi-Fan Bao
- Key Laboratory of Grains and Oils Quality Control and Processing, College of Food Science and Engineering, Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing University of Finance and Economics, Nanjing, China
| | - Jia-Jun Si
- Key Laboratory of Grains and Oils Quality Control and Processing, College of Food Science and Engineering, Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing University of Finance and Economics, Nanjing, China
| | - Yu Duan
- Basic Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ze-Bin Weng
- Basic Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xin-Chun Shen
- Key Laboratory of Grains and Oils Quality Control and Processing, College of Food Science and Engineering, Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing University of Finance and Economics, Nanjing, China
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Comparison of the Intestinal Microbial Community in Ducks Reared Differently through High-Throughput Sequencing. BIOMED RESEARCH INTERNATIONAL 2019; 2019:9015054. [PMID: 30956988 PMCID: PMC6431443 DOI: 10.1155/2019/9015054] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/09/2019] [Accepted: 02/13/2019] [Indexed: 02/07/2023]
Abstract
Birds are an important source of fecal contamination in environment. Many of diseases are spread through water contamination caused by poultry droppings. A study was conducted to compare the intestinal microbial structure of Shaoxing ducks with and without water. Thirty 1-day-old Shaoxing ducks (Qingke No. 3) were randomly divided into two groups; one group had free access to water (CC), while the other one was restricted from water (CT). After 8 months of breeding, caecal samples of 10 birds from each group were obtained on ice for high-throughput sequencing. A total of 1507978 valid sequences were examined and clustered into 1815 operational taxonomic units (OTUs). At phylum level, Firmicutes (41.37%), Bacteroidetes (33.26%), Proteobacteria (13.67%), and Actinobacteria (8.26%) were found to dominate the microbial community in CC birds, while Firmicutes (53.62%), Bacteroidetes (33.06%), and Actinobacteria (11.13%) were uncovered to be the prime phyla in CT ducks. At genus level, Bacteroides (25.02%), Escherichia-Shigella (11.02%), Peptococcus (7.73%) and Parabacteroides (5.86%) were revealed to be the mainly genera in the CC group ducks, while Bacteroides (18.11%), Erysipelatoclostridium (10.94%), Ruminococcaceae_unclassified (10.43%), Lachnospiraceae_unclassified (5.26%), Coriobacteriales_unclassified (5.89%), and Faecalibacterium (4.2%) were detected to staple the microbial flora in the CT birds. One phylum and 13 genera were found to have the significant difference between the two bird groups (p<0.05). At phylum level, Proteobacteria in CT ducks were found to be obviously lower than ducks in CC birds (p<0.05). At genus level, Escherichia-Shigella (p<0.05) and Peptococcus (p<0.05) were found to be notably lower in CT birds, while Erysipelatoclostridium (p<0.05), Ruminococcaceae_unclassified (p<0.01), Coriobacteriales_unclassified (p<0.05), Faecalibacterium (p<0.01), Atopobiaceae_unclassified (p<0.01), Alistipes (p<0.05), Eggerthellaceae_unclassified (p<0.05), Prevotella_7 (<0.05), Rikenellaceae_RC9_gut_group (p<0.05), Prevotellaceae_uncultured (p<0.05), and Shuttleworthia (p<0.05) were observed to be prominently higher in CT ducks. In conclusion, the present study revealed the effects of keeping ducks away from swimming with obvious changes in the microbial community. Though higher microbial richness was found in the ducks without swimming, more pathogenic genera including Eggerthella, Erysipelatoclostridium, Alistipes, Prevotella_7, and Shuttleworthia; zoonotic genera including Eggerthella and Shuttleworthia; inflammatory genus Alistipes; anti-inflammatory Faecalibacterium genus; and tumor genus Rikenellaceae were examined in these ducks. The CT ducks also showed significant changes at genera level regarding the metabolism (Peptococcus, Ruminococcaceae, and Coriobacteriales).
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Fitzgerald CB, Shkoporov AN, Sutton TDS, Chaplin AV, Velayudhan V, Ross RP, Hill C. Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa. BMC Genomics 2018; 19:931. [PMID: 30547746 PMCID: PMC6295017 DOI: 10.1186/s12864-018-5313-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/27/2018] [Indexed: 02/08/2023] Open
Abstract
Background Faecalibacterium prausnitzii is a ubiquitous member of the human gut microbiome, constituting up to 15% of the total bacteria in the human gut. Substantial evidence connects decreased levels of F. prausnitzii with the onset and progression of certain forms of inflammatory bowel disease, which has been attributed to its anti-inflammatory potential. Two phylogroups of F. prausnitzii have been identified, with a decrease in phylogroup I being a more sensitive marker of intestinal inflammation. Much of the genomic and physiological data available to date was collected using phylogroup II strains. Little analysis of F. prausnitzii genomes has been performed so far and genetic differences between phylogroups I and II are poorly understood. Results In this study we sequenced 11 additional F. prausnitzii genomes and performed comparative genomics to investigate intraspecies diversity, functional gene complement and the mobilome of 31 high-quality draft and complete genomes. We reveal a very low level of average nucleotide identity among F. prausnitzii genomes and a high level of genome plasticity. Two genomogroups can be separated based on differences in functional gene complement, albeit that this division does not fully agree with separation based on conserved gene phylogeny, highlighting the importance of horizontal gene transfer in shaping F. prausnitzii genomes. The difference between the two genomogroups is mainly in the complement of genes associated with catabolism of carbohydrates (such as a predicted sialidase gene in genomogroup I) and amino acids, as well as defense mechanisms. Conclusions Based on the combination of ANI of genomic sequences, phylogenetic analysis of core proteomes and functional differences we propose to separate the species F. prausnitzii into two new species level taxa: F. prausnitzii sensu stricto (neotype strain A2–165T = DSM 17677T = JCM 31915T) and F. moorei sp. nov. (type strain ATCC 27768T = NCIMB 13872T). Electronic supplementary material The online version of this article (10.1186/s12864-018-5313-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cormac Brian Fitzgerald
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | | | | | - Andrei V Chaplin
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland. .,Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Ireland. .,School of Microbiology, University College Cork, Cork, Ireland.
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