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Jost SM, Cardona L, Rohrbach E, Mathis A, Holliger C, Verhulst NO. Environment rather than breed or body site shapes the skin bacterial community of healthy sheep as revealed by metabarcoding. Vet Dermatol 2024; 35:273-283. [PMID: 38082464 DOI: 10.1111/vde.13223] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 09/11/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024]
Abstract
BACKGROUND The skin is inhabited by a variety of micro-organisms, with bacteria representing the predominant taxon of the skin microbiome. In sheep, the skin bacterial community of healthy animals has been addressed in few studies, only with culture-based methods or sequencing of cloned amplicons. OBJECTIVES The objectives of this study were to determine the sheep skin bacterial community composition by using metabarcoding for a detailed characterisation and to determine the effect of body part, breed and environment. MATERIALS AND METHODS Overall, 267 samples were taken from 89 adult female sheep, belonging to three different breeds and kept on nine different farms in Switzerland. From every individual, one sample each was taken from belly, left ear and left leg and metabarcoding of the 16S rRNA V3-V4 hypervariable region was performed. RESULTS The main phyla identified were Actinobacteriota, Firmicutes, Proteobacteria and Bacteriodota. The alpha diversity as determined by Shannon's diversity index was significantly different between sheep from different farms. Beta diversity analysis by principal coordinate analysis (PCoA) showed clustering of the samples by farm and body site, while breed had only a marginal influence. A sparse partial least squares discriminant analysis (sPLS-DA) revealed seven main groups of operational taxonomic units (OTUs) of which groups of OTUs were specific for some farms. CONCLUSIONS AND CLINICAL RELEVANCE These findings indicate that environment has a larger influence on skin microbial variability than breed, although the sampled breeds, the most abundant ones in Switzerland, are phenotypically similar. Future studies on the sheep skin microbiome may lead to novel insights in skin diseases and prevention.
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Affiliation(s)
- Stéphanie M Jost
- Vetsuisse and Medical Faculty, Vector Entomology unit, National Centre for Vector Entomology, Institute of Parasitology, University of Zürich, Zürich, Switzerland
| | - Laëtitia Cardona
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Emmanuelle Rohrbach
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Alexander Mathis
- Vetsuisse and Medical Faculty, Vector Entomology unit, National Centre for Vector Entomology, Institute of Parasitology, University of Zürich, Zürich, Switzerland
| | - Christof Holliger
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Niels O Verhulst
- Vetsuisse and Medical Faculty, Vector Entomology unit, National Centre for Vector Entomology, Institute of Parasitology, University of Zürich, Zürich, Switzerland
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Smith KS, Morris MM, Morrow CD, Novak JR, Roberts MD, Frugé AD. Mood disturbance, but not overall diet quality, is associated with fecal microbiome diversity in free-living adults. Nutr Neurosci 2024; 27:451-459. [PMID: 37183583 DOI: 10.1080/1028415x.2023.2213484] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
OBJECTIVES To investigate the gut-brain axis, we explored the relationships among mood disturbance (MD), diet quality (DQ), and fecal microbiota in free-living adults. METHODS A cross-sectional analysis was conducted with data from 75 healthy adults enrolled in two studies. Anthropometrics, 16s rRNA gene sequencing of fecal microbes, DQ as assessed by Healthy Eating Index-2015 (HEI), and MD determined by Profile of Mood States (POMS) were included. Alpha-diversity and DQ differences were explored between low (n = 37) and high MD (n = 38) groups. Spearman correlations were used to investigate relationships between alpha-diversity, DQ, and POMS subscales. Moderation analysis explored the effect of HEI score on the relationship between MD and alpha-diversity. RESULTS Participants were mostly white (67%), 54.5 years old (±11.8), and overweight (28.5 ± 6.5 kg/m2). Shannon and Simpson indices indicate higher alpha-diversity in participants with low MD compared to high MD (p = 0.004 and p = 0.008, respectively). Simpson and Shannon indices were correlated with subscale of anger (rho = -0.303, p = 0.011; rho = -0.265, p = 0.027, respectively)and total MD (rho = -0.404, p = 0.001; rho = -0.357, p = 0.002, respectively). Refined grains were associated with fatigue and tension subscales (rho = 0.428, p < 0.001; rho = 0.302, p = 0.014, respectively). DQ did not significantly moderate the relationship between alpha-diversity and mood disturbance (F(7, 53) = 2.00, p = 0.072, R2 = 0.209). Shannon index was a significant predictor of MD (b = -4.39, t(53) = -2.55, p = 0.014), but total HEI score and the interaction (Shannon index*HEI score) were not significant. DISCUSSION Greater bacterial diversity was associated with lower MD, and DQ was associated with various mood state subscales in this sample of adults.
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Affiliation(s)
- Kristen S Smith
- Department of Nutritional Sciences, Auburn University, Auburn, AL, USA
| | - Molly M Morris
- College of Science and Mathematics, Auburn University, Auburn, AL, USA
| | - Casey D Morrow
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Josh R Novak
- Department of Human Development and Family Science, Auburn University, Auburn, AL, USA
| | | | - Andrew D Frugé
- Department of Nutritional Sciences, Auburn University, Auburn, AL, USA
- College of Nursing, Auburn University, Auburn, AL, USA
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Fidino M, Sander HA, Lewis JS, Lehrer EW, Rivera K, Murray MH, Adams HC, Kase A, Flores A, Stankowich T, Schell CJ, Salsbury CM, Rohnke AT, Jordan MJ, Green AM, R. Gramza A, Zellmer AJ, Williamson J, Surasinghe TD, Storm H, Sparks KL, Ryan TJ, Remine KR, Pendergast ME, Mullen K, Minier DE, Middaugh CR, Mertl AL, McClung MR, Long RA, Larson RN, Kohl MT, Harris LR, Hall CT, Haight JD, Drake D, Davidge AM, Cheek AO, Bloch CP, Biro EG, Anthonysamy WJB, Angstmann JL, Allen ML, Adalsteinsson SA, Short Gianotti AG, LaMontagne JM, Gelmi-Candusso TA, Magle SB. Gentrification drives patterns of alpha and beta diversity in cities. Proc Natl Acad Sci U S A 2024; 121:e2318596121. [PMID: 38621142 PMCID: PMC11047091 DOI: 10.1073/pnas.2318596121] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/30/2024] [Indexed: 04/17/2024] Open
Abstract
While there is increasing recognition that social processes in cities like gentrification have ecological consequences, we lack nuanced understanding of the ways gentrification affects urban biodiversity. We analyzed a large camera trap dataset of mammals (>500 g) to evaluate how gentrification impacts species richness and community composition across 23 US cities. After controlling for the negative effect of impervious cover, gentrified parts of cities had the highest mammal species richness. Change in community composition was associated with gentrification in a few cities, which were mostly located along the West Coast. At the species level, roughly half (11 of 21 mammals) had higher occupancy in gentrified parts of a city, especially when impervious cover was low. Our results indicate that the impacts of gentrification extend to nonhuman animals, which provides further evidence that some aspects of nature in cities, such as wildlife, are chronically inaccessible to marginalized human populations.
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Affiliation(s)
- Mason Fidino
- Conservation and Science Department, Lincoln Park Zoo, Chicago, IL60614
| | - Heather A. Sander
- Department of Geographical and Sustainability Sciences, University of Iowa, Iowa City, IA52242
| | - Jesse S. Lewis
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ85287
| | | | - Kimberly Rivera
- Conservation and Science Department, Lincoln Park Zoo, Chicago, IL60614
| | - Maureen H. Murray
- Conservation and Science Department, Lincoln Park Zoo, Chicago, IL60614
| | - Henry C. Adams
- Conservation and Science Department, Lincoln Park Zoo, Chicago, IL60614
| | - Anna Kase
- Conservation and Science Department, Lincoln Park Zoo, Chicago, IL60614
| | - Andrea Flores
- Conservation and Science Department, Lincoln Park Zoo, Chicago, IL60614
| | - Theodore Stankowich
- Department of Biological Sciences, California State University, Long Beach, CA90840
| | - Christopher J. Schell
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA94720
| | - Carmen M. Salsbury
- Department of Biological Sciences, Butler University, Indianapolis, IN46208
| | - Adam T. Rohnke
- Department of Wildlife, Fisheries, and Aquaculture, Mississippi State University, Jackson, MS39759
| | - Mark J. Jordan
- Department of Biology, Seattle University, Seattle, WA98112
| | - Austin M. Green
- Science Research Initiative, University of Utah, Salt Lake City, UT84112
| | | | - Amanda J. Zellmer
- Department of Biology, Occidental College, Los Angeles, CA90042
- Arroyos & Foothills Conservancy, Pasadena, CA91102
| | | | - Thilina D. Surasinghe
- Department of Biological Sciences, Bridgewater State University, Bridgewater, MA02325
| | - Hunter Storm
- University Honors College, Portland State University, Portland, OR97201
| | - Kimberly L. Sparks
- Research Division, Arkansas Game and Fish Commission, Little Rock, AR72205
| | - Travis J. Ryan
- Department of Biological Sciences, Butler University, Indianapolis, IN46208
| | - Katie R. Remine
- Wildlife Conservation Division, Woodland Park Zoo, Seattle, WA98103
| | | | - Kayleigh Mullen
- Conservation Department, Utah’s Hogle Zoo, Salt Lake City, UT84108
| | | | | | - Amy L. Mertl
- Department of Natural Sciences and Mathematics, Lesley University, Cambridge, MA02138
| | | | - Robert A. Long
- Wildlife Conservation Division, Woodland Park Zoo, Seattle, WA98103
| | - Rachel N. Larson
- Department of Geographical and Sustainability Sciences, University of Iowa, Iowa City, IA52242
| | - Michel T. Kohl
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA30602
| | - Lavendar R. Harris
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA30602
| | - Courtney T. Hall
- Conservation Operations Department, Memorial Park Conservancy, Houston, TX77007
| | | | - David Drake
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI53706
| | - Alyssa M. Davidge
- Department of Integrative Biology, University of Colorado, Denver, CO80204
| | - Ann O. Cheek
- Department of Biology and Biochemistry, University of Houston, Houston, TX77004
| | - Christopher P. Bloch
- Department of Biological Sciences, Bridgewater State University, Bridgewater, MA02325
| | - Elizabeth G. Biro
- Tyson Research Center, Washington University in St. Louis, Eureka, MO63025
| | | | - Julia L. Angstmann
- Center for Urban Ecology and Sustainability, Butler University, Indianapolis, IN42608
| | - Maximilian L. Allen
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL61820
| | | | | | - Jalene M. LaMontagne
- Conservation and Science Department, Lincoln Park Zoo, Chicago, IL60614
- Department of Biological Sciences, DePaul University, Chicago, IL60614
| | | | - Seth B. Magle
- Conservation and Science Department, Lincoln Park Zoo, Chicago, IL60614
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Zhao Y, Liu T, Wu S, Zhang D, Xiao Z, Ren Z, Li L, Liu S, Xiao Y, Tang Q. Insight into the soil bacterial community succession of Nicotiana benthamiana in response to Tobacco mosaic virus. Front Microbiol 2024; 15:1341296. [PMID: 38357345 PMCID: PMC10864551 DOI: 10.3389/fmicb.2024.1341296] [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: 11/21/2023] [Accepted: 01/15/2024] [Indexed: 02/16/2024] Open
Abstract
Background Tobacco mosaic virus (TMV) is one famous plant virus responsible for substantial economic losses worldwide. However, the roles of bacterial communities in response to TMV in the tobacco rhizosphere remain unclear. Methods We explored the soil physicochemical properties and bacterial community succession of the healthy (YTH) and diseased (YTD) plants with TMV infection by 16S rRNA gene sequencing and bioinformatics analysis. Results We found that soil pH in the YTD group was significantly lower than in the YTH group, and the soil available nutrients were substantially higher. The bacterial community analysis found that the diversity and structure significantly differed post-TMV disease onset. With TMV inoculated, the alpha diversity of the bacterial community in the YTD was markedly higher than that in the YTH group at the early stage. However, the alpha diversity in the YTD group subsequently decreased to lower than in the YTH group. The early bacterial structure of healthy plants exhibited higher susceptibility to TMV infection, whereas, in the subsequent stages, there was an enrichment of beneficial bacterial (e.g., Ramlibacter, Sphingomonas, Streptomyces, and Niastella) and enhanced energy metabolism and nucleotide metabolism in bacteria. Conclusion The initial soil bacterial community exhibited susceptibility to TMV infection, which might contribute to strengthening resistance of Tobacco to TMV.
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Affiliation(s)
- Yuqiang Zhao
- College of Plant Protection and College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | | | | | - Deyong Zhang
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | | | - Zuohua Ren
- College of Plant Protection and College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Lingling Li
- College of Plant Protection and College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Suoni Liu
- College of Plant Protection and College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Yunhua Xiao
- College of Plant Protection and College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Qianjun Tang
- College of Plant Protection and College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
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An ZG, Shang HS, Cui ZJ, Huang YF, Wu R, Li RH. Arbuscular mycorrhizal fungal communities in soils where astragalus had grown for 2 years were similar to those in the abandoned farmland. Front Microbiol 2024; 14:1293496. [PMID: 38239725 PMCID: PMC10794390 DOI: 10.3389/fmicb.2023.1293496] [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: 09/13/2023] [Accepted: 11/14/2023] [Indexed: 01/22/2024] Open
Abstract
Purpose Astragalus-cultivated soils are enriched in arbuscular mycorrhizal fungi (AMF); however, the community changes of AMF between years in stragalus-cultivated soils are still unclear. Methods To illustrate this, using high-throughput amplicon sequencing and quantitative real-time PCR, we analyzed the AMF communities of the abandoned farmlands and interannual astragalus-cultivated soils for 1-, 2-, 3-, and 4-years, including community composition, dominant, core, specific and significantly fluctuating AMF, co-occurrence network, alpha diversity, and beta diversity. Results A total of 74 OTUs were classified into one phylum, Glomeromycota; one class, Glomeromycetes; four orders; four families; and six genera. The 2-year soil had the highest number of reads among the interannual soils. Only one OTU was shared among all interannual soils. The treatments significantly affected the Ace, Shannoneven, and Shannon estimators of the communities. The 2-year soil had the highest richness, evenness, and diversity among all interannual soils and was the closest to the abandoned farmland in terms of alpha diversity. Glomus of the family Glomeraceae was the dominant genus present in all treatments, and the composition of the dominant genus in interannual soils was different. Both Glomus and Diversispora were the core AMF in interannual soils, and specific AMF existed in different interannual soils. Glomus is a genus that exhibits significant interannual variation. The interannual time significantly affected the network connectivity. The results of the principal coordinate analysis showed that the community composition of the interannual soils was close to each other and separated from the abandoned farmland, and that the interannual time significantly affected the community composition. Conclusion Among the interannual soils, the 2-year soil may be more suitable for A. sinensis seedling rotation.
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Affiliation(s)
- Zhi-Gang An
- College of Public Health, Gansu University of Chinese Medicine, Lanzhou, China
- Pharmacy Department, Gansu University of Chinese Medicine, Dingxi, China
| | - Hu-Shan Shang
- Chinese Herbal Medicine Institute, Dingxi Academy of Agricultural Sciences, Dingxi, China
| | - Zhi-Jia Cui
- Pharmacy Department, Gansu University of Chinese Medicine, Dingxi, China
| | - Yu-Fang Huang
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, China
| | - Rui Wu
- Pharmacy Department, Gansu University of Chinese Medicine, Dingxi, China
| | - Run-Hong Li
- Pharmacy Department, Gansu University of Chinese Medicine, Dingxi, China
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Liu K, Xie N, Wang Y. Quantifying mitochondrial heteroplasmy diversity: A computational approach. Mol Ecol Resour 2024; 24:e13874. [PMID: 37815422 DOI: 10.1111/1755-0998.13874] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/22/2023] [Indexed: 10/11/2023]
Abstract
Biodiversity plays a pivotal role in sustaining ecosystem processes, encompassing diverse biological species, genetic types and the intricacies of ecosystem composition. However, the precise definition of biodiversity at the individual level remains a challenging endeavour. Hill numbers, derived from Rényi's entropy, have emerged as a popular measure of diversity, with a recent unified framework extending their application across various levels, from genetics to ecosystems. In this study, we employ a computational approach to exploring the diversity of mitochondrial heteroplasmy using real-world data. By adopting Hill numbers with q = 2, we demonstrate the feasibility of quantifying mitochondrial heteroplasmy diversity within and between individuals and populations. Furthermore, we investigate the alpha diversity of mitochondrial heteroplasmy among different species, revealing heterogeneity at multiple levels, including mitogenome components and protein-coding genes (PCGs). Our analysis explores large-scale mitochondrial heteroplasmy data in humans, examining the relationship between alpha diversity at the mitogenome components and PCGs level. Notably, we do not find a significant correlation between these two levels. Additionally, we observe significant correlations in alpha diversity between mothers and children in blood samples, exceeding the reported R2 value for allele frequency correlations. Moreover, our investigation of beta diversity and local overlay similarity demonstrates that heteroplasmy variant distributions in different tissues of children more closely resemble those of their mothers. Through systematic quantification and analysis of mitochondrial heteroplasmy diversity, this study enhances our understanding of heterogeneity at multiple levels, from individuals to populations, providing new insights into this fundamental dimension of biodiversity.
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Affiliation(s)
- Kai Liu
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Nan Xie
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Yuxi Wang
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
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Sun ZB, Hu YF, Song HJ, Cong SB, Wang L. Cry1Ac Mixed with Gentamicin Influences the Intestinal Microbial Diversity and Community Composition of Pink Bollworms. Life (Basel) 2023; 14:58. [PMID: 38255673 PMCID: PMC10820413 DOI: 10.3390/life14010058] [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: 11/29/2023] [Revised: 12/25/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
Pink bollworms severely affect the production of cotton. The method currently used for pink bollworm control is the planting of Bt (Bacillus thuringiensis) protein-expressing transgenic cotton. However, pink bollworms can develop strong resistance to Bt proteins in transgenic cotton because of the large planting area and long planting time of this crop, which severely affects the control of pink bollworms. Intestinal microorganisms play very important roles in insect growth, development and Bt resistance. However, the effect of intestinal microorganisms on pink bollworm Bt resistance is still unclear. The current study aimed to analyze the effect of intestinal microorganisms on the Bt resistance of pink bollworms. Intestinal microorganisms associated with Bt resistance were initially screened through Illumina MiSeq sequencing and analysis. The results showed that feeding with a mixture of gentamicin, Cry1Ac and an artificial diet could significantly increase the mortality of pink bollworm larvae compared with feeding with of a mixture of Cry1Ac and an artificial diet or an artificial diet alone. The microbial diversity, community structure and composition of the pink bollworm larval intestine were significantly influenced by feeding with a mixture of gentamicin, Cry1Ac and an artificial diet. Several intestinal bacteria with significantly altered abundances after treatment with gentamicin were preliminarily screened as potential resources for addressing Bt toxicity. This study provides useful strategies for addressing the Bt resistance of pink bollworms.
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Affiliation(s)
- Zhan-Bin Sun
- China Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing 100048, China
| | - Ya-Feng Hu
- China Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing 100048, China
| | - Han-Jian Song
- China Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing 100048, China
| | - Sheng-Bo Cong
- Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Ling Wang
- Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
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Erhunmwunse AS, Guerra VA, Liu JC, Mackowiak CL, Blount ARS, Dubeux JCB, Liao HL. Soil Bacterial Diversity Responds to Long-Term Establishment of Perennial Legumes in Warm-Season Grassland at Two Soil Depths. Microorganisms 2023; 11:3002. [PMID: 38138146 PMCID: PMC10745480 DOI: 10.3390/microorganisms11123002] [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: 10/31/2023] [Revised: 11/24/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
The introduction of rhizoma peanut (RP Arachis glabrata Benth) into bahiagrass (Paspalum notatum Flüggé) may require time to develop stable plant-soil microbe interactions as the microbial legacy of the previous plant community may be long-lasting. A previous study showed that <2 years of introducing rhizoma peanut into bahiagrass pastures minimally affected soil bacterial diversity and community composition. In this study, we compared the effects of the long-term inclusion of rhizoma peanut (>8 years) into bahiagrass on soil bacterial diversity and community composition against their monocultures at 0 to 15 and 15 to 30 cm soil depths using next-generation sequencing to target bacterial 16S V3-V4 regions. We observed that a well-established RP-bahiagrass mixed stand led to a 36% increase in bacterial alpha diversity compared to the bahiagrass monoculture. There was a shift from a soil bacterial community dominated by Proteobacteria (~26%) reported in other bahiagrass and rhizoma peanut studies to a soil bacterial community dominated by Firmicutes (39%) in our study. The relative abundance of the bacterial genus Crossiella, known for its antimicrobial traits, was enhanced in the presence of RP. Differences in soil bacterial diversity and community composition were substantial between 0 to 15 and 15 to 30 cm soil layers, with N2-fixing bacteria belonging to the phylum Proteobacteria concentrated in 0 to 15 cm. Introducing RP into bahiagrass pastures is a highly sustainable alternative to mineral N fertilizer inputs. Our results provide evidence that this system also promotes greater soil microbial diversity and is associated with unique taxa that require further study to better understand their contributions to healthy pastures.
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Affiliation(s)
- Adesuwa Sylvia Erhunmwunse
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL 32351, USA (H.-L.L.)
- Soil, Water and Ecosystem Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Victor Alonso Guerra
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL 32351, USA (H.-L.L.)
- Soil, Water and Ecosystem Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Jung-Chen Liu
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL 32351, USA (H.-L.L.)
- Soil, Water and Ecosystem Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Cheryl L. Mackowiak
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL 32351, USA (H.-L.L.)
- Soil, Water and Ecosystem Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Ann Rachel Soffes Blount
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL 32351, USA (H.-L.L.)
| | - José Carlos Batista Dubeux
- North Florida Research and Education Center, University of Florida, 3925 Highway 71, Marianna, FL 32446, USA;
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL 32351, USA (H.-L.L.)
- Soil, Water and Ecosystem Sciences Department, University of Florida, Gainesville, FL 32611, USA
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Ouyang ML, Zou SP, Cheng Q, Shi X, Zhao YZ, Sun MH. Effect of potassium-competitive acid blockers on human gut microbiota: a systematic review and meta-analysis. Front Pharmacol 2023; 14:1269125. [PMID: 38192408 PMCID: PMC10773775 DOI: 10.3389/fphar.2023.1269125] [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: 07/29/2023] [Accepted: 11/30/2023] [Indexed: 01/10/2024] Open
Abstract
Background: Vonoprazan has been reported to exert more potent and long-lasting gastric acid inhibition than proton pump inhibitors, potentially leading to a greater impact on the gut microbiota. This study aimed to clarify changes in microbial diversity and bacterial composition after VPZ treatments. Methods: We searched from PubMed, Embase, WOS, Scopus, Cochrane Library, and ClinicalTrials.gov (all years up to May 2023). The primary outcomes were alpha and beta diversity, as well as differences in gut microbiota composition between before and after VPZ treatments. We performed a meta-analysis to uncover the potential changes in human gut microbiota among VPZ users by pooled mean difference (MD) with a 95% confidence interval (CI). The risk of bias was assessed using the ROBINS-I tool. Results: A total of 12 studies were included to compare differences before and after VPZ treatments. Compared with baseline, alpha diversity was significantly reduced after VPZ treatments and gradually returned to baseline with longer follow-up. At the phylum level, there was a decrease in the relative abundance of Firmicutes and Actinobacteria, while Bacteroidetes increased compared with baseline. At the genus level, we found a significant decrease in the relative abundance of Coprococcus and Bifidobacterium and a significant increase in the relative abundance of Bacteroides compared with those before treatment. In subgroup analyses according to country and participants, we found differences in microbial changes after VPZ treatments. Conclusion: Vonoprazan can affect the changes of gut microbiota, which may be potentially associated with its strong ability of acid inhibition. However, due to the large heterogeneity, further studies are required to validate these findings. Systematic Review Registration: https://www.crd.york.ac.uk/prospero/, identifier CRD42023412265.
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Affiliation(s)
| | | | | | | | | | - Ming-Hui Sun
- Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Wang M, Pu W, Wang S, Zeng X, Sui X, Wang X. pH-Related Changes in Soil Bacterial Communities in the Sanjiang Plain, Northeast China. Microorganisms 2023; 11:2950. [PMID: 38138094 PMCID: PMC10745975 DOI: 10.3390/microorganisms11122950] [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: 10/25/2023] [Revised: 11/16/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Soil bacteria are crucial components of terrestrial ecosystems, playing an important role in soil biogeochemical cycles. Although bacterial community diversity and composition are regulated by many abiotic and biotic factors, how soil physiochemical properties impact the soil bacteria community diversity and composition in wetland ecosystems remains largely unknown. In this study, we used high-throughput sequencing technology to investigate the diversity and composition of a soil bacterial community, as well as used the structural equation modeling (SEM) method to investigate the relationships of the soil's physicochemical properties (i.e., soil pH, soil organic carbon (SOC), total nitrogen (TN), ammonium nitrogen (NH4+N), electrical conductivity (EC) and nitrate nitrogen (NO3-N)), and soil bacterial community structures in three typical wetland sites in the Sanjiang Plain wetland. Our results showed that the soil physicochemical properties significantly changed the α and β-diversity of the soil bacteria communities, e.g., soil TN, NH4+N, NO3-N, and SOC were the main soil factors affecting the soil bacterial α-diversity. The soil TN and pH were the key soil factors affecting the soil bacterial community. Our results suggest that changes in soil pH indirectly affect soil bacterial communities by altering the soil nitrogenous nutrient content.
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Affiliation(s)
- Mingyu Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China; (M.W.); (W.P.); (S.W.)
| | - Wenmiao Pu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China; (M.W.); (W.P.); (S.W.)
| | - Shenzheng Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China; (M.W.); (W.P.); (S.W.)
| | - Xiannan Zeng
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin 150088, China;
| | - Xin Sui
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China; (M.W.); (W.P.); (S.W.)
| | - Xin Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China; (M.W.); (W.P.); (S.W.)
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11
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Huovinen V, Aatsinki AK, Kataja EL, Munukka E, Keskitalo A, Lamichhane S, Raunioniemi P, Bridgett DJ, Lahti L, O'Mahony SM, Dickens A, Korja R, Karlsson H, Nolvi S, Karlsson L. Infant gut microbiota and negative and fear reactivity. Dev Psychopathol 2023:1-16. [PMID: 37974473 DOI: 10.1017/s0954579423001396] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
BACKGROUND Studies indicate that gut microbiota is related to neurodevelopmental and behavioral outcomes. Accordingly, early gut microbiota composition (GMC) has been linked to child temperament, but research is still scarce. The aim of this study was to examine how early GMC at 2.5 months is associated with child negative and fear reactivity at 8 and 12 months since they are potentially important intermediate phenotypes of later child psychiatric disorders. METHODS Our study population was 330 infants enrolled in the longitudinal FinnBrain Birth Cohort Study. Gut microbiota composition was analyzed using stool sample 16s rRNA sequencing. Negative and fear reactivity were assessed using the Laboratory Temperament Assessment Battery (Lab-TAB) at child's age of 8 months (n =150) and the Infant Behavior Questionnaire-Revised Short Form (IBQ-R SF) at child's age of 12 months (n = 276). CONCLUSIONS We found a positive association between alpha diversity and reported fear reactivity and differing microbial community composition based on negative reactivity for boys. Isobutyric acid correlated with observed negative reactivity, however, this association attenuated in the linear model. Several genera were associated with the selected infant temperament traits. This study adds to the growing literature on links between infant gut microbiota and temperament informing future mechanistic studies.
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Affiliation(s)
- Venla Huovinen
- Department of Clinical Medicine, Psychiatry, FinnBrain Birth Cohort Study, Turku Brain and Mind Center, University of Turku, Turku, Finland
| | - Anna-Katariina Aatsinki
- Department of Clinical Medicine, Psychiatry, FinnBrain Birth Cohort Study, Turku Brain and Mind Center, University of Turku, Turku, Finland
- Centre for Population Health Research, Turku University Hospital and University of Turku, Turku, Finland
| | - Eeva-Leena Kataja
- Department of Clinical Medicine, Psychiatry, FinnBrain Birth Cohort Study, Turku Brain and Mind Center, University of Turku, Turku, Finland
| | - Eveliina Munukka
- Microbiome Biobank, Research Center for Infections and Immunity Institute of Biomedicine, University of Turku and Turku University, Hospital, Turku, Finland
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Anniina Keskitalo
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Santosh Lamichhane
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Peppi Raunioniemi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - David J Bridgett
- Department of Psychology, Northern Illinois University, DeKalb, IL, USA
| | - Leo Lahti
- Department of Computing, Faculty of Technology, University of Turku, Turku, Finland
| | - Siobhain M O'Mahony
- Department of Anatomy and Neuroscience, APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Alex Dickens
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Riikka Korja
- Department of Clinical Medicine, Psychiatry, FinnBrain Birth Cohort Study, Turku Brain and Mind Center, University of Turku, Turku, Finland
- Department of Psychology and Speech-Language Pathology, University of Turku, Turku, Finland
| | - Hasse Karlsson
- Department of Clinical Medicine, Psychiatry, FinnBrain Birth Cohort Study, Turku Brain and Mind Center, University of Turku, Turku, Finland
- Centre for Population Health Research, Turku University Hospital and University of Turku, Turku, Finland
| | - Saara Nolvi
- Department of Clinical Medicine, Psychiatry, FinnBrain Birth Cohort Study, Turku Brain and Mind Center, University of Turku, Turku, Finland
- Department of Psychology and Speech-Language Pathology, University of Turku, Turku, Finland
- Turku Institute for Advanced Studies, University of Turku, Turku, Finland
| | - Linnea Karlsson
- Department of Clinical Medicine, Psychiatry, FinnBrain Birth Cohort Study, Turku Brain and Mind Center, University of Turku, Turku, Finland
- Centre for Population Health Research, Turku University Hospital and University of Turku, Turku, Finland
- Department of Clinical Medicine, Pediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
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12
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Ferrarini A, Gustin M, Celada C. Simulation Modeling Unveils the Unalike Effects of Alternative Strategies for Waterbird Conservation in the Coastal Wetlands of Sardinia (Italy). Biology (Basel) 2023; 12:1440. [PMID: 37998040 PMCID: PMC10669041 DOI: 10.3390/biology12111440] [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] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/12/2023] [Accepted: 11/14/2023] [Indexed: 11/25/2023]
Abstract
The Sardinian wetlands (Italy) act as stopover sites for many migratory birds along the central eastern Mediterranean bird flyway. These wetlands are now severely threatened by human activities and climate change. Accordingly, we built a simulation framework to predict the effects of several counterfactual and management scenarios on the level of avian diversity in the coastal wetlands of Sardinia. We found that the alpha avian diversity (i.e., the mean number of avian species per wetland) is destined to (a) decrease due to the most likely increase in water salinity, water discharges, and tourism pressure; and (b) halve (from 14.9 to 7.4, with 9 wetlands out of 22 predicted to host only between two and five waterbird species) in the worst possible scenario. However, the results also showed that proper management strategies could prevent and reverse such outcomes. Restrictions on tourism activities, water desalination, prevention of future saltwater intrusions, and the prohibition of water discharges could markedly favor the avian diversity in these wetlands, with an expected increase in the alpha avian diversity from 14.9 to 24.8 (and 10 wetlands out of 22 predicted to host from 29 to 32 waterbird species) in the best possible scenario. The importance of our results could be emphasized in the management plans of these important wetlands, most of which belong to the Natura 2000 network.
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13
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Cantu-Jungles TM, Hamaker BR. Tuning Expectations to Reality: Don't Expect Increased Gut Microbiota Diversity with Dietary Fiber. J Nutr 2023; 153:3156-3163. [PMID: 37690780 DOI: 10.1016/j.tjnut.2023.09.001] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/01/2023] [Indexed: 09/12/2023] Open
Abstract
Dietary approaches, particularly those including fiber supplementation, can be used to promote health benefits by shaping gut microbial communities. Whereas community diversity measures, such as richness and evenness, are often used in microbial ecology to make sense of these complex and vast microbial ecosystems, it is less clear how these concepts apply when dietary fiber supplementation is given. In this perspective, we summarize and demonstrate how factors including experimental approach, number of bacteria sharing a dietary fiber, and initial relative abundances of bacteria that use a fiber can significantly affect diversity outcomes in fiber fermentation studies. We also show that a reduction in alpha diversity is possible, and perhaps expected, for most approaches that use fermentable fibers to beneficially shape the gut microbial community while still achieving health-related improvements.
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Affiliation(s)
- Thaisa M Cantu-Jungles
- Department of Food Science, Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, United States.
| | - Bruce R Hamaker
- Department of Food Science, Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, United States
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14
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Chen G, Zhou X, Zhu Y, Shi W, Kong L. Gut microbiome characteristics in subjective cognitive decline, mild cognitive impairment and Alzheimer's disease: a systematic review and meta-analysis. Eur J Neurol 2023; 30:3568-3580. [PMID: 37399128 DOI: 10.1111/ene.15961] [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: 11/16/2022] [Revised: 05/08/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023]
Abstract
BACKGROUND AND PURPOSE The gut microbiome has been reported to be closely related to Alzheimer's disease (AD) progression. Here, a comprehensive meta-analysis of gut microbial characteristics in AD, mild cognitive impairment (MCI) and subjective cognitive decline (SCD) was performed to compare gut microbial alterations at each stage. METHODS A total of 10 databases (CNKI, WanFang, VIP, SinoMed, WOS, PubMed, Embase, Cochrane Library, PsycINFO and Void) were searched and 34 case-control studies were included. α and β diversity and the relative abundance of gut microbiota were analysed as outcome indices. Data analysis was performed using Review Manager (5.4.1) and R. RESULTS Chao1 and Shannon index levels in AD were significantly lower compared with healthy controls (HCs), and the Chao1 index was significantly lower in MCI compared with HCs. There was a significant difference in β diversity of gut microbiomes in patients (SCD, MCI, AD) compared with HCs. The relative abundance of Firmicutes at the phylum level was significantly lower in patients with AD and MCI than HCs. However, the relative abundance of Bacteroidetes at the phylum level was significantly higher in patients with MCI than HCs. There was an increasing trend for Enterobacteriaceae and a decreasing trend for Ruminococcaceae, Lachnospiraceae and Lactobacillus during AD; Lactobacillus showed a decreasing trend early in SCD. CONCLUSION Our results indicated that there were gut microbiological abnormalities in AD, even as early as the SCD stage. The dynamic, consistent changes in gut microbes with the disease process showed that they might serve as potential biomarkers for early identification and diagnosis of AD.
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Affiliation(s)
- Guanlin Chen
- Department of Psychology, Shanghai Normal University, Shanghai, China
| | - Xiaoqi Zhou
- Center for Global Change and Ecological Forecasting, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Yikang Zhu
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wendian Shi
- Department of Psychology, Shanghai Normal University, Shanghai, China
| | - Li Kong
- Department of Psychology, Shanghai Normal University, Shanghai, China
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15
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Zhang L, Ren W, Bi Y, Zhang J, Cheng Y, Xu X. Effects of different feeding patterns on the rumen bacterial community of tan lambs, based on high-throughput sequencing of 16S rRNA amplicons. Front Microbiol 2023; 14:1228935. [PMID: 37928689 PMCID: PMC10621797 DOI: 10.3389/fmicb.2023.1228935] [Citation(s) in RCA: 2] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/06/2023] [Indexed: 11/07/2023] Open
Abstract
Introduction The mutton quality of Chinese Tan lambs (Ovis aries) has declined as feeding patterns have shifted from pasturing to pen rationing. While pen-fed can enhance the growth performance of sheep, it falls short in terms of meat quality attributes such as meat color and tenderness. Furthermore, compared to pen-fed, pasture-fed husbandry increases the proportion of oxidative muscle fibers, decreases the proportion of glycolytic muscle fibers, and reduces LDH (lactate dehydrogenase) activity. Mutton quality is affected by fatty acids, and rumen microorganisms play a role in the synthesis of short-chain fatty acids, long-chain fatty acids, and conjugated linoleic acids. Methods We used 16S rRNA sequencing to analyze the effects of two feeding patterns on the rumen bacteria of Tan lambs. In a randomized block design with 24 newborn Tan lambs, 12 lambs were fed by ewes in pasture and 12 were fed by pen-fed ewes. At 2 months, the biceps femoris and the longissimus dorsi were analyzed by gas chromatography for intramuscular fat content and fatty acids composition, and DNA in the rumen contents was extracted and used to analyze the structure of the bacterial community. Results Different feeding patterns had no significant effect on the intramuscular fat content of the biceps femoris and longissimus dorsi of the lambs, but there was a significant effect on fatty acids composition. The fatty acids c18:3n3 and c20:5n3 were significantly higher in the biceps femoris and longissimus dorsi of the pasture group than the pen-ration group. The alpha diversity of rumen bacteria was significantly greater in the pasture group compared to the pen-ration group. The ACE index, Chao1 index, Shannon index, and Simpson index were all notably higher in the pasture group than in the pen-ration group. Utilizing beta diversity analysis to examine the differences in rumen bacteria between the pasture group and pen-ration group, it was observed that the homogeneity of bacteria in the pasture group was lower than that in the pen-ration group. Furthermore, the diversity of rumen bacteria in the pasture group was greater than that in the pen-ration group. Twenty-one phyla were identified in the pasture group, and 14 phyla were identified in the pen-ration group. The dominant phyla in the pasture group were Bacteroidetes and Fibrobacteres; the dominant phyla in the pen-ration group were Proteobacteria and Bacteroidetes. The relative abundance of Proteobacteria was significantly higher in the pen-ration group than in the pasture group (p < 0.01). Diversity at the genus level was also higher in the pasture group, with 176 genera in the pasture group and 113 genera in the pen-ration group. The dominant genera in the pasture group were Prevotella_1, Rikenellaceae_RC9_gut_group, and Bacteroidales_BS11_gut_group_Na; the dominant genera in the pen-ration group were Prevotella_1, Prevotella_7, Succinivibrionaceae_UCG-001, and Succinivibrionaceae_NA. Discussion The rumen bacterial community of Tan sheep is significantly influenced by pen-ration and pasture-fed conditions, leading to variations in fatty acid content in the muscle, which in turn affects the flavor and nutritional value of the meat to some extent. Pasture-fed conditions have been shown to enhance the diversity of rumen bacterial community structure in Tan sheep, thereby increasing the nutritional value of their meat.
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Affiliation(s)
- Lili Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Wenyi Ren
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Yanliang Bi
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Yuchen Cheng
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Xiaofeng Xu
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
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Persely A, Beszedics B, Paloczi K, Piroska M, Alijanpourotaghsara A, Strelnikov D, Vessal A, Szabo H, Hernyes A, Zoldi L, Jokkel Z, Fekete A, Juhasz J, Makra N, Szabo D, Buzas E, Tarnoki AD, Tarnoki DL. Analysis of Genetic and MRI Changes, Blood Markers, and Risk Factors in a Twin Pair Discordant of Progressive Supranuclear Palsy. Medicina (Kaunas) 2023; 59:1696. [PMID: 37893413 PMCID: PMC10608279 DOI: 10.3390/medicina59101696] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/14/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023]
Abstract
Background and Objectives: Progressive supranuclear palsy (PSP) is a neurodegenerative disease, a tauopathy, which results in a wide clinical spectrum of neurological symptoms. The diagnosis is mostly based on clinical signs and neuroimaging; however, possible biomarkers for screening have been under investigation, and the role of the gut microbiome is unknown. The aim of our study was to identify potential blood biomarkers and observe variations in the gut microbiome within a PSP discordant monozygotic twin pair. Materials and Methods: Anthropometric measurements, neuropsychological tests, and the neurological state were evaluated. Blood was collected for metabolic profiling and for the detection of neurodegenerative and vascular biomarkers. Both the gut microbiome and brain MRI results were thoroughly examined. Results: We found a relevant difference between alpha-synuclein levels and moderate difference in the levels of MMP-2, MB, Apo-A1, Apo-CIII, and Apo-H. With respect to the ratios, a small difference was observed for ApoA1/SAA and ApoB/ApoA1. Using a microbiome analysis, we also discovered a relative dysbiosis, and the MRI results revealed midbrain and frontoparietal cortical atrophy along with a reduction in overall brain volumes and an increase in white matter lesions in the affected twin. Conclusions: We observed significant differences between the unaffected and affected twins in some risk factors and blood biomarkers, along with disparities in the gut microbiome. Additionally, we detected abnormalities in brain MRI results and alterations in cognitive functions.
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Affiliation(s)
- Aliz Persely
- Medical Imaging Centre, Semmelweis University, 1082 Budapest, Hungary; (A.P.); (B.B.); (M.P.); (A.A.); (D.S.); (A.V.); (H.S.); (A.H.); (L.Z.); (Z.J.); (A.F.); (A.D.T.)
- Neurology Department, Medical Centre Hungarian Defence Forces, 1134 Budapest, Hungary
| | - Beatrix Beszedics
- Medical Imaging Centre, Semmelweis University, 1082 Budapest, Hungary; (A.P.); (B.B.); (M.P.); (A.A.); (D.S.); (A.V.); (H.S.); (A.H.); (L.Z.); (Z.J.); (A.F.); (A.D.T.)
| | - Krisztina Paloczi
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, 1085 Budapest, Hungary; (K.P.); (E.B.)
| | - Marton Piroska
- Medical Imaging Centre, Semmelweis University, 1082 Budapest, Hungary; (A.P.); (B.B.); (M.P.); (A.A.); (D.S.); (A.V.); (H.S.); (A.H.); (L.Z.); (Z.J.); (A.F.); (A.D.T.)
| | - Amirreza Alijanpourotaghsara
- Medical Imaging Centre, Semmelweis University, 1082 Budapest, Hungary; (A.P.); (B.B.); (M.P.); (A.A.); (D.S.); (A.V.); (H.S.); (A.H.); (L.Z.); (Z.J.); (A.F.); (A.D.T.)
| | - David Strelnikov
- Medical Imaging Centre, Semmelweis University, 1082 Budapest, Hungary; (A.P.); (B.B.); (M.P.); (A.A.); (D.S.); (A.V.); (H.S.); (A.H.); (L.Z.); (Z.J.); (A.F.); (A.D.T.)
| | - Arsalan Vessal
- Medical Imaging Centre, Semmelweis University, 1082 Budapest, Hungary; (A.P.); (B.B.); (M.P.); (A.A.); (D.S.); (A.V.); (H.S.); (A.H.); (L.Z.); (Z.J.); (A.F.); (A.D.T.)
| | - Helga Szabo
- Medical Imaging Centre, Semmelweis University, 1082 Budapest, Hungary; (A.P.); (B.B.); (M.P.); (A.A.); (D.S.); (A.V.); (H.S.); (A.H.); (L.Z.); (Z.J.); (A.F.); (A.D.T.)
- Central Radiological Diagnostic Department, Medical Centre Hungarian Defence Forces, 1134 Budapest, Hungary
| | - Anita Hernyes
- Medical Imaging Centre, Semmelweis University, 1082 Budapest, Hungary; (A.P.); (B.B.); (M.P.); (A.A.); (D.S.); (A.V.); (H.S.); (A.H.); (L.Z.); (Z.J.); (A.F.); (A.D.T.)
| | - Luca Zoldi
- Medical Imaging Centre, Semmelweis University, 1082 Budapest, Hungary; (A.P.); (B.B.); (M.P.); (A.A.); (D.S.); (A.V.); (H.S.); (A.H.); (L.Z.); (Z.J.); (A.F.); (A.D.T.)
| | - Zsofia Jokkel
- Medical Imaging Centre, Semmelweis University, 1082 Budapest, Hungary; (A.P.); (B.B.); (M.P.); (A.A.); (D.S.); (A.V.); (H.S.); (A.H.); (L.Z.); (Z.J.); (A.F.); (A.D.T.)
| | - Andrea Fekete
- Medical Imaging Centre, Semmelweis University, 1082 Budapest, Hungary; (A.P.); (B.B.); (M.P.); (A.A.); (D.S.); (A.V.); (H.S.); (A.H.); (L.Z.); (Z.J.); (A.F.); (A.D.T.)
| | - Janos Juhasz
- Institute of Medical Microbiology, Semmelweis University, 1085 Budapest, Hungary; (J.J.); (N.M.); (D.S.)
- Faculty of Information Technology and Bionics, Pazmany Peter Catholic University, 1085 Budapest, Hungary
| | - Nora Makra
- Institute of Medical Microbiology, Semmelweis University, 1085 Budapest, Hungary; (J.J.); (N.M.); (D.S.)
| | - Dora Szabo
- Institute of Medical Microbiology, Semmelweis University, 1085 Budapest, Hungary; (J.J.); (N.M.); (D.S.)
| | - Edit Buzas
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, 1085 Budapest, Hungary; (K.P.); (E.B.)
| | - Adam Domonkos Tarnoki
- Medical Imaging Centre, Semmelweis University, 1082 Budapest, Hungary; (A.P.); (B.B.); (M.P.); (A.A.); (D.S.); (A.V.); (H.S.); (A.H.); (L.Z.); (Z.J.); (A.F.); (A.D.T.)
| | - David Laszlo Tarnoki
- Medical Imaging Centre, Semmelweis University, 1082 Budapest, Hungary; (A.P.); (B.B.); (M.P.); (A.A.); (D.S.); (A.V.); (H.S.); (A.H.); (L.Z.); (Z.J.); (A.F.); (A.D.T.)
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Howe S, Kegley B, Powell J, Chen S, Zhao J. Effect of bovine respiratory disease on the respiratory microbiome: a meta-analysis. Front Cell Infect Microbiol 2023; 13:1223090. [PMID: 37743862 PMCID: PMC10516580 DOI: 10.3389/fcimb.2023.1223090] [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] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
Background Bovine respiratory disease (BRD) is the most devastating disease affecting beef and dairy cattle producers in North America. An emerging area of interest is the respiratory microbiome's relationship with BRD. However, results regarding the effect of BRD on respiratory microbiome diversity are conflicting. Results To examine the effect of BRD on the alpha diversity of the respiratory microbiome, a meta-analysis analyzing the relationship between the standardized mean difference (SMD) of three alpha diversity metrics (Shannon's Diversity Index (Shannon), Chao1, and Observed features (OTUs, ASVs, species, and reads) and BRD was conducted. Our multi-level model found no difference in Chao1 and Observed features SMDs between calves with BRD and controls. The Shannon SMD was significantly greater in controls compared to that in calves with BRD. Furthermore, we re-analyzed 16S amplicon sequencing data from four previously published datasets to investigate BRD's effect on individual taxa abundances. Additionally, based on Bray Curtis and Jaccard distances, health status, sampling location, and dataset were all significant sources of variation. Using a consensus approach based on RandomForest, DESeq2, and ANCOM-BC2, we identified three differentially abundant amplicon sequence variants (ASVs) within the nasal cavity, ASV5_Mycoplasma, ASV19_Corynebacterium, and ASV37_Ruminococcaceae. However, no ASVs were differentially abundant in the other sampling locations. Moreover, based on SECOM analysis, ASV37_Ruminococcaceae had a negative relationship with ASV1_Mycoplasma_hyorhinis, ASV5_Mycoplasma, and ASV4_Mannheimia. ASV19_Corynebacterium had negative relationships with ASV1_Mycoplasma_hyorhinis, ASV4_Mannheimia, ASV54_Mycoplasma, ASV7_Mycoplasma, and ASV8_Pasteurella. Conclusions Our results confirm a relationship between bovine respiratory disease and respiratory microbiome diversity and composition, which provide additional insight into microbial community dynamics during BRD development. Furthermore, as sampling location and sample processing (dataset) can also affect results, consideration should be taken when comparing results across studies.
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Affiliation(s)
- Samantha Howe
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, United States
| | - Beth Kegley
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, United States
| | - Jeremy Powell
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, United States
| | - Shicheng Chen
- Medical Laboratory Sciences Program, College of Health and Human Sciences, Northern Illinois University, DeKalb, IL, United States
| | - Jiangchao Zhao
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, United States
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Park J, Bushita H, Nakano A, Hara A, Ueno HM, Ozato N, Hosomi K, Kawashima H, Chen YA, Mohsen A, Ohno H, Konishi K, Tanisawa K, Nanri H, Murakami H, Miyachi M, Kunisawa J, Mizuguchi K, Araki M. Ramen Consumption and Gut Microbiota Diversity in Japanese Women: Cross-Sectional Data from the NEXIS Cohort Study. Microorganisms 2023; 11:1892. [PMID: 37630452 PMCID: PMC10458504 DOI: 10.3390/microorganisms11081892] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/20/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
A cross-sectional study involving 224 healthy Japanese adult females explored the relationship between ramen intake, gut microbiota diversity, and blood biochemistry. Using a stepwise regression model, ramen intake was inversely associated with gut microbiome alpha diversity after adjusting for related factors, including diets, Age, BMI, and stool habits (β = -0.018; r = -0.15 for Shannon index). The intake group of ramen was inversely associated with dietary nutrients and dietary fiber compared with the no-intake group of ramen. Sugar intake, Dorea as a short-chain fatty acid (SCFA)-producing gut microbiota, and γ-glutamyl transferase as a liver function marker were directly associated with ramen intake after adjustment for related factors including diets, gut microbiota, and blood chemistry using a stepwise logistic regression model, whereas Dorea is inconsistently less abundant in the ramen group. In conclusion, the increased ramen was associated with decreased gut bacterial diversity accompanying a perturbation of Dorea through the dietary nutrients, gut microbiota, and blood chemistry, while the methodological limitations existed in a cross-sectional study. People with frequent ramen eating habits need to take measures to consume various nutrients to maintain and improve their health, and dietary management can be applied to the dietary feature in ramen consumption.
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Affiliation(s)
- Jonguk Park
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, 3-17 Senrioka-shinmachi, Settsu 566-0002, Osaka, Japan
- International Life Sciences Institute (ILSI) Japan, Gobel Building 3-13-5, Morishita, Koto 135-0004, Tokyo, Japan
| | - Hiroto Bushita
- International Life Sciences Institute (ILSI) Japan, Gobel Building 3-13-5, Morishita, Koto 135-0004, Tokyo, Japan
- Health & Wellness Products Research Laboratories, Kao Corporation, Tokyo 131-8501, Japan
| | - Ayatake Nakano
- International Life Sciences Institute (ILSI) Japan, Gobel Building 3-13-5, Morishita, Koto 135-0004, Tokyo, Japan
- Milk Science Research Institute, Megmilk Snow Brand Co., Ltd., 1-1-2 Minamidai, Kawagoe 350-1165, Saitama, Japan
| | - Ai Hara
- International Life Sciences Institute (ILSI) Japan, Gobel Building 3-13-5, Morishita, Koto 135-0004, Tokyo, Japan
- Future Design Division, The KAITEKI Institute, Inc., Palace Building 1-1, Marunouchi 1-chome, Chiyoda 100-8251, Tokyo, Japan
| | - Hiroshi M. Ueno
- International Life Sciences Institute (ILSI) Japan, Gobel Building 3-13-5, Morishita, Koto 135-0004, Tokyo, Japan
- Milk Science Research Institute, Megmilk Snow Brand Co., Ltd., 1-1-2 Minamidai, Kawagoe 350-1165, Saitama, Japan
| | - Naoki Ozato
- International Life Sciences Institute (ILSI) Japan, Gobel Building 3-13-5, Morishita, Koto 135-0004, Tokyo, Japan
- Health & Wellness Products Research Laboratories, Kao Corporation, Tokyo 131-8501, Japan
| | - Koji Hosomi
- Laboratory of Vaccine Materials and Laboratory of Gut Environmental System, Microbial Research Center for Health and Medicine, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki 567-0085, Osaka, Japan
| | - Hitoshi Kawashima
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, 3-17 Senrioka-shinmachi, Settsu 566-0002, Osaka, Japan
| | - Yi-An Chen
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, 3-17 Senrioka-shinmachi, Settsu 566-0002, Osaka, Japan
| | - Attayeb Mohsen
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, 3-17 Senrioka-shinmachi, Settsu 566-0002, Osaka, Japan
| | - Harumi Ohno
- Department of Physical Activity Research, National Institutes of Biomedical Innovation, Health and Nutrition, 3-17 Senrioka-shinmachi, Settsu 566-0002, Osaka, Japan
- Department of Nutrition, Kiryu University, 606-7 Azami, Kasakake-machi, Midori 379-2392, Gunma, Japan
| | - Kana Konishi
- Department of Physical Activity Research, National Institutes of Biomedical Innovation, Health and Nutrition, 3-17 Senrioka-shinmachi, Settsu 566-0002, Osaka, Japan
- Faculty of Food and Nutritional Sciences, Toyo University, 1-1-1 Izumino, Itakura, Oura 374-0193, Gunma, Japan
| | - Kumpei Tanisawa
- Department of Physical Activity Research, National Institutes of Biomedical Innovation, Health and Nutrition, 3-17 Senrioka-shinmachi, Settsu 566-0002, Osaka, Japan
- Faculty of Sport Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa 359-1192, Saitama, Japan
| | - Hinako Nanri
- Department of Physical Activity Research, National Institutes of Biomedical Innovation, Health and Nutrition, 3-17 Senrioka-shinmachi, Settsu 566-0002, Osaka, Japan
| | - Haruka Murakami
- Department of Physical Activity Research, National Institutes of Biomedical Innovation, Health and Nutrition, 3-17 Senrioka-shinmachi, Settsu 566-0002, Osaka, Japan
- Faculty of Sport and Health Science, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu 525-8577, Shiga, Japan
| | - Motohiko Miyachi
- Department of Physical Activity Research, National Institutes of Biomedical Innovation, Health and Nutrition, 3-17 Senrioka-shinmachi, Settsu 566-0002, Osaka, Japan
- Faculty of Sport Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa 359-1192, Saitama, Japan
| | - Jun Kunisawa
- Laboratory of Vaccine Materials and Laboratory of Gut Environmental System, Microbial Research Center for Health and Medicine, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki 567-0085, Osaka, Japan
- International Research and Development Center for Mucosal Vaccines, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato 108-8639, Tokyo, Japan
- Graduate School of Medicine, Graduate School of Pharmaceutical Sciences, Graduate School of Dentistry, Graduate School of Sciences, Osaka University, 1-1 Yamadaoka, Suita 565-0871, Osaka, Japan
- Department of Microbiology and Immunology, Graduate School of Medicine, Kobe University, 7-5-1 Kusunoki, Chuo, Kobe 650-0017, Hyogo, Japan
- Research Organization for Nano and Life Innovation, Waseda University, 513 Waseda-Tsurumaki, Shinjuku 162-0041, Tokyo, Japan
| | - Kenji Mizuguchi
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, 3-17 Senrioka-shinmachi, Settsu 566-0002, Osaka, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Michihiro Araki
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, 3-17 Senrioka-shinmachi, Settsu 566-0002, Osaka, Japan
- Graduate School of Medicine, Kyoto University, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Hyogo, Japan
- National Cerebral and Cardiovascular Center, 6-1 Kishibe-Shinmachi, Suita 564-8565, Osaka, Japan
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Wang X, Li G, Wang H, Liu Y, Yang Y, Wang C, Gong S, He D. Feeding whole-plant ensiled corn stover affects growth performance, blood parameters, and Cecal microbiota of Holdobagy goose. Front Vet Sci 2023; 10:1210706. [PMID: 37397002 PMCID: PMC10310790 DOI: 10.3389/fvets.2023.1210706] [Citation(s) in RCA: 4] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 05/19/2023] [Indexed: 07/04/2023] Open
Abstract
Introduction The aim of this study was to investigate the effects of adding whole-plant ensiled corn stalks (WECS) to the diet of Holdorbagy geese on their growth performance, serum parameters, and cecal microbiota. Geese farming is an important agricultural practice, and optimizing their diet can contribute to better growth and health outcomes. However, there is limited research on the utilization of WECS as a feed source for geese. Understanding the potential effects of WECS on growth, blood parameters, and cecal microbiota can provide valuable insights into its feasibility and impact on geese farming practices. Methods A total of 144 six-week-old Holdorbagy geese were randomly assigned to one of three groups: a control group (0% WECS), a group fed 15% WECS and 85% concentrated feed (15% WECS), and a group fed 30% WECS and 70% concentrated feed (30% WECS). The trial period lasted for three weeks, during which the growth performance, serum parameters, and cecal microbiota were assessed. Results The results revealed significant findings in different aspects. Firstly, the feed-to-gain ratio (F/G ratio) of the 15% WECS group was significantly higher than that of the control group (p<0.05), indicating potential challenges in feed efficiency. Additionally, the average daily feed intake (ADFI) of both the 15% and 30% WECS groups was significantly higher than that of the control group (p<0.05), suggesting increased appetite or palatability of the diet containing WECS. In terms of serum parameters, the level of lactate dehydrogenase (LDH) in the 30% WECS group was significantly lower than that in the control group (p<0.05). Moreover, there was a tendency for increasing Fe levels and decreasing Zn levels with higher levels of WECS supplementation, although the differences were not statistically significant (p<0.05). Furthermore, the principal coordinate analysis showed significant differences in the composition of cecal microbiota among the three groups (p < 0.01). The observed_species, Shannon, and Pielou_e indices of the 30% WECS group were significantly higher than those of the 0% and 15% WECS groups (p<0.05), while the Simpson index of the 15% WECS group was significantly lower than that of the control group (p<0.05). Discussion The results indicate that the addition of WECS to the geese diet has both positive and negative effects. The study suggests that WECS can be a long-term stable feed source for geese, which can contribute to reducing feeding costs. However, it is important to monitor the amount of WECS added as it can affect the absorption of Zn by geese. Supplementation of Zn in the diet might be necessary to meet the needs of geese. Notably, adding 30% WECS to the diet can increase the richness, evenness, and diversity of the cecal microbiota, indicating potential benefits to gut health. In conclusion, this study highlights the potential of WECS as a feed source for geese. It provides valuable insights into the effects of WECS on growth performance, serum parameters, and cecal microbiota. These findings contribute to optimizing geese farming practices, improving feed utilization, and enhancing overall productivity and well-being of geese. Further research is needed to determine the optimal inclusion level of WECS and to explore strategies for mitigating any negative effects.
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Affiliation(s)
| | | | | | | | | | | | | | - Daqian He
- *Correspondence: Daqian He, ; Huiying Wang,
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Kong J, Feng J, Sun L, Zhang S. Evaluating the Reproducibility of Amplicon Sequencing Data Derived from Deep-Sea Cold Seep Sediment-Associated Microbiota. Microbiol Spectr 2023; 11:e0404822. [PMID: 37074190 PMCID: PMC10269476 DOI: 10.1128/spectrum.04048-22] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 03/24/2023] [Indexed: 04/20/2023] Open
Abstract
Benefiting from the rapid developments and wide applications of high-throughput sequencing, great advancements have been made in investigating microbiota, which are highly diverse and play key roles in both element cycling and the energy flow of ecosystems. There have been inherent limitations of amplicon sequencing that could introduce uncertainty and raise concerns about the accuracy and reproducibility of this technology. However, studies focusing on the reproducibility of amplicon sequencing are limited, especially in characterizing microbial communities in deep-sea sediments. To evaluate reproducibility, 118 deep-sea sediment samples were used for 16S rRNA gene sequencing in technical replicates (repeated measurements of the same sample) that demonstrate the variability of amplicon sequencing. The average occurrence-based overlaps were 35.98% and 27.02% between two and among three technical replicates, respectively, whereas their abundance-based overlaps reached 84.88% and 83.16%, respectively. Although variations of alpha and beta diversity indices were found between/among technical replicates, alpha diversity indices were similar across samples, and the average beta diversity indices were much smaller for technical replicates than among samples. Moreover, clustering methods (i.e., operational taxonomic units [OTUs] and amplicon sequence variants [ASVs]) were shown to have little impact on the alpha and beta diversity patterns of microbial communities. Taken together, although there are variations between/among technical replicates, amplicon sequencing is still a powerful tool with which to reveal diversity patterns of microbiota in deep-sea sediments. IMPORTANCE The reproducibility of amplicon sequencing is vital for whether the diversities of microbial communities could be accurately estimated. Thus, reproducibility influences the drawing of sound ecological conclusions. Nevertheless, few studies have focused on the reproducibility of microbial communities that are characterized by amplicon sequencing, and studies focusing on microbiota in deep-sea sediments have been especially lacking. In this study, we evaluated the reproducibility of amplicon sequencing targeting microbiota in deep-sea sediments of cold seep. Our results revealed that there were variations between/among technical replicates and that amplicon sequencing was still a powerful tool with which to characterize the diversities of microbial communities in deep-sea sediments. This study provides valuable guidelines for the reproducibility evaluation of future work in experimental design and interpretation.
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Affiliation(s)
- Jie Kong
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangdong, China
| | - Jingchun Feng
- Guangdong University of Technology, Guangzhou, China
| | - Liwei Sun
- Guangdong University of Technology, Guangzhou, China
| | - Si Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangdong, China
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21
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Turroni S, Provensi G. Editorial: Gut biodiversity and its influence in brain health. Front Neurosci 2023; 17:1221543. [PMID: 37325038 PMCID: PMC10267479 DOI: 10.3389/fnins.2023.1221543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 06/17/2023] Open
Affiliation(s)
- Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Gustavo Provensi
- Department of Neuroscience, Psychology, Drug Research and Child Health (NEUROFARBA), Section of Pharmacology of Toxicology, University of Florence, Florence, Italy
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22
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Prewer E, Vilaça ST, Bird S, Kutz S, Leclerc L, Kyle CJ. Metabarcoding of fecal pellets in wild muskox populations reveals negative relationships between microbiome and diet alpha diversity. Ecol Evol 2023; 13:e10192. [PMID: 37325724 PMCID: PMC10261903 DOI: 10.1002/ece3.10192] [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: 01/19/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 06/17/2023] Open
Abstract
Microbiome diversity and diet composition concomitantly influence species health, fitness, immunity, and digestion. In environments where diet varies spatially and temporally, microbiome plasticity may promote rapid host adaptation to available resources. For northern ungulates in particular, metabarcoding of noninvasively collected fecal pellets presents unprecedented insights into their diverse ecological requirements and niches by clarifying the interrelationships of microbiomes, key to deriving nutrients, in context of altered forage availability in changing climates. Muskoxen (Ovibos moschatus) are Arctic-adapted species that experience fluctuating qualities and quantities of vegetation. Geography and seasonality have been noted to influence microbiome composition and diversity in muskoxen, yet it is unclear how their microbiomes intersect with diet. Following observations from other species, we hypothesized increasing diet diversity would result in higher microbiome diversity in muskoxen. We assessed diet composition in muskoxen using three common plant metabarcoding markers and explored correlations with microbiome data. Patterns of dietary diversity and composition were not fully concordant among the markers used, yet all reflected the primary consumption of willows and sedges. Individuals with similar diets had more similar microbiomes, yet in contrast to most literature, yielded negative relationships between microbiome and diet alpha diversity. This negative correlation may reflect the unique capacities of muskoxen to survive solely on high-fiber Arctic forage and provide insight into their resiliency to exploit changing dietary resources in a rapidly warming Arctic altering vegetation diversity.
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Affiliation(s)
- Erin Prewer
- Environmental and Life Sciences Graduate ProgramTrent UniversityPeterboroughOntarioCanada
| | - Sibelle T. Vilaça
- Environmental and Life Sciences Graduate ProgramTrent UniversityPeterboroughOntarioCanada
| | - Samantha Bird
- Forensic Science DepartmentTrent UniversityPeterboroughOntarioCanada
| | - Susan Kutz
- Department of Ecosystem and Public Health, Faculty of Veterinary MedicineUniversity of CalgaryCalgaryAlbertaCanada
| | | | - Christopher J. Kyle
- Environmental and Life Sciences Graduate ProgramTrent UniversityPeterboroughOntarioCanada
- Forensic Science DepartmentTrent UniversityPeterboroughOntarioCanada
- Natural Resources DNA Profiling and Forensic CentrePeterboroughOntarioCanada
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23
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Baeshen NN, Baz L, Shami AY, Ashy RA, Jalal RS, Abulfaraj AA, Refai M, Majeed MA, Abuzahrah SS, Abdelkader H, Baeshen NA, Baeshen MN. Composition, Abundance, and Diversity of the Soil Microbiome Associated with the Halophytic Plants Tamarix aphylla and Halopeplis perfoliata on Jeddah Seacoast, Saudi Arabia. Plants (Basel) 2023; 12:plants12112176. [PMID: 37299153 DOI: 10.3390/plants12112176] [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] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023]
Abstract
The coast of the Red Sea in Jeddah City is home to a unique microbial community that has adapted to extreme environmental conditions. Therefore, it is essential to characterize the microbial community in this unique microbiome to predict how environmental changes will affect it. The aim of this study was to conduct metagenomic sequencing of 16S rRNA and ITS rRNA genes for the taxonomic classification of the microbial community in soil samples associated with the halophytic plants Tamarix aphylla and Halopeplis perfoliata. Fifteen soil samples were collected in triplicate to enhance robustness and minimize sampling bias. Firstly, to identify novel microbial candidates, the gDNAs were isolated from the saline soil samples surrounding each plant, and then bacterial 16S (V3-V4) and fungal ITS1 regions were sequenced utilizing a high-throughput approach (next-generation sequencing; NGS) on an Illumina MiSeq platform. Quality assessment of the constructed amplicon libraries was conducted using Agilent Bioanalyzer and fluorometric quantification methods. The raw data were processed and analyzed using the Pipeline (Nova Lifetech, Singapore) for bioinformatics analysis. Based on the total number of readings, it was determined that the phylum Actinobacteriota was the most prevalent in the soil samples examined, followed by the phylum Proteobacteria. Based on ITS rRNA gene analysis, the alpha and beta fungal diversity in the studied soil samples revealed that the fungal population is structured into various groups according to the crust (c) and/or rhizosphere (r) plant parts. Fungal communities in the soil samples indicated that Ascomycota and Basidiomycota were the two most abundant phyla based on the total amount of sequence reads. Secondly, heat-map analysis of the diversity indices showed that the bacterial alpha diversity, as measured by Shannon, Simpson, and InvSimpson, was associated with soil crust (Hc and Tc enclosing H. perfoliata and T. aphylla, respectively) and that the soil rhizosphere (Hr and Tr) was strongly correlated with bacterial beta diversity. Finally, fungal-associated Tc and Hc samples clustered together, according to observations made using the Fisher and Chao1 methods, and Hr and Tr samples clustered together according to Shannon, Simpson, and InvSimpson analyses. As a result of the soil investigation, potential agents that have been identified could lead to innovative agricultural, medical, and industrial applications.
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Affiliation(s)
- Naseebh N Baeshen
- Department of Biology, College of Sciences and Arts at Khulais, University of Jeddah, Jeddah 21959, Saudi Arabia
| | - Lina Baz
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ashwag Y Shami
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh 11617, Saudi Arabia
| | - Ruba A Ashy
- Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
| | - Rewaa S Jalal
- Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
| | - Aala A Abulfaraj
- Biological Sciences Department, College of Science & Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia
| | - Mohammed Refai
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
| | - Mazen A Majeed
- Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
| | - Samah S Abuzahrah
- Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
| | - Hayam Abdelkader
- Virus Research Department, Molecular Biology Laboratory, PPRI, ARC, Giza 12613, Egypt
| | - Nabih A Baeshen
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mohammed N Baeshen
- Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
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24
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Vaziri GJ, Jones MM, Carr HA, Nuñez CMV. Out of the stable: Social disruption and concurrent shifts in the feral mare ( Equus caballus) fecal microbiota. Ecol Evol 2023; 13:e10079. [PMID: 37187967 PMCID: PMC10175550 DOI: 10.1002/ece3.10079] [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: 12/30/2022] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/17/2023] Open
Abstract
The disruption of animals' symbiotic bacterial communities (their microbiota) has been associated with myriad factors including changes to the diet, hormone levels, and various stressors. The maintenance of healthy bacterial communities may be especially challenging for social species as their microbiotas are also affected by group membership, social relationships, microbial transfer between individuals, and social stressors such as increased competition and rank maintenance. We investigated the effects of increased social instability, as determined by the number of group changes made by females, on the microbiota in free-living, feral horses (Equus caballus) on Shackleford Banks, a barrier island off the North Carolina coast. Females leaving their groups to join new ones had fecal microbial communities that were similarly diverse but compositionally different than those of females that did not change groups. Changing groups was also associated with the increased abundance of a several bacterial genera and families. These changes may be significant as horses are heavily dependent upon their microbial communities for nutrient absorption. Though we cannot identify the particular mechanism(s) driving these changes, to the best of our knowledge, ours is the first study to demonstrate an association between acute social perturbations and the microbiota in a free-ranging mammal.
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Affiliation(s)
- Grace J. Vaziri
- Ecology and Evolutionary BiologyUniversity of ConnecticutMansfieldConnecticutUSA
| | - Maggie M. Jones
- Department of Natural Resource Ecology and ManagementIowa State UniversityAmes, IowaUSA
- Present address:
School of Natural Resources and EnvironmentUniversity of FloridaGainesvilleFloridaUSA
| | - Haley A. Carr
- Department of Natural Resource Ecology and ManagementIowa State UniversityAmes, IowaUSA
| | - Cassandra M. V. Nuñez
- Department of Natural Resource Ecology and ManagementIowa State UniversityAmes, IowaUSA
- Department of Biological SciencesThe University of MemphisMemphisTennesseeUSA
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25
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Oddi S, Mantziari A, Huber P, Binetti A, Salminen S, Collado MC, Vinderola G. Human Milk Microbiota Profile Affected by Prematurity in Argentinian Lactating Women. Microorganisms 2023; 11:microorganisms11041090. [PMID: 37110513 PMCID: PMC10145235 DOI: 10.3390/microorganisms11041090] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/10/2023] [Accepted: 03/30/2023] [Indexed: 04/29/2023] Open
Abstract
To study (16S rRNA-sequencing) the impact of gestational and corrected ages on the microbiota profile of human milk (HM) of mothers that delivered full-term and pre-term children, HM samples were obtained and classified according to the gestational age as group T (full-term births ≥37 weeks), and group P (pre-term births <37 weeks). Group P was longitudinally followed, and the samples were collected at the full-term corrected gestational age: when the chronological age plus the gestational age were ≥37 weeks (PT group). The HM microbiota composition differed depending on the gestational age (T vs. P). Group T had lower levels of Staphylococcus and higher levels of Rothia and Streptococcus, as compared to group P. The alpha Simpson diversity value was higher in group T than in P, whereas no differences were found between groups T and PT, suggesting a microbial evolution of the composition of group P towards group T over chronological age. Full-term delivery was associated with a greater diversity of microbes in HM. The microbial composition of pre-term HM, at the corrected age, did not show significant differences, as compared to the samples obtained from the full-term group, suggesting that it would be appropriate to consider the corrected age in terms of the composition and the diversity of the milk in future studies.
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Affiliation(s)
- Sofía Oddi
- Instituto de Lactología Industrial (INLAIN, UNL-CONICET), Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Anastasia Mantziari
- Functional Foods Forum, Faculty of Medicine, University of Turku, 20520 Turku, Finland
| | - Paula Huber
- Laboratorio de Plancton, Instituto Nacional de Limnología (INALI, UNL-CONICET), Universidad Nacional del Litoral, Santa Fe 3000, Argentina
- Departamento de Hydrobiologia, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos 13565-905, SP, Brazil
| | - Ana Binetti
- Instituto de Lactología Industrial (INLAIN, UNL-CONICET), Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Seppo Salminen
- Functional Foods Forum, Faculty of Medicine, University of Turku, 20520 Turku, Finland
| | - Maria Carmen Collado
- Department of Biotechnology, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), 46980 Valencia, Spain
| | - Gabriel Vinderola
- Instituto de Lactología Industrial (INLAIN, UNL-CONICET), Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
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26
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Deschamps L, Proulx R, Rheault G, Gross N, Watson C, Maire V. Species richness drives selection of individuals within wetlands based on traits related to acquisition and utilization of light. Ecol Evol 2023; 13:e9959. [PMID: 37038518 PMCID: PMC10082176 DOI: 10.1002/ece3.9959] [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: 08/03/2022] [Revised: 03/10/2023] [Accepted: 03/14/2023] [Indexed: 04/12/2023] Open
Abstract
Selection within natural communities has mainly been studied along large abiotic gradients, while the selection of individuals within populations should occur locally in response to biotic filters. To better leverage the role of the latter, we considered the hierarchal nature of environmental selection for the multiple dimensions of the trait space across biological levels, that is, from the species to the community and the ecosystem levels. We replicated a natural species richness gradient where communities included from two to 16 species within four wetlands (bog, fen, meadow, and marsh) contrasting in plant productivity. We sampled functional traits from individuals in each community and used hierarchical distributional modeling in order to analyze the independent variation of the mean and dispersion of functional trait space at ecosystem, community, and species levels. The plant productivity gradient observed between wetlands led to species turnover and selection of traits related to leaf nutrient conservation/acquisition strategy. Within wetlands, plant species richness drove trait variation across both communities and species. Among communities, variation of species richness correlated with the selection of individuals according to their use of vertical space and leaf adaptations to light conditions. Within species, intraspecific light-related trait variation in response to species richness was associated with stable population density for some species, while others reached low population density in more diverse communities. Within ecosystems, variation in biotic conditions selects individuals along functional dimensions that are independent of those selected across ecosystems. Within-species variations of light-related traits are related to demographic responses, linking biotic selection of individuals within communities to eco-evolutionary dynamics of species.
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Affiliation(s)
- Lucas Deschamps
- Département des sciences de l'environnementUniversité du Québec à Trois‐RivièresTrois RivièresCanada
| | - Raphaël Proulx
- Département des sciences de l'environnementUniversité du Québec à Trois‐RivièresTrois RivièresCanada
| | - Guillaume Rheault
- Département des sciences de l'environnementUniversité du Québec à Trois‐RivièresTrois RivièresCanada
| | - Nicolas Gross
- Université Clermont Auvergne, INRAE, VetAgro SupUnité Mixte de Recherche Ecosystème PrairialClermont‐FerrandFrance
| | - Christopher Watson
- Département des sciences de l'environnementUniversité du Québec à Trois‐RivièresTrois RivièresCanada
| | - Vincent Maire
- Département des sciences de l'environnementUniversité du Québec à Trois‐RivièresTrois RivièresCanada
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Fenn J, Taylor C, Goertz S, Wanelik KM, Paterson S, Begon M, Jackson J, Bradley J. Discrete patterns of microbiome variability across timescales in a wild rodent population. BMC Microbiol 2023; 23:87. [PMID: 36997846 PMCID: PMC10061908 DOI: 10.1186/s12866-023-02824-x] [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: 08/22/2022] [Accepted: 03/15/2023] [Indexed: 04/01/2023] Open
Abstract
Mammalian gastrointestinal microbiomes are highly variable, both within individuals and across populations, with changes linked to time and ageing being widely reported. Discerning patterns of change in wild mammal populations can therefore prove challenging. We used high-throughput community sequencing methods to characterise the microbiome of wild field voles (Microtus agrestis) from faecal samples collected across 12 live-trapping field sessions, and then at cull. Changes in α- and β-diversity were modelled over three timescales. Short-term differences (following 1–2 days captivity) were analysed between capture and cull, to ascertain the degree to which the microbiome can change following a rapid change in environment. Medium-term changes were measured between successive trapping sessions (12–16 days apart), and long-term changes between the first and final capture of an individual (from 24 to 129 days). The short period between capture and cull was characterised by a marked loss of species richness, while over medium and long-term in the field, richness slightly increased. Changes across both short and long timescales indicated shifts from a Firmicutes-dominant to a Bacteroidetes-dominant microbiome. Dramatic changes following captivity indicate that changes in microbiome diversity can be rapid, following a change of environment (food sources, temperature, lighting etc.). Medium- and long-term patterns of change indicate an accrual of gut bacteria associated with ageing, with these new bacteria being predominately represented by Bacteroidetes. While the patterns of change observed are unlikely to be universal to wild mammal populations, the potential for analogous shifts across timescales should be considered whenever studying wild animal microbiomes. This is especially true if studies involve animal captivity, as there are potential ramifications both for animal health, and the validity of the data itself as a reflection of a ‘natural’ state of an animal.
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Affiliation(s)
- Jonathan Fenn
- grid.4563.40000 0004 1936 8868School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Christopher Taylor
- grid.4563.40000 0004 1936 8868School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Sarah Goertz
- grid.4563.40000 0004 1936 8868School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Klara M. Wanelik
- grid.10025.360000 0004 1936 8470University of Liverpool, Liverpool, UK
| | - Steve Paterson
- grid.10025.360000 0004 1936 8470University of Liverpool, Liverpool, UK
| | - Mike Begon
- grid.10025.360000 0004 1936 8470University of Liverpool, Liverpool, UK
| | - Joe Jackson
- grid.8752.80000 0004 0460 5971University of Salford, Salford, UK
| | - Jan Bradley
- grid.4563.40000 0004 1936 8868School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
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Byrd DA, Vogtmann E, Ortega-Villa AM, Wan Y, Gomez M, Hogue S, Warner A, Zhu B, Dagnall C, Jones K, Hicks B, Albert PS, Murphy G, Sinha R. Prospective and Cross-sectional Associations of the Rectal Tissue Microbiome with Colorectal Adenoma Recurrence. Cancer Epidemiol Biomarkers Prev 2023; 32:435-443. [PMID: 36525653 PMCID: PMC9992132 DOI: 10.1158/1055-9965.epi-22-0608] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/19/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The gut microbiome is plausibly associated with colorectal cancer risk; however, previous studies mostly investigated this association cross-sectionally. We investigated cross-sectional and prospective associations of the rectal tissue microbiome with adenoma recurrence in the Polyp Prevention Trial (PPT). METHODS PPT is a 4-year randomized clinical trial of the effect of a dietary intervention on adenoma recurrence among community members. We extracted DNA from rectal biopsies at baseline, end of year 1, and end of year 4 among 455 individuals and sequenced the V4 region of the 16S rRNA gene. At each timepoint, we investigated associations of alpha diversity, beta diversity, and presence and relative abundance of select taxa with adenoma recurrence using multivariable logistic regression. RESULTS Variation in beta diversity was primarily explained by subject and minimally by year of collection or time between biopsy and colonoscopy. Cross-sectionally, year 4 alpha diversity was strongly, inversely associated with adenoma prevalence [ORQ3 vs. Q1 Shannon index = 0.40 (95% confidence interval, CI: 0.21-0.76)]. Prospective alpha diversity associations (i.e., baseline/year 1 alpha diversity with adenoma recurrence 3-4 years later) were weak or null, as were cross-sectional and prospective beta diversity-adenoma associations. Bacteroides abundance was more strongly, positively associated with adenoma prevalence cross-sectionally than prospectively. CONCLUSIONS Rectal tissue microbiome profiles may be associated with prevalent adenomas, with little evidence supporting prospective associations. IMPACT Additional prospective studies, with serial fecal and tissue samples, to explore microbiome-colorectal cancer associations are needed. Eventually, it may be possible to use microbiome characteristics as intervenable risk factors or screening tools.
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Affiliation(s)
- Doratha A. Byrd
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Emily Vogtmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Ana M. Ortega-Villa
- Division of Clinical Research, National Institute of Allergy and Infectious Diseases, Rockville, MD, USA
| | - Yunhu Wan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Maria Gomez
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Stephanie Hogue
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Andrew Warner
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Casey Dagnall
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Paul S. Albert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Gwen Murphy
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Rashmi Sinha
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
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Aranguren R, Voyron S, Ungaro F, Cañón J, Lumini E. Metabarcoding Reveals Impact of Different Land Uses on Fungal Diversity in the South-Eastern Region of Antioquia, Colombia. Plants (Basel) 2023; 12:1126. [PMID: 36903986 PMCID: PMC10005449 DOI: 10.3390/plants12051126] [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] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/20/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
Changes in soil fungal communities caused by land use have not been sufficiently studied in South American Andosols, which are considered key food production areas. Since fungal communities play an important role in soil functionality, this study analysed 26 soil samples of Andosols collected from locations devoted to conservation, agriculture and mining activities in Antioquia, Colombia, to establish differences between fungal communities as indicators of soil biodiversity loss using Illumina MiSeq metabarcoding on nuclear ribosomal ITS2 region. A non-metric multidimensional scaling allowed to explore driver factors of changes in fungal communities, while the significance of these variations was assessed by PERMANOVA. Furthermore, the effect size of land use over relevant taxa was quantified. Our results suggest a good coverage of fungal diversity with a detection of 353,312 high-quality ITS2 sequences. We found strong correlations of Shannon and Fisher indexes with dissimilarities on fungal communities (r = 0.94). These correlations allow grouping soil samples according to land use. Variations in temperature, air humidity and organic matter content lead to changes in abundances of relevant orders (Wallemiales and Trichosporonales). The study highlights specific sensitivities of fungal biodiversity features in tropical Andosols, which may serve as a basis for robust assessments of soil quality in the region.
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Affiliation(s)
- Raul Aranguren
- GAIA Research Group, Universidad de Antioquia, Medellín 050010, Colombia
| | - Samuele Voyron
- Department of Life Sciences and Systems Biology, University of Turin, 10124 Turin, Italy
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), 10125 Turin, Italy
| | - Fabrizio Ungaro
- Institute for Bio-Economy (IBE), National Research Council (CNR), 50018 Florence, Italy
| | - Julio Cañón
- GAIA Research Group, Universidad de Antioquia, Medellín 050010, Colombia
| | - Erica Lumini
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), 10125 Turin, Italy
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Sayres LC, Younge NE, Rikard B, Corcoran DL, Modliszewski JL, Hughes BL. The gestational membrane microbiome in the presence or absence of intraamniotic infection. Am J Obstet Gynecol MFM 2023; 5:100837. [PMID: 36623808 DOI: 10.1016/j.ajogmf.2022.100837] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 12/06/2022] [Indexed: 01/09/2023]
Abstract
BACKGROUND Data regarding the microbiome of the gestational membranes are emerging and conflicting. Shifts in the microbial communities in the setting of labor, rupture of membranes, and intraamniotic infection are yet to be understood. OBJECTIVE This study aimed to characterize the microbiome of the gestational membranes of women in labor or with ruptured membranes, including those with and without intraamniotic infection. STUDY DESIGN Women with a singleton pregnancy at ≥28 weeks' gestation undergoing unscheduled cesarean delivery in the setting of labor or rupture of membranes were included. Demographic and clinical variables were collected. We defined suspected intraamniotic infection by standard clinical criteria; placentae and gestational membranes were also reviewed for histologic evidence of infection. Sterile swabs were collected from membranes at the time of delivery. Bacteria were cultured from the swabs, and the isolates were sequenced. DNA extraction and 16S sequencing of the swabs were also performed. Bacterial taxonomy was assigned to each sequence. Alpha diversity indices and beta-diversity metrics were calculated to test for differences in microbial community diversity and composition between uninfected and infected groups. Differential abundance of bacteria between infected and uninfected groups was tested at the class, family, and genus level. RESULTS Samples were collected from 34 participants. Clinical intraamniotic infection was diagnosed in 38% of participants, although 50% of placentae and membranes demonstrated histologic signs of infection. Of all samples, 68% grew bacteria on culture; this included 62% of the uninfected samples and 77% of the infected samples (P=.83). Multiple measures of alpha diversity were not significantly different between uninfected and infected groups. Similarly, analysis of beta diversity revealed that the microbial community was not significantly different between the uninfected and infected group. Several bacteria traditionally characterized as pathogenic, including Actinomyces and Streptococcus agalactiae, were identified in both infected and uninfected samples. CONCLUSION The pathogenesis and clinical implications of intraamniotic infection remain poorly understood. Diverse bacteria are present in both infected and uninfected gestational membranes. A unique microbiologic signature may exist among the gestational membranes following labor or rupture of membranes, and further characterization of the pathogens specifically implicated in intraamniotic infection may allow for targeted therapy.
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Affiliation(s)
- Lauren C Sayres
- Department of Obstetrics and Gynecology, Duke University, Durham, NC (Dr Sayres).
| | - Noelle E Younge
- Department of Pediatrics, Duke University, Durham, NC (Dr Younge and Ms Rikard)
| | - Blaire Rikard
- Department of Pediatrics, Duke University, Durham, NC (Dr Younge and Ms Rikard)
| | - David L Corcoran
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC (Dr Corcoran)
| | | | - Brenna L Hughes
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Duke University, Durham, NC (Dr Hughes)
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31
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Walters WA, Granados AC, Ley C, Federman S, Stryke D, Santos Y, Haggerty T, Sotomayor-Gonzalez A, Servellita V, Ley RE, Parsonnet J, Chiu CY. Longitudinal comparison of the developing gut virome in infants and their mothers. Cell Host Microbe 2023; 31:187-198.e3. [PMID: 36758519 PMCID: PMC9950819 DOI: 10.1016/j.chom.2023.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 11/15/2022] [Accepted: 01/05/2023] [Indexed: 02/10/2023]
Abstract
The human gut virome and its early life development are poorly understood. Prior studies have captured single-point assessments with the evolution of the infant virome remaining largely unexplored. We performed viral metagenomic sequencing on stool samples collected longitudinally from a cohort of 53 infants from age 2 weeks to 3 years (80.7 billion reads), and from their mothers (9.8 billion reads) to examine and compare viromes. The asymptomatic infant virome consisted of bacteriophages, nonhuman dietary/environmental viruses, and human-host viruses, predominantly picornaviruses. In contrast, human-host viruses were largely absent from the maternal virome. Previously undescribed, sequence-divergent vertebrate viruses were detected in the maternal but not infant virome. As infants aged, the phage component evolved to resemble the maternal virome, but by age 3, the human-host component remained dissimilar from the maternal virome. Thus, early life virome development is determined predominantly by dietary, infectious, and environmental factors rather than direct maternal acquisition.
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Affiliation(s)
- William A Walters
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Andrea C Granados
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Catherine Ley
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Doug Stryke
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Yale Santos
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Thomas Haggerty
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Julie Parsonnet
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA; Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA.
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Yu C, Guo Z, Lei Z, Mao X, Chen S, Wang K. Comparison of fecal microbiota of SPF and non-SPF Beagle dogs. Front Vet Sci 2023; 10:1021371. [PMID: 36825235 PMCID: PMC9941619 DOI: 10.3389/fvets.2023.1021371] [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: 08/17/2022] [Accepted: 01/19/2023] [Indexed: 02/10/2023] Open
Abstract
Microbial colonization of animal intestine impacts host metabolism and immunity. The study was aimed to investigate the diversity of the intestinal microflora in specific pathogen free (SPF) and non-SPF Beagle dogs of different ages by direct sequencing analysis of the 16S rRNA gene. Stool samples were collected from four non-SPF and four SPF healthy Beagle dogs. From a total of 792 analyzed Operation taxonomic units, four predominant bacterial phyla were identified: Firmicutes (75.23%), Actinobacteria (10.98%), Bacteroidetes (9.33%), and Proteobacteria (4.13%). At the genus level, Streptococcus, Lactobacillus, and Bifidobacterium were dominated. Among which, Alloprevotella, Prevotella_9, and Faecalibacterium were presented exclusively in non-SPF beagles, with potentially anti-inflammatory capability, which could protect non-SPF beagles from complex microbial environment. The number and diversity of intestinal flora for non-SPF Beagle dogs were the highest at birth and gradually decreased with growth, whereas the results for the SPF beagle samples were the opposite, with the number and diversity of intestinal microbiota gradually increases as beagles grow. In a nutshell, the microbial complexity of the rearing environment can enrich the gut microbiota of beagles, many of which are anti-inflammatory microbiota with the potential to increase the adaptability of the animal to the environment. However, the gut microbiota of SPF beagles was more sensitive to environmental changes than that of non-SPF beagles. This study is of great significance for understanding the bionomics of intestinal microflora in non-SPF and SPF beagles, improving the experimental accuracy in scientific research.
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Affiliation(s)
- Cuilian Yu
- School of Laboratory Animal and Shandong Laboratory Animal Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Zhongkun Guo
- School of Laboratory Animal and Shandong Laboratory Animal Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Zhan Lei
- School of Laboratory Animal and Shandong Laboratory Animal Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Xiaolong Mao
- School of Laboratory Animal and Shandong Laboratory Animal Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Shumin Chen
- Shandong Provincial Center for Animal Disease Control and Prevention (Zoonoses Surveillance Center of Shandong Province), Jinan, China
| | - Kezhou Wang
- School of Laboratory Animal and Shandong Laboratory Animal Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China,*Correspondence: Kezhou Wang ✉
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Bonin A, Guerrieri A, Ficetola GF. Optimal sequence similarity thresholds for clustering of molecular operational taxonomic units in DNA metabarcoding studies. Mol Ecol Resour 2023; 23:368-381. [PMID: 36052659 DOI: 10.1111/1755-0998.13709] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 08/08/2022] [Accepted: 08/25/2022] [Indexed: 01/04/2023]
Abstract
Clustering approaches are pivotal to handle the many sequence variants obtained in DNA metabarcoding data sets, and therefore they have become a key step of metabarcoding analysis pipelines. Clustering often relies on a sequence similarity threshold to gather sequences into molecular operational taxonomic units (MOTUs), each of which ideally represents a homogeneous taxonomic entity (e.g., a species or a genus). However, the choice of the clustering threshold is rarely justified, and its impact on MOTU over-splitting or over-merging even less tested. Here, we evaluated clustering threshold values for several metabarcoding markers under different criteria: limitation of MOTU over-merging, limitation of MOTU over-splitting, and trade-off between over-merging and over-splitting. We extracted sequences from a public database for nine markers, ranging from generalist markers targeting Bacteria or Eukaryota, to more specific markers targeting a class or a subclass (e.g., Insecta, Oligochaeta). Based on the distributions of pairwise sequence similarities within species and within genera, and on the rates of over-splitting and over-merging across different clustering thresholds, we were able to propose threshold values minimizing the risk of over-splitting, that of over-merging, or offering a trade-off between the two risks. For generalist markers, high similarity thresholds (0.96-0.99) are generally appropriate, while more specific markers require lower values (0.85-0.96). These results do not support the use of a fixed clustering threshold. Instead, we advocate careful examination of the most appropriate threshold based on the research objectives, the potential costs of over-splitting and over-merging, and the features of the studied markers.
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Affiliation(s)
- Aurélie Bonin
- Department of Environmental Science and Policy, University of Milan, Milan, Italy.,Argaly, Bâtiment Clean space, Sainte-Hélène-du-Lac, France
| | - Alessia Guerrieri
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - Gentile Francesco Ficetola
- Department of Environmental Science and Policy, University of Milan, Milan, Italy.,LECA, Laboratoire d'Ecologie Alpine, Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, Grenoble, France
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Paden H, Kurbatfinski N, Poelstra JW, Ormiston K, Orchard T, Ilic S. Dietary Impacts on Changes in Diversity and Abundance of the Murine Microbiome during Progression and Treatment of Cancer. Nutrients 2023; 15:724. [PMID: 36771430 PMCID: PMC9920799 DOI: 10.3390/nu15030724] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/14/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
The intestinal microbial population is recognized for its impact on cancer treatment outcomes. Little research has reported microbiome changes during cancer progression or the interplay of disease progression, dietary sugar/fat intake, and the microbiome through surgery and chemotherapy. In this study, the murine gut microbiome was used as a model system, and changes in microbiome diversity, richness, and evenness over the progression of the cancer and treatment were analyzed. Mice were categorized into four diet cohorts, combinations of either high or low sucrose and high or low omega-3 fatty acids, and two treatment cohorts, saline vehicle or chemotherapy, for a total of eight groups. Fecal samples were collected at specific timepoints to assess changes due to diet implementation, onset of cancer, lumpectomy, and chemotherapy. Akkermansia muciniphila abundance was very high in some samples and negatively correlated with overall Amplicon Sequence Variant (ASV) richness (r(64) = -0.55, p = 3 × 10-8). Throughout the disease progression, ASV richness significantly decreased and was impacted by diet and treatment. Alpha-diversity and differential microbial abundance were significantly affected by disease progression, diet, treatment, and their interactions. These findings help establish a baseline for understanding how cancer progression, dietary macronutrients, and specific treatments impact the murine microbiome, which may influence outcomes.
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Affiliation(s)
- Holly Paden
- Department of Human Sciences, Ohio State University, Columbus, OH 43210, USA
| | - Nikola Kurbatfinski
- Department of Human Sciences, Ohio State University, Columbus, OH 43210, USA
| | - Jelmer W. Poelstra
- Molecular and Cellular Imaging Center (MCIC), Ohio State University, Wooster, OH 44691, USA
| | - Kate Ormiston
- Department of Human Sciences, Ohio State University, Columbus, OH 43210, USA
| | - Tonya Orchard
- Department of Human Sciences, Ohio State University, Columbus, OH 43210, USA
| | - Sanja Ilic
- Department of Human Sciences, Ohio State University, Columbus, OH 43210, USA
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35
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Lu G, Huang X, Li L, Chen C, Li P. Effects of ambient temperature and available sugar on bacterial community of Pennisetum sinese leaf: An in vitro study. Front Microbiol 2023; 13:1072666. [PMID: 36687585 PMCID: PMC9853076 DOI: 10.3389/fmicb.2022.1072666] [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: 10/17/2022] [Accepted: 12/08/2022] [Indexed: 01/09/2023] Open
Abstract
The present in vitro study investigated the effects of temperature and available sugar on the bacterial community of Pennisetum sinese leaf during fermentation. P. sinese leaves were cultured in MRS broth containing 0.4 and 1.6 g sugar and incubated at 25°C and 45°C for 9, 18, and 36 h. The results showed that the dominant phyla during sugar fermentation were Firmicutes, followed by Proteobacteria and Bacteroidetes. Compared to a low incubation temperature (25°C), a high incubation temperature (45°C) decreased the relative abundances of Exiguobacterium and Acinetobacter and increased those of Bacillus and Paenibacillus. Leaf samples incubated at 25°C showed higher bacterial alpha diversity indices than those incubated at 45°C. Principal coordinate analysis revealed that the bacterial community structure was altered by the high incubation temperature. Sugar concentration of 1.6 g/50 ml increased the relative abundances of Bacillus and Klebsiella but decreased those of Paenibacillus and Serratia as compared to sugar concentration of 0.4 g/50 ml. pH was the primary factor that influenced the succession of bacterial communities during sugar fermentation in P. sinese leaves. In conclusion, ambient temperatures (25°C and 45°C) and high sugar concentration restructured the bacterial communities on P. sinese leaves by facilitating the dominance of Bacillus and Paenibacillus. This study provided insights into the mechanisms by which bacterial communities on P. sinese leaves are enriched.
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Affiliation(s)
- Guangrou Lu
- College of Animal Science, Guizhou University, Guiyang, China
| | - Xiaokang Huang
- College of Animal Science, Guizhou University, Guiyang, China
| | - Lin Li
- College of Animal Science, Guizhou University, Guiyang, China
| | - Chao Chen
- College of Animal Science, Guizhou University, Guiyang, China,Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou, China
| | - Ping Li
- College of Animal Science, Guizhou University, Guiyang, China,Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, Guizhou, China,*Correspondence: Ping Li,
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Munley JA, Kelly LS, Pons EE, Kannan KB, Coldwell PS, Whitley EM, Gillies GS, Efron PA, Nagpal R, Mohr AM. Multicompartmental traumatic injury and the microbiome: Shift to a pathobiome. J Trauma Acute Care Surg 2023; 94:15-22. [PMID: 36203239 PMCID: PMC9805505 DOI: 10.1097/ta.0000000000003803] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Previous animal models have demonstrated altered gut microbiome after mild traumatic injury; however, the impact of injury severity and critical illness is unknown. We hypothesized that a rodent model of severe multicompartmental injuries and chronic stress would demonstrate microbiome alterations toward a "pathobiome" characterized by an overabundance of pathogenic organisms, which would persist 1 week after injury. METHODS Male Sprague-Dawley rats (n = 8 per group) were subjected to either multiple injuries (PT) (lung contusion, hemorrhagic shock, cecectomy, and bifemoral pseudofractures), PT plus daily chronic restraint stress for 2 hours (PT/CS), or naive controls. Fecal microbiome was measured on days 0, 3, and 7 using high-throughput 16S rRNA sequencing and Quantitative Insights Into Microbial Ecology 2 bioinformatics analysis. Microbial α diversity was assessed using Chao1 and Shannon indices, and β diversity with principle coordinate analysis. Intestinal permeability was evaluated by plasma occludin; ileum and descending colon tissues were reviewed for injury. Analyses were performed in GraphPad (GraphPad Software, La Jolla, CA) and R (R Foundation for Statistical Computing, Vienna, Austria), with significance defined as p < 0.05. RESULTS There were significant alterations in β diversity at day 3 and between all groups. By day 3, both PT and PT/CS demonstrated significantly depleted bacterial diversity (Chao1) ( p = 0.01 and p = 0.001, respectively) versus naive, which persisted up to day 7 in PT/CS only ( p = 0.001). Anaerostipes and Rothia dominated PT and Lactobacillus bloomed in PT/CS cohorts by day 7. Plasma occludin was significantly elevated in PT/CS compared with naive ( p = 0.04), and descending colon of both PT and PT/CS showed significantly higher injury compared with naive ( p = 0.005, p = 0.006). CONCLUSIONS Multiple injuries with and without chronic stress induces significant alterations in microbiome diversity and composition within 3 days; these changes are more prominent and persist for 1 week postinjury with stress. This rapid and persistent transition to a "pathobiome" phenotype represents a critical phenomenon that may influence outcomes after severe trauma and critical illness.
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Affiliation(s)
- Jennifer A. Munley
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, Florida
| | - Lauren S. Kelly
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, Florida
| | - Erick E. Pons
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, Florida
| | - Kolenkode B. Kannan
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, Florida
| | - Preston S. Coldwell
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, Florida
| | | | - Gwendolyn S. Gillies
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, Florida
| | - Philip A. Efron
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, Florida
| | - Ravinder Nagpal
- Department of Nutrition & Integrative Physiology, Florida State University College of Health and Human Sciences, Tallahassee, Florida
| | - Alicia M. Mohr
- Department of Surgery and Sepsis and Critical Illness Research Center, University of Florida College of Medicine, Gainesville, Florida
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Robas Mora M, Fernández Pastrana VM, Probanza Lobo A, Jiménez Gómez PA. Valorization as a biofertilizer of an agricultural residue leachate: Metagenomic characterization and growth promotion test by PGPB in the forage plant Medicago sativa (alfalfa). Front Microbiol 2022; 13:1048154. [PMID: 36620069 PMCID: PMC9815802 DOI: 10.3389/fmicb.2022.1048154] [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: 09/19/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
The abuse of chemical fertilizers in intensive agriculture has turned out in the contamination of ground and the soil on which they are applied. Likewise, the generation, storage, and destruction of plant residues from the agri-food industry poses a threat to the environment and human health. The current situation of growing demand for food implies the urgent need to find sustainable alternatives to chemical fertilizers and the management of agricultural waste. Valorization of this plant residue to produce natural biofertilizers using microbiological treatments is presented as a sustainable alternative. The microbial activity allows the transformation into simple molecules that are easily absorbed by plants, as well as the stimulation of plant growth. This double direct and indirect action induced significant increases against the variables of germination, viability, and biomass (dry weight). To guarantee biosafety, it is necessary to use new bio-technological tools, such as metagenomics, which allow the taxonomic analysis of microbial communities, detecting the absence of pathogens. In the present paper, a physicochemical and metagenomic characterization of a fertilizer obtained from agricultural plant waste valorization is carried out. Likewise, fertigation treatments were tested to which the Plant Growth Promoting Bacteria (PGPB) Pseudomonas agronomica and Bacillus pretiosus were added, both independently and in consortium. Metagenomic analysis has identified taxa belonging to the kingdoms Bacteria and Archaea; 10 phyla, 25 families, 32 genera and 34 species, none of them previously described as pathogenic. A 1/512 dilution of the fertilizer increased the germination rate of Medicago sativa (alfalfa) by 16% at 144 h, compared to the treatment without fertilizer. Both the fertilizer and the addition of PGPB in a double direct and indirect action induced significant increases against the variables of germination, viability, and biomass (dry weight). Therefore, the use of an agricultural residue is proposed, which after the addition of two new species is transformed into a biofertilizer that significantly induces plant growth in Mendicago sativa plants.
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Rodriguez DM, Hintze KJ, Rompato G, Wettere AJV, Ward RE, Phatak S, Neal C, Armbrust T, Stewart EC, Thomas AJ, Benninghoff AD. Dietary Supplementation with Black Raspberries Altered the Gut Microbiome Composition in a Mouse Model of Colitis-Associated Colorectal Cancer, although with Differing Effects for a Healthy versus a Western Basal Diet. Nutrients 2022; 14. [PMID: 36558431 DOI: 10.3390/nu14245270] [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: 11/23/2022] [Revised: 11/30/2022] [Accepted: 12/03/2022] [Indexed: 12/14/2022] Open
Abstract
Black raspberries (BRB) are rich in anthocyanins with purported anti-inflammatory properties. However, it is not known whether dietary supplementation would ameliorate Western-diet enhanced gut inflammation and colon tumorigenesis. We employed a mouse model of colitis-associated colorectal cancer (CAC) to determine the effects of dietary supplementation with 5 to 10% (w/w) whole, freeze-dried BRB in male C57BL/6J mice fed either a standard healthy diet (AIN93G) or the total Western diet (TWD). In a pilot study, BRB suppressed colitis and colon tumorigenesis while also shifting the composition of the fecal microbiome in favor of taxa with purported health benefits, including Bifidobacterium pseudolongum. In a follow-up experiment using a 2 × 2 factorial design with AIN and TWD basal diets with and without 10% (w/w) BRB, supplementation with BRB reduced tumor multiplicity and increased colon length, irrespective of the basal diet, but it did not apparently affect colitis symptoms, colon inflammation or mucosal injury based on histopathological findings. However, BRB intake increased alpha diversity, altered beta diversity and changed the relative abundance of Erysipelotrichaceae, Bifidobacteriaceae, Streptococcaceae, Rikenellaceae, Ruminococcaceae and Akkermansiaceae, among others, of the fecal microbiome. Notably, changes in microbiome profiles were inconsistent with respect to the basal diet consumed. Overall, these studies provide equivocal evidence for in vivo anti-inflammatory effects of BRB on colitis and colon tumorigenesis; yet, BRB supplementation led to dynamic changes in the fecal microbiome composition over the course of disease development.
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Wu AH, Vigen C, Tseng C, Garcia AA, Spicer D. Effect of Chemotherapy on the Gut Microbiome of Breast Cancer Patients During the First Year of Treatment. Breast Cancer (Dove Med Press) 2022; 14:433-451. [PMID: 36532254 PMCID: PMC9747861 DOI: 10.2147/bctt.s305486] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/26/2022] [Indexed: 10/24/2023]
Abstract
INTRODUCTION There is accumulating information of the effects of chemotherapy and weight changes on the gut microbiome of breast cancer patients. METHODS In this 1-year follow-up study, we investigated gut microbiome of 33 breast cancer patients who donated fecal samples at baseline and after completion of treatment. We compared alpha diversity and mean taxa abundance at baseline and absolute taxa abundance changes (final-baseline) by treatment (16 neoadjuvant [neoADJ], 13 adjuvant [ADJ], 4 no chemotherapy [noC]) and specific chemotherapy agent using Wilcoxon rank sum and negative binomial mixed model (NBMM) analysis. RESULTS All four gut alpha diversity measures changed in association with chemotherapy treatment; they increased in the neoADJ (+16.4% OTU p = 0.03; +51.6% Chao1 p = 0.03; +7.0% Shannon index p = 0.02; +11.0% PD whole tree p = 0.09) but not in the ADJ and noC group (ADJ+noC). The difference in Chao1 index change between groups was statistically significant (pneoADJ vs. ADJ+noC=0.04). Wilcoxon p values of 0.03-0.003 were observed for five taxa. In NBMM analysis, changes in taxa abundance differed (Bonferroni-adjusted p ≤ 0.0007) for two Bacteroidetes taxa (g_Alistipes, f_S24-7) and two Firmicutes taxa (g_Catenibacterium, g_Eubacterium). NBMM analysis results remained unchanged with adjustment for weight changes. Alpha diversity changes were also found by receipt of chemotherapy agents. Consistent increases in alpha diversity were observed among those treated with TCHP (OTU p = 0.009; Chao1 p = 0.02; Shannon p = 0.02; PD whole tree p = 0.05) but not AC, Taxol or Herceptin. Those treated with TCHP or Herceptin showed increases in Verrucomicrobia (g_Akkermansia) but decreases of Bacteroidetes(g_Alistipes); the differences in changes in taxa abundance were statistically significant. CONCLUSION Results from this pilot longitudinal study support an effect of chemotherapy, particularly neoADJ on the gut microbiome of breast cancer patients even after adjustment for weight changes. Further investigations are needed to confirm these findings in larger studies and with longer follow-up and to assess the impact of these microbiome changes on patient outcome.
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Affiliation(s)
- Anna H Wu
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Cheryl Vigen
- Mrs. TH Chan Division of Occupational Science and Occupational Therapy, University of Southern California, Los Angeles, CA, USA
| | - Chiuchen Tseng
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Agustin A Garcia
- Department of Medicine, Louisiana State University School of Medicine, New Orleans, LA, USA
| | - Darcy Spicer
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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Almeida HMDS, Sonalio K, Mechler-Dreibi ML, Petri FAM, Storino GY, Maes D, de Oliveira LG. Experimental Infection with Mycoplasma hyopneumoniae Strain 232 in Swine Influences the Lower Respiratory Microbiota. Vet Sci 2022; 9:vetsci9120674. [PMID: 36548835 PMCID: PMC9788024 DOI: 10.3390/vetsci9120674] [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: 10/20/2022] [Revised: 11/21/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Mycoplasma (M.) hyopneumoniae, the etiological agent of swine enzootic pneumonia, has been reported to increase the susceptibility to secondary infections and modulate the respiratory microbiota in infected pigs. However, no studies have assessed the influence of M. hyopneumoniae on the respiratory microbiota diversity under experimental conditions. Therefore, this study evaluated the impact of M. hyopneumoniae infection on the respiratory microbiota of experimentally infected swine over time. To accomplish this, 12 weaned pigs from a M. hyopneumoniae-free farm were divided into two groups: M. hyopneumoniae strain 232 infected (n = 8) and non-infected (n = 4). The first group received 10 mL of Friis medium containing 107 CCU/mL of M. hyopneumoniae while the control group received 10 mL of sterile Friis medium. Inoculation of both groups was performed intratracheally when the animals were 35 days old (d0). At 28 days post-inoculation (dpi) and 56 dpi, 4 infected animals plus 2 controls were humanely euthanized, and biopsy samples of nasal turbinates (NT) and bronchus-alveolar lavage fluid (BALF) samples were collected. The DNA was extracted from the individual samples, and each group had the samples pooled and submitted to next-generation sequencing. Taxonomic analysis, alpha and beta diversity indexes, weighted unifrac, and unweighted unifrac distances were calculated. A high relative frequency (99%) of M. hyopneumoniae in BALF samples from infected animals was observed with no significant variation between time points. The infection did not seem to alter the diversity and evenness of bacterial communities in NT, thus, M. hyopneumoniae relative frequency was low in NT pools from infected animals (28 dpi-0.83%; 56 dpi-0.89%). PCoA diagrams showed that BALF samples from infected pigs were grouped and far from the control samples, whereas NT from infected animals were not separated from the control. Under the present coditions, M. hyopneumoniae infection influenced the lower respiratory microbiota, which could contribute to the increased susceptibility of infected animals to respiratory infections.
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Affiliation(s)
| | - Karina Sonalio
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal 14884-900, São Paul, Brazil
- Unit of Porcine Health Management, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Marina Lopes Mechler-Dreibi
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal 14884-900, São Paul, Brazil
| | - Fernando Antônio Moreira Petri
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal 14884-900, São Paul, Brazil
| | - Gabriel Yuri Storino
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal 14884-900, São Paul, Brazil
| | - Dominiek Maes
- Unit of Porcine Health Management, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Luís Guilherme de Oliveira
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal 14884-900, São Paul, Brazil
- Correspondence:
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Chen A, Li Z, Zheng Y, Zhan J, Yang B, Yang Z. Decreasing Species Richness with Increase in Elevation and Positive Rapoport Effects of Crambidae (Lepidoptera) on Mount Taibai. Insects 2022; 13:1125. [PMID: 36555035 PMCID: PMC9783943 DOI: 10.3390/insects13121125] [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] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Rapoport's rule proposes that a species' range size increases with the increase in a gradient (such as latitude, altitude or water depth). However, altitudinal distributions and Rapoport's rule have rarely been tested for Asian Lepidoptera. Pyraustinae and Spilomelinae (Lepidoptera: Crambidae) are extremely diverse in temperate Asia, including on Mount Taibai, which is considered a hotspot area for studying the vertical distribution patterns of insect species. Based on the investigation of altitudinal distribution data with identification by using both DNA barcoding and the morphological classification of Pyraustinae and Spilomelinae, this paper determines the altitudinal gradient pattern for these two subfamilies on the north slope of Mount Taibai, and provides a test of the universality of Rapoport's rule in Lepidoptera by using four methods, including Stevens' method, Pagel's method, Rohde's method, and the cross-species method. Our results show that the alpha diversity of Pyraustinae and Spilomelinae both decrease with rising altitude. By contrast, the species' ranges increase with rising altitude. Three of the four methods used to test Rapoport's rule yielded positive results, while Rohde's results show a unimodal distribution model and do not support Rapoport's rule. Our findings fill the research gap on the elevational diversity of Lepidoptera in temperate Asia.
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Affiliation(s)
- Anping Chen
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Northwest A&F University, Xianyang 712100, China
- Entomological Museum, College of Plant Protection, Northwest A&F University, Xianyang 712100, China
| | - Zhijie Li
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Northwest A&F University, Xianyang 712100, China
- Entomological Museum, College of Plant Protection, Northwest A&F University, Xianyang 712100, China
| | - Yufeng Zheng
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Northwest A&F University, Xianyang 712100, China
- Entomological Museum, College of Plant Protection, Northwest A&F University, Xianyang 712100, China
| | - Jinyu Zhan
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Northwest A&F University, Xianyang 712100, China
- Entomological Museum, College of Plant Protection, Northwest A&F University, Xianyang 712100, China
| | - Bolan Yang
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Northwest A&F University, Xianyang 712100, China
- Entomological Museum, College of Plant Protection, Northwest A&F University, Xianyang 712100, China
| | - Zhaofu Yang
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Northwest A&F University, Xianyang 712100, China
- Entomological Museum, College of Plant Protection, Northwest A&F University, Xianyang 712100, China
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Smith KS, Morris MM, Morrow CD, Novak JR, Roberts MD, Frugé AD. Associations between Changes in Fat-Free Mass, Fecal Microbe Diversity, and Mood Disturbance in Young Adults after 10-Weeks of Resistance Training. Microorganisms 2022; 10:microorganisms10122344. [PMID: 36557597 PMCID: PMC9785032 DOI: 10.3390/microorganisms10122344] [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: 10/19/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The gut microbiome contributes to numerous physiological processes in humans, and diet and exercise are known to alter both microbial composition and mood. We sought to explore the effect of a 10-week resistance training (RT) regimen with or without peanut protein supplementation (PPS) in untrained young adults on fecal microbiota and mood disturbance (MD). METHODS Participants were randomized into PPS (n = 25) and control (CTL [no supplement]; n = 24) groups and engaged in supervised, full-body RT twice a week. Measures included body composition, fecal microbe relative abundance, alpha- and beta-diversity from 16 s rRNA gene sequencing with QIIME2 processing, dietary intake at baseline and following the 10-week intervention, and post-intervention MD via the profile of mood states (POMS) questionnaire. Independent samples t-tests were used to determine differences between PPS and CTL groups. Paired samples t-tests investigated differences within groups. RESULTS Our sample was mostly female (69.4%), white (87.8%), normal weight (body mass index 24.6 ± 4.2 kg/m2), and 21 ± 2.0 years old. Shannon index significantly increased from baseline in all participants (p = 0.040), with no between-group differences or pre-post beta-diversity dissimilarities. Changes in Blautia abundance were associated with the positive POMS subscales, Vigor and self-esteem-related-affect (SERA) (rho = -0.451, p = 0.04; rho = -0.487, p = 0.025, respectively). Whole tree phylogeny changes were negatively correlated with SERA and Vigor (rho = -0.475, p = 0.046; rho = -0.582, p = 0.011, respectively) as well as change in bodyfat percentage (rho = -0.608, p = 0.007). Mediation analysis results indicate changes in PD Whole Tree Phylogeny was not a significant mediator of the relationship between change in fat-free mass and total MD. CONCLUSIONS Mood state subscales are associated with changes in microbial taxa and body composition. PD Whole Tree Phylogeny increased following the 10-week RT regimen; further research is warranted to explore how RT-induced changes in microbial diversity are related to changes in body composition and mood disturbance.
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Affiliation(s)
- Kristen S. Smith
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL 36849, USA
- Correspondence:
| | - Molly M. Morris
- College of Science and Mathematics, Auburn University, Auburn, AL 36849, USA
| | - Casey D. Morrow
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Josh R. Novak
- Department of Human Development and Family Sciences, Auburn University, Auburn, AL 36849, USA
| | | | - Andrew Dandridge Frugé
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL 36849, USA
- College of Nursing, Auburn University, Auburn, AL 36849, USA
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Abstract
BACKGROUND Numerous studies have examined the gut microbial ecology of patients with Crohn's disease (CD) and ulcerative colitis, but inflammatory bowel disease-associated taxa and ecological effect sizes are not consistent between studies. METHODS We systematically searched PubMed and Google Scholar and performed a meta-analysis of 13 studies to analyze how variables such as sample type (stool, biopsy, and lavage) affect results in inflammatory bowel disease gut microbiome studies, using uniform bioinformatic methods for all primary data. RESULTS Reduced alpha diversity was a consistent feature of both CD and ulcerative colitis but was more pronounced in CD. Disease contributed significantly variation in beta diversity in most studies, but effect size varied, and the effect of sample type was greater than the effect of disease. Fusobacterium was the genus most consistently associated with CD, but disease-associated genera were mostly inconsistent between studies. Stool studies had lower heterogeneity than biopsy studies, especially for CD. CONCLUSIONS Our results indicate that sample type variation is an important contributor to study variability that should be carefully considered during study design, and stool is likely superior to biopsy for CD studies due to its lower heterogeneity.
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Affiliation(s)
| | - Xochitl C Morgan
- Address correspondence to: Xochitl C. Morgan, PhD, Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, Dunedin 9010 New Zealand ()
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Costa-Roura S, Villalba D, Balcells J, De la Fuente G. First Steps into Ruminal Microbiota Robustness. Animals (Basel) 2022; 12:2366. [PMID: 36139226 PMCID: PMC9495070 DOI: 10.3390/ani12182366] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/01/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Despite its central role in ruminant nutrition, little is known about ruminal microbiota robustness, which is understood as the ability of the microbiota to cope with disturbances. The aim of the present review is to offer a comprehensive description of microbial robustness, as well as its potential drivers, with special focus on ruminal microbiota. First, we provide a briefing on the current knowledge about ruminal microbiota. Second, we define the concept of disturbance (any discrete event that disrupts the structure of a community and changes either the resource availability or the physical environment). Third, we discuss community resistance (the ability to remain unchanged in the face of a disturbance), resilience (the ability to return to the initial structure following a disturbance) and functional redundancy (the ability to maintain or recover initial function despite compositional changes), all of which are considered to be key properties of robust microbial communities. Then, we provide an overview of the currently available methodologies to assess community robustness, as well as its drivers (microbial diversity and network complexity) and its potential modulation through diet. Finally, we propose future lines of research on ruminal microbiota robustness.
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Jiang LM, Sattar K, Lü GH, Hu D, Zhang J, Yang XD. Different contributions of plant diversity and soil properties to the community stability in the arid desert ecosystem. Front Plant Sci 2022; 13:969852. [PMID: 36092411 PMCID: PMC9453452 DOI: 10.3389/fpls.2022.969852] [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] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
As a one of the focuses of ecological research, understanding the regulation of plant diversity on community stability is helpful to reveal the adaption of plant to environmental changes. However, the relationship between plant diversity and community stability is still controversial due to the scale effect of its influencing factors. In this study, we compared the changes in community stability and different plant diversity (i.e., species, functional, and phylogenetic diversities) between three communities (i.e., riparian forest, ecotone community, and desert shrubs), and across three spatial scales (i.e., 100, 400, and 2500 m2), and then quantified the contribution of soil properties and plant diversity to community stability by using structural equation model (SEM) in the Ebinur Lake Basin Nature Reserve of the Xinjiang Uygur Autonomous Region in the NW China. The results showed that: (1) community stability differed among three communities (ecotone community > desert shrubs > riparian forest). The stability of three communities all decreased with the increase of spatial scale (2) species diversity, phylogenetic richness and the mean pairwise phylogenetic distance were higher in ecotone community than that in desert shrubs and riparian forest, while the mean nearest taxa distance showed as riparian forest > ecotone community > desert shrubs. (3) Soil ammonium nitrogen and total phosphorus had the significant direct negative and positive effects on the community stability, respectively. Soil ammonium nitrogen and total phosphorus also indirectly affected community stability by adjusting plant diversity. The interaction among species, functional and phylogenetic diversities also regulated the variation of community stability across the spatial scales. Our results suggested that the effect of plant diversities on community stability were greater than that of soil factors. The asynchronous effect caused by the changes in species composition and functional traits among communities had a positive impact on the stability. Our study provided a theoretical support for the conservation and management of biodiversity and community functions in desert areas.
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Affiliation(s)
- La-Mei Jiang
- College of Ecology and Environment, Xinjiang University, Ürümqi, China
- Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Ürümqi, China
- Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Jinghe, China
| | - Kunduz Sattar
- Xinjiang Uygur Autonomous Region Forestry Planning Institute, Ürümqi, China
| | - Guang-Hui Lü
- College of Ecology and Environment, Xinjiang University, Ürümqi, China
- Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Ürümqi, China
- Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Jinghe, China
| | - Dong Hu
- College of Life Science, Northwest University, Xi’an, China
| | - Jie Zhang
- College of Ecology and Environment, Xinjiang University, Ürümqi, China
- Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Ürümqi, China
- Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Jinghe, China
| | - Xiao-Dong Yang
- College of Geography and Tourism Culture, Ningbo University, Ningbo, China
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Aira M, Pérez-Losada M, Crandall KA, Domínguez J. Host taxonomy determines the composition, structure, and diversity of the earthworm cast microbiome under homogenous feeding conditions. FEMS Microbiol Ecol 2022; 98:6655979. [PMID: 35927583 DOI: 10.1093/femsec/fiac093] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/21/2022] [Accepted: 08/02/2022] [Indexed: 11/12/2022] Open
Abstract
Host evolutionary history is a key factor shaping the earthworm cast microbiome, although its effect can be shadowed by the earthworm's diet. To untangle dietary from taxon effects, we raised nine earthworm species on a uniform diet of cow manure and compared cast microbiome across species while controlling for diet. Our results showed that, under controlled laboratory conditions, earthworm microbiomes are species-specific, more diverse than that of the controlled diet, and mainly comprised of native bacteria (i.e., not acquired from the diet). Furthermore, diet has a medium to large convergence effect on microbiome composition since earthworms shared 16 to 74% of their bacterial amplicon sequence variants (ASV). The inter-species core microbiome included 10 ASVs, while their intra-species core microbiomes were larger and varied in ASV richness (24-48%) and sequence abundance across earthworm species. This specificity in core microbiomes and variable degree of similarity in bacterial composition suggest that phylosymbiosis could determine earthworm microbiome assembly. However, lack of congruence between the earthworm phylogeny and the microbiome dendrogram suggests that a consistent diet fed over several generations may have weakened potential phylosymbiotic effects. Thus, cast microbiome assembly in earthworms seem to be the result of an interplay among host phylogeny and diet.
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Affiliation(s)
- Manuel Aira
- Grupo de Ecoloxía Animal (GEA), Universidad de Vigo, Ourense E-36310, España
| | - Marcos Pérez-Losada
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC 20052, USA.,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Keith A Crandall
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC 20052, USA
| | - Jorge Domínguez
- Grupo de Ecoloxía Animal (GEA), Universidad de Vigo, Ourense E-36310, España
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Linkens AMA, van Best N, Niessen PM, Wijckmans NEG, de Goei EEC, Scheijen JLJM, van Dongen MCJM, van Gool CCJAW, de Vos WM, Houben AJHM, Stehouwer CDA, Eussen SJMP, Penders J, Schalkwijk CG. A 4-Week Diet Low or High in Advanced Glycation Endproducts Has Limited Impact on Gut Microbial Composition in Abdominally Obese Individuals: The deAGEing Trial. Int J Mol Sci 2022; 23. [PMID: 35628138 DOI: 10.3390/ijms23105328] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 11/25/2022] Open
Abstract
Dietary advanced glycation endproducts (AGEs), abundantly present in Westernized diets, are linked to negative health outcomes, but their impact on the gut microbiota has not yet been well investigated in humans. We investigated the effects of a 4-week isocaloric and macronutrient-matched diet low or high in AGEs on the gut microbial composition of 70 abdominally obese individuals in a double-blind parallel-design randomized controlled trial (NCT03866343). Additionally, we investigated the cross-sectional associations between the habitual intake of dietary dicarbonyls, reactive precursors to AGEs, and the gut microbial composition, as assessed by 16S rRNA amplicon-based sequencing. Despite a marked percentage difference in AGE intake, we observed no differences in microbial richness and the general community structure. Only the Anaerostipes spp. had a relative abundance >0.5% and showed differential abundance (0.5 versus 1.11%; p = 0.028, after low- or high-AGE diet, respectively). While the habitual intake of dicarbonyls was not associated with microbial richness or a general community structure, the intake of 3-deoxyglucosone was especially associated with an abundance of several genera. Thus, a 4-week diet low or high in AGEs has a limited impact on the gut microbial composition of abdominally obese humans, paralleling its previously observed limited biological consequences. The effects of dietary dicarbonyls on the gut microbiota composition deserve further investigation.
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Choi Y, Hoops SL, Thoma CJ, Johnson AJ. A Guide to Dietary Pattern-Microbiome Data Integration. J Nutr 2022; 152:1187-1199. [PMID: 35348723 PMCID: PMC9071309 DOI: 10.1093/jn/nxac033] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/27/2022] [Accepted: 02/11/2022] [Indexed: 11/13/2022] Open
Abstract
The human gut microbiome is linked to metabolic and cardiovascular disease risk. Dietary modulation of the human gut microbiome offers an attractive pathway to manipulate the microbiome to prevent microbiome-related disease. However, this promise has not been realized. The complex system of diet and microbiome interactions is poorly understood. Integrating observational human diet and microbiome data can help researchers and clinicians untangle the complex systems of interactions that predict how the microbiome will change in response to foods. The use of dietary patterns to assess diet-microbiome relations holds promise to identify interesting associations and result in findings that can directly translate into actionable dietary intake recommendations and eating plans. In this article, we first highlight the complexity inherent in both dietary and microbiome data and introduce the approaches generally used to explore diet and microbiome simultaneously in observational studies. Second, we review the food group and dietary pattern-microbiome literature focusing on dietary complexity-moving beyond nutrients. Our review identified a substantial and growing body of literature that explores links between the microbiome and dietary patterns. However, there was very little standardization of dietary collection and assessment methods across studies. The 54 studies identified in this review used ≥7 different methods to assess diet. Coupled with the variation in final dietary parameters calculated from dietary data (e.g., dietary indices, dietary patterns, food groups, etc.), few studies with shared methods and assessment techniques were available for comparison. Third, we highlight the similarities between dietary and microbiome data structures and present the possibility that multivariate and compositional methods, developed initially for microbiome data, could have utility when applied to dietary data. Finally, we summarize the current state of the art for diet-microbiome data integration and highlight ways dietary data could be paired with microbiome data in future studies to improve the detection of diet-microbiome signals.
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Affiliation(s)
- Yuni Choi
- Division of Epidemiology and Community Health, University of Minnesota, School of Public Health, Minneapolis, MN
| | - Susan L Hoops
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, MN
| | - Calvin J Thoma
- BioTechnology Institute, University of Minnesota, Saint Paul, MN
| | - Abigail J Johnson
- Division of Epidemiology and Community Health, University of Minnesota, School of Public Health, Minneapolis, MN
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Molinero N, Taladrid D, Zorraquín-Peña I, de Celis M, Belda I, Mira A, Bartolomé B, Moreno-Arribas MV. Ulcerative Colitis Seems to Imply Oral Microbiome Dysbiosis. Curr Issues Mol Biol 2022; 44:1513-1527. [PMID: 35723361 PMCID: PMC9164047 DOI: 10.3390/cimb44040103] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/19/2022] [Accepted: 03/29/2022] [Indexed: 12/12/2022] Open
Abstract
Ulcerative colitis (UC) is a recurrent pathology of complex etiology that has been occasionally associated with oral lesions, but the overall composition of the oral microbiome in UC patients and its role in the pathogenesis of the disease are still poorly understood. In this study, the oral microbiome of UC patients and healthy individuals was compared to ascertain the possible changes in the oral microbial communities associated with UC. For this, the salivary microbiota of 10 patients diagnosed with an active phase of UC and 11 healthy controls was analyzed by 16S rRNA gene sequencing (trial ref. ISRCTN39987). Metataxonomic analysis revealed a decrease in the alpha diversity and an imbalance in the relative proportions of some key members of the oral core microbiome in UC patients. Additionally, Staphylococcus members and four differential species or phylotypes were only present in UC patients, not being detected in healthy subjects. This study provides a global snapshot of the existence of oral dysbiosis associated with UC, and the possible presence of potential oral biomarkers.
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Affiliation(s)
- Natalia Molinero
- Institute of Food Science Research (CIAL), CSIC-UAM, Campus de Cantoblanco, Nicolás Cabrera 9, 28049 Madrid, Spain; (N.M.); (D.T.); (I.Z.-P.); (B.B.)
| | - Diego Taladrid
- Institute of Food Science Research (CIAL), CSIC-UAM, Campus de Cantoblanco, Nicolás Cabrera 9, 28049 Madrid, Spain; (N.M.); (D.T.); (I.Z.-P.); (B.B.)
| | - Irene Zorraquín-Peña
- Institute of Food Science Research (CIAL), CSIC-UAM, Campus de Cantoblanco, Nicolás Cabrera 9, 28049 Madrid, Spain; (N.M.); (D.T.); (I.Z.-P.); (B.B.)
| | - Miguel de Celis
- Department of Genetics, Physiology and Microbiology, Complutense University of Madrid, 28040 Madrid, Spain; (M.d.C.); (I.B.)
| | - Ignacio Belda
- Department of Genetics, Physiology and Microbiology, Complutense University of Madrid, 28040 Madrid, Spain; (M.d.C.); (I.B.)
| | - Alex Mira
- Center for Advanced Research in Public Health, Department of Health and Genomics, FISABIO Foundation, 46020 Valencia, Spain;
| | - Begoña Bartolomé
- Institute of Food Science Research (CIAL), CSIC-UAM, Campus de Cantoblanco, Nicolás Cabrera 9, 28049 Madrid, Spain; (N.M.); (D.T.); (I.Z.-P.); (B.B.)
| | - M. Victoria Moreno-Arribas
- Institute of Food Science Research (CIAL), CSIC-UAM, Campus de Cantoblanco, Nicolás Cabrera 9, 28049 Madrid, Spain; (N.M.); (D.T.); (I.Z.-P.); (B.B.)
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Preisser WC, Welicky RL, Leslie KL, Mastick NC, Fiorenza EA, Maslenikov KP, Tornabene L, Kinsella JM, Wood CL. Parasite communities in English Sole ( Parophrys vetulus) have changed in composition but not richness in the Salish Sea, Washington, USA since 1930. Parasitology 2022; 149:1-51. [PMID: 35238289 PMCID: PMC10090603 DOI: 10.1017/s0031182022000233] [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: 08/23/2021] [Revised: 02/18/2022] [Accepted: 02/23/2022] [Indexed: 11/06/2022]
Abstract
Earth is rapidly losing free-living species. Is the same true for parasitic species? To reveal temporal trends in biodiversity, historical data are needed, but often such data do not exist for parasites. Here, parasite communities of the past were reconstructed by identifying parasites in fluid-preserved specimens held in natural history collections. Approximately 2500 macroparasites were counted from 109 English Sole (Parophrys vetulus ) collected between 1930 and 2019 in the Salish Sea, Washington, USA. Alpha and beta diversity were measured to determine if and how diversity changed over time. Species richness of parasite infracommunities and community dispersion did not vary over time, but community composition of decadal component communities varied significantly over the study period. Community dissimilarity also varied: prior to the mid-20th century, parasites shifted in abundance in a seemingly stochastic manner and, after this time period, a canalization of community change was observed, where species' abundances began to shift in consistent directions. Further work is needed to elucidate potential drivers of these changes and to determine if these patterns are present in the parasite communities of other fishes of the Salish Sea.
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Affiliation(s)
- Whitney C. Preisser
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Rachel L. Welicky
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
- Unit for Environmental Sciences and Management, North–West University, Potchefstroom, South Africa
| | - Katie L. Leslie
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Natalie C. Mastick
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Evan A. Fiorenza
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
- Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA
| | - Katherine P. Maslenikov
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
- Burke Museum Ichthyology Collection, University of Washington, Seattle, WA, USA
| | - Luke Tornabene
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
- Burke Museum Ichthyology Collection, University of Washington, Seattle, WA, USA
| | | | - Chelsea L. Wood
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
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