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Pallen MJ. Valid publication of names for bacterial species from the chicken gut. Int J Syst Evol Microbiol 2024; 74. [PMID: 38967644 DOI: 10.1099/ijsem.0.006445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024] Open
Abstract
This article is a follow-up to Gilroy R, Ravi A, Getino M, Pursley I, Horton DL, et al. PeerJ 2021;9:e10941, detailing accession numbers from culture collections to ensure that names for 33 new species conform to the Rules of the International Code of Nomenclature of Prokaryotes required for valid publication of names for cultured species. The following species names are now proposed to be recognized as validly published: Acinetobacter pecorum sp. nov., Arthrobacter gallicola sp. nov., Arthrobacter pullicola sp. nov., Bacillus norwichensis sp. nov., Brevibacterium gallinarum sp. nov., Brevundimonas guildfordensis sp. nov., Cellulomonas avistercoris sp. nov., Clostridium gallinarum sp. nov., Comamonas avium sp. nov., Corynebacterium gallinarum sp. nov., Cytobacillus stercorigallinarum sp. nov., Escherichia whittamii sp. nov., Kaistella pullorum sp. nov., Luteimonas colneyensis sp. nov., Microbacterium commune sp. nov., Microbacterium gallinarum sp. nov., Microbacterium pullorum sp. nov., Oceanitalea stevensii sp. nov., Ochrobactrum gallinarum sp. nov., Oerskovia douganii sp. nov., Oerskovia gallyi sp. nov., Oerskovia merdavium sp. nov., Oerskovia rustica sp. nov., Paenibacillus gallinarum sp. nov., Phocaeicola gallinarum sp. nov., Planococcus wigleyi sp. nov., Psychrobacter communis sp. nov., Serpens gallinarum sp. nov., Solibacillus faecavium sp. nov., Sporosarcina gallistercoris sp. nov., Sporosarcina quadrami sp. nov., Stenotrophomonas pennii sp. nov. and Ureibacillus galli sp. nov.
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Affiliation(s)
- Mark J Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
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2
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Goris T, Braune A. Genomics and physiology of Catenibacillus, human gut bacteria capable of polyphenol C-deglycosylation and flavonoid degradation. Microb Genom 2024; 10:001245. [PMID: 38785231 PMCID: PMC11170127 DOI: 10.1099/mgen.0.001245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 04/16/2024] [Indexed: 05/25/2024] Open
Abstract
The genus Catenibacillus (family Lachnospiraceae, phylum Bacillota) includes only one cultivated species so far, Catenibacillus scindens, isolated from human faeces and capable of deglycosylating dietary polyphenols and degrading flavonoid aglycones. Another human intestinal Catenibacillus strain not taxonomically resolved at that time was recently genome-sequenced. We analysed the genome of this novel isolate, designated Catenibacillus decagia, and showed its ability to deglycosylate C-coupled flavone and xanthone glucosides and O-coupled flavonoid glycosides. Most of the resulting aglycones were further degraded to the corresponding phenolic acids. Including the recently sequenced genome of C. scindens and ten faecal metagenome-assembled genomes assigned to the genus Catenibacillus, we performed a comparative genome analysis and searched for genes encoding potential C-glycosidases and other polyphenol-converting enzymes. According to genome data and physiological characterization, the core metabolism of Catenibacillus strains is based on a fermentative lifestyle with butyrate production and hydrogen evolution. Both C. scindens and C. decagia encode a flavonoid O-glycosidase, a flavone reductase, a flavanone/flavanonol-cleaving reductase and a phloretin hydrolase. Several gene clusters encode enzymes similar to those of the flavonoid C-deglycosylation system of Dorea strain PUE (DgpBC), while separately located genes encode putative polyphenol-glucoside oxidases (DgpA) required for C-deglycosylation. The diversity of dgpA and dgpBC gene clusters might explain the broad C-glycoside substrate spectrum of C. scindens and C. decagia. The other Catenibacillus genomes encode only a few potential flavonoid-converting enzymes. Our results indicate that several Catenibacillus species are well-equipped to deglycosylate and degrade dietary plant polyphenols and might inhabit a corresponding, specific niche in the gut.
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Affiliation(s)
- Tobias Goris
- Research Group Intestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany
| | - Annett Braune
- Research Group Intestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany
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3
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Moinet M, Collis RM, Rogers L, Devane ML, Biggs PJ, Stott R, Marshall J, Muirhead R, Cookson AL. Development of a multiplex droplet digital PCR assay for simultaneous detection and quantification of Escherichia coli, E. marmotae, and E. ruysiae in water samples. J Microbiol Methods 2024; 220:106909. [PMID: 38432551 DOI: 10.1016/j.mimet.2024.106909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/05/2024]
Abstract
Escherichia coli are widely used by water quality managers as Fecal Indicator Bacteria, but current quantification methods do not differentiate them from benign, environmental Escherichia species such as E. marmotae (formerly named cryptic clade V) or E. ruysiae (cryptic clades III and IV). Reliable and specific techniques for their identification are required to avoid confounding microbial water quality assessments. To address this, a multiplex droplet digital PCR (ddPCR) assay targeting lipB (E. coli and E. ruysiae) and bglC (E. marmotae) was designed. The ddPCR performance was assessed using in silico analysis; genomic DNA from 40 local, international, and reference strains of target and non-target coliforms; and spiked water samples in a range relevant to water quality managers (1 to 1000 cells/100 mL). Results were compared to an analogous quantitative PCR (qPCR) and the Colilert method. Both PCR assays showed excellent sensitivity with a limit of detection of 0.05 pg/μL and 0.005 pg/μl for ddPCR and qPCR respectively, and of quantification of 0.5 pg/μL of genomic DNA. The ddPCR allowed differentiation and quantification of three Escherichia species per run by amplitude multiplexing and showed a high concordance with concentrations measured by Colilert once proportional bias was accounted for. In silico specificity testing underlined the possibility to further detect and distinguish Escherichia cryptic clade VI. Finally, the applicability of the ddPCR was successfully tested on environmental water samples where E. marmotae and E. ruysiae potentially confound E. coli counts based on the Most Probable Number method, highlighting the utility of this novel ddPCR as an efficient and rapid discriminatory test to improve water quality assessments.
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Affiliation(s)
- Marie Moinet
- AgResearch Ltd., Food Systems Integrity Team, Hopkirk Research Institute, Tennent Drive, 4442 Palmerston North, New Zealand.
| | - Rose M Collis
- AgResearch Ltd., Food Systems Integrity Team, Hopkirk Research Institute, Tennent Drive, 4442 Palmerston North, New Zealand.
| | - Lynn Rogers
- AgResearch Ltd., Food Systems Integrity Team, Hopkirk Research Institute, Tennent Drive, 4442 Palmerston North, New Zealand; Massey University, (m)EpiLab, School of Veterinary Science, Hopkirk Research Institute, Tennent Drive, 4442 Palmerston North, New Zealand.
| | - Megan L Devane
- Institute of Environmental Science and Research Ltd. (ESR), 27 Creyke Rd, Ilam, 8041 Christchurch, New Zealand.
| | - Patrick J Biggs
- Massey University, (m)EpiLab, School of Veterinary Science, Hopkirk Research Institute, Tennent Drive, 4442 Palmerston North, New Zealand; Massey University, School of Natural Sciences, Tennent Drive, 4442 Palmerston North, New Zealand.
| | - Rebecca Stott
- National Institute of Water and Atmospheric Research (NIWA), Gate 10 Silverdale Road, Hillcrest, 3216 Hamilton, New Zealand.
| | - Jonathan Marshall
- Massey University, School of Mathematical and Computational Sciences, Tennent Drive, 4442 Palmerston North, New Zealand.
| | - Richard Muirhead
- AgResearch Ltd., Ethical Agriculture, Invermay, 176 Puddle Alley, 9092, Mosgiel, New Zealand.
| | - Adrian L Cookson
- AgResearch Ltd., Food Systems Integrity Team, Hopkirk Research Institute, Tennent Drive, 4442 Palmerston North, New Zealand; Massey University, (m)EpiLab, School of Veterinary Science, Hopkirk Research Institute, Tennent Drive, 4442 Palmerston North, New Zealand.
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Riva A, Sahin E, Volpedo G, Petretto A, Lavarello C, Di Sapia R, Barbarossa D, Zaniani NR, Craparotta I, Barbera MC, Sezerman U, Vezzani A, Striano P, Ravizza T. Identification of an epilepsy-linked gut microbiota signature in a pediatric rat model of acquired epilepsy. Neurobiol Dis 2024; 194:106469. [PMID: 38485093 DOI: 10.1016/j.nbd.2024.106469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/04/2024] [Accepted: 03/06/2024] [Indexed: 03/21/2024] Open
Abstract
A dysfunctional gut microbiota-brain axis is emerging as a potential pathogenic mechanism in epilepsy, particularly in pediatric forms of epilepsy. To add new insights into gut-related changes in acquired epilepsy that develops early in life, we used a multi-omics approach in a rat model with a 56% incidence of epilepsy. The presence of spontaneous seizures was assessed in adult rats (n = 46) 5 months after status epilepticus induced by intra-amygdala kainate at postnatal day 13, by 2 weeks (24/7) ECoG monitoring. Twenty-six rats developed epilepsy (Epi) while the remaining 20 rats (No-Epi) did not show spontaneous seizures. At the end of ECoG monitoring, all rats and their sham controls (n = 20) were sacrificed for quantitative histopathological and immunohistochemical analyses of the gut structure, glia and macrophages, as well as RTqPCR analysis of inflammation/oxidative stress markers. By comparing Epi, No-Epi rats, and sham controls, we found structural, cellular, and molecular alterations reflecting a dysfunctional gut, which were specifically associated with epilepsy. In particular, the villus height-to-crypt depth ratio and number of Goblet cells were reduced in the duodenum of Epi rats vs both No-Epi rats and sham controls (p < 0.01). Villus height and crypt depth in the duodenum and jejunum (p < 0.01) were increased in No-Epi vs both Epi and sham controls. We also detected enhanced Iba1-positive macrophages, together with increased IL1b and NFE2L2 transcripts and TNF protein, in the small intestine of Epi vs both No-Epi and sham control rats (p < 0.01), denoting the presence of inflammation and oxidative stress. Astroglial GFAP-immunostaining was similar in all experimental groups. Metagenomic analysis in the feces collected 5 months after status epilepticus showed that the ratio of two dominant phyla (Bacteroidota-to-Firmicutes) was similarly increased in Epi and No-Epi rats vs sham control rats. Notably, the relative abundance of families, genera, and species associated with SCFA production differed in Epi vs No-Epi rats, describing a bacterial imprint associated with epilepsy. Furthermore, Epi rats showed a blood metabolic signature characterized by changes in lipid metabolism compared to both No-Epi and sham control rats. Our study provides new evidence of long-term gut alterations, along with microbiota-related metabolic changes, occurring specifically in rats that develop epilepsy after brain injury early in life.
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Affiliation(s)
- Antonella Riva
- IRCCS Istituto Giannina Gaslini, Genova, Italy; Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università degli Studi di Genova, Genova, Italy
| | - Eray Sahin
- Acıbadem University, Faculty of Medicine, Department of Biostatistics and Medical Informatics, Istanbul, Turkey
| | - Greta Volpedo
- IRCCS Istituto Giannina Gaslini, Genova, Italy; Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università degli Studi di Genova, Genova, Italy
| | | | | | - Rossella Di Sapia
- Department of Acute Brain and Cardiovascular Injury, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Davide Barbarossa
- Department of Acute Brain and Cardiovascular Injury, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Nasibeh Riahi Zaniani
- Department of Acute Brain and Cardiovascular Injury, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Ilaria Craparotta
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Maria Chiara Barbera
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Uğur Sezerman
- Acıbadem University, Faculty of Medicine, Department of Biostatistics and Medical Informatics, Istanbul, Turkey
| | - Annamaria Vezzani
- Department of Acute Brain and Cardiovascular Injury, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Pasquale Striano
- IRCCS Istituto Giannina Gaslini, Genova, Italy; Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università degli Studi di Genova, Genova, Italy
| | - Teresa Ravizza
- Department of Acute Brain and Cardiovascular Injury, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy.
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Durán-Viseras A, Lindner BG, Hatt JK, Lai A, Wallace R, Ginn O, Brown J, Konstantinidis KT. Metagenomic insights into the impact of litter from poultry Concentrated Animal Feeding Operations (CAFOs) to adjacent soil and water microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 920:170772. [PMID: 38346660 DOI: 10.1016/j.scitotenv.2024.170772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/02/2024] [Accepted: 02/04/2024] [Indexed: 02/20/2024]
Abstract
In recent decades, human food consumption has led to an increased demand for animal-based foods, particularly chicken meat production. The state of Georgia, USA is one of the top broiler chicken producers in the United States, where animals are raised in Concentrated Animal Feeding Operations (CAFOs). Without proper management, CAFOs could negatively impact the environment and become a public health risk as a source of water and air pollution and/or by spreading antimicrobial resistance genes. In this study, we used metagenome sequencing to investigate the impact of the application of the CAFO's litter on adjacent soils and downstream creek waters in terms of microbial diversity and antimicrobial resistance profile changes. Our data indicate that while a few microbial groups increased in abundance within a short period of time after litter application, these populations subsequently decreased to levels similar to those found prior to the litter application or to below the detection limit of our metagenome sequencing effort. Microbial taxonomic composition analyses, relative abundance of Metagenome-Assembled Genomes (MAGs) and detection of Antimicrobial Resistance Genes (ARGs) allow us to conclude that this practice of litter application had a negligible effect on the microbiome or resistome profile of these soils and nearby waterways, likely due to its dilution in the field and/or outcompetition by indigenous microbes, revealing a minimal impact of these poultry facilities on the natural microbial communities.
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Affiliation(s)
- Ana Durán-Viseras
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla 41012, Spain; School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Blake G Lindner
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Amanda Lai
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Robert Wallace
- Georgia Tech Research Institute, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Olivia Ginn
- Chemical, Materials and Biomedical Engineering Department and Institute for Bioinformatics, University of Georgia, Athens, GA 30601, USA
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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Chuang SC, Dobhal S, Alvarez AM, Arif M. Three new species, Xanthomonas hawaiiensis sp. nov., Stenotrophomonas aracearum sp. nov., and Stenotrophomonas oahuensis sp. nov., isolated from the Araceae family. Front Microbiol 2024; 15:1356025. [PMID: 38655077 PMCID: PMC11035887 DOI: 10.3389/fmicb.2024.1356025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/18/2024] [Indexed: 04/26/2024] Open
Abstract
Xanthomonas and Stenotrophomonas are closely related genera in the family Lysobacteraceae. In our previous study of aroid-associated bacterial strains, most strains isolated from anthurium and other aroids were reclassified as X. phaseoli and other Xanthomonas species. However, two strains isolated from Spathiphyllum and Colocasia were phylogenetically distant from other strains in the Xanthomonas clade and two strains isolated from Anthurium clustered within the Stenotrophomonas clade. Phylogenetic trees based on 16S rRNA and nine housekeeping genes placed the former strains with the type strain of X. sacchari from sugarcane and the latter strains with the type strain of S. bentonitica from bentonite. In pairwise comparisons with type strains, the overall genomic relatedness indices required delineation of new species; digital DNA-DNA hybridization and average nucleotide identity values were lower than 70 and 95%, respectively. Hence, three new species are proposed: S. aracearum sp. nov. and S. oahuensis sp. nov. for two strains from anthurium and X. hawaiiensis sp. nov. for the strains from spathiphyllum and colocasia, respectively. The genome size of X. hawaiiensis sp. nov. is ~4.88 Mbp and higher than S. aracearum sp. nov. (4.33 Mbp) and S. oahuensis sp. nov. (4.68 Mbp). Gene content analysis revealed 425 and 576 core genes present in 40 xanthomonads and 25 stenotrophomonads, respectively. The average number of unique genes in Stenotrophomonas spp. was higher than in Xanthomonas spp., implying higher genetic diversity in Stenotrophomonas.
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Affiliation(s)
| | | | | | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaiʻi at Mānoa, Honolulu, HI, United States
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Deryabin D, Lazebnik C, Vlasenko L, Karimov I, Kosyan D, Zatevalov A, Duskaev G. Broiler Chicken Cecal Microbiome and Poultry Farming Productivity: A Meta-Analysis. Microorganisms 2024; 12:747. [PMID: 38674691 PMCID: PMC11052200 DOI: 10.3390/microorganisms12040747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 03/31/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
The cecal microbial community plays an important role in chicken growth and development via effective feed conversion and essential metabolite production. The aim of this study was to define the microbial community's variants in chickens' ceca and to explore the most significant association between the microbiome compositions and poultry farming productivity. The meta-analysis included original data from 8 control broiler chicken groups fed with a standard basic diet and 32 experimental groups supplemented with various feed additives. Standard Illumina 16S-RNA gene sequencing technology was used to characterize the chicken cecal microbiome. Zootechnical data sets integrated with the European Production Effectiveness Factor (EPEF) were collected. Analysis of the bacterial taxa abundance and co-occurrence in chicken cecal microbiomes revealed two alternative patterns: Bacteroidota-dominated with decreased alpha biodiversity; and Bacillota-enriched, which included the Actinomycetota, Cyanobacteriota and Thermodesulfobacteriota phyla members, with increased biodiversity indices. Bacillota-enriched microbiome groups showed elevated total feed intake (especially due to the starter feed intake) and final body weight, and high EPEF values, while Bacteroidota-dominated microbiomes were negatively associated with poultry farming productivity. The meta-analysis results lay the basis for the development of chicken growth-promoting feed supplementations, aimed at the stimulation of beneficial and inhibition of harmful bacterial patterns, where relevant metagenomic data can be a tool for their control and selection.
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Affiliation(s)
- Dmitry Deryabin
- Federal Research Centre of Biological Systems and Agrotechnologies of the Russian Academy of Sciences, January 9 Street, 29, 460000 Orenburg, Russia; (C.L.); (L.V.); (D.K.); (G.D.)
| | - Christina Lazebnik
- Federal Research Centre of Biological Systems and Agrotechnologies of the Russian Academy of Sciences, January 9 Street, 29, 460000 Orenburg, Russia; (C.L.); (L.V.); (D.K.); (G.D.)
| | - Ludmila Vlasenko
- Federal Research Centre of Biological Systems and Agrotechnologies of the Russian Academy of Sciences, January 9 Street, 29, 460000 Orenburg, Russia; (C.L.); (L.V.); (D.K.); (G.D.)
| | - Ilshat Karimov
- Orenburg State Medical University of the Ministry of Health of Russia, Sovetskaya Street, 6, 460014 Orenburg, Russia;
| | - Dianna Kosyan
- Federal Research Centre of Biological Systems and Agrotechnologies of the Russian Academy of Sciences, January 9 Street, 29, 460000 Orenburg, Russia; (C.L.); (L.V.); (D.K.); (G.D.)
| | - Alexander Zatevalov
- G.N. Gabrichevsky Research Institute for Epidemiology and Microbiology, Admiral Makarov Street, 10, 125212 Moscow, Russia;
| | - Galimzhan Duskaev
- Federal Research Centre of Biological Systems and Agrotechnologies of the Russian Academy of Sciences, January 9 Street, 29, 460000 Orenburg, Russia; (C.L.); (L.V.); (D.K.); (G.D.)
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Rosch MEG, Rehner J, Schmartz GP, Manier SK, Becker U, Müller R, Meyer MR, Keller A, Becker SL, Keller V. Time series of chicken stool metagenomics and egg metabolomics in changing production systems: preliminary insights from a proof-of-concept. ONE HEALTH OUTLOOK 2024; 6:4. [PMID: 38549118 PMCID: PMC10979557 DOI: 10.1186/s42522-024-00100-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 03/06/2024] [Indexed: 04/01/2024]
Abstract
BACKGROUND Different production systems of livestock animals influence various factors, including the gut microbiota. METHODS We investigated whether changing the conditions from barns to free-range chicken farming impacts the microbiome over the course of three weeks. We compared the stool microbiota of chicken from industrial barns after introducing them either in community or separately to a free-range environment. RESULTS Over the six time points, 12 taxa-mostly lactobacilli-changed significantly. As expected, the former barn chicken cohort carries more resistances to common antibiotics. These, however, remained positive over the observed period. At the end of the study, we collected eggs and compared metabolomic profiles of the egg white and yolk to profiles of eggs from commercial suppliers. Here, we observed significant differences between commercial and fresh collected eggs as well as differences between the former barn chicken and free-range chicken. CONCLUSION Our data indicate that the gut microbiota can undergo alterations over time in response to changes in production systems. These changes subsequently exert an influence on the metabolites found in the eggs. The preliminary results of our proof-of-concept study motivate larger scale observations with more individual chicken and longer observation periods.
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Affiliation(s)
- Michael E G Rosch
- Medical Doctor program Human Medicine, Saarland University/ Saarland University Medical Center, 66123/66421, Saarbrücken/Homburg, Germany
| | - Jacqueline Rehner
- Institute of Medical Microbiology and Hygiene, Saarland University, 66421, Homburg/Saar, Germany
| | - Georges P Schmartz
- Department of Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Sascha K Manier
- Department of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Saarland University, Center for Molecular Signaling (PZMS), 66421, Homburg/Saar, Germany
| | - Uta Becker
- MIP Pharma GmbH, 66386, Sankt Ingbert, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
| | - Markus R Meyer
- Department of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Saarland University, Center for Molecular Signaling (PZMS), 66421, Homburg/Saar, Germany
| | - Andreas Keller
- Department of Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Sören L Becker
- Institute of Medical Microbiology and Hygiene, Saarland University, 66421, Homburg/Saar, Germany
| | - Verena Keller
- Department of Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany.
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Maghini DG, Oduaran OH, Wirbel J, Olubayo LAI, Smyth N, Mathema T, Belger CW, Agongo G, Boua PR, Choma SSR, Gómez-Olivé FX, Kisiangani I, Mashaba GR, Micklesfield L, Mohamed SF, Nonterah EA, Norris S, Sorgho H, Tollman S, Wafawanaka F, Tluway F, Ramsay M, Bhatt AS, Hazelhurst S. Expanding the human gut microbiome atlas of Africa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584859. [PMID: 38559015 PMCID: PMC10980044 DOI: 10.1101/2024.03.13.584859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Population studies are crucial in understanding the complex interplay between the gut microbiome and geographical, lifestyle, genetic, and environmental factors. However, populations from low- and middle-income countries, which represent ~84% of the world population, have been excluded from large-scale gut microbiome research. Here, we present the AWI-Gen 2 Microbiome Project, a cross-sectional gut microbiome study sampling 1,803 women from Burkina Faso, Ghana, Kenya, and South Africa. By intensively engaging with communities that range from rural and horticultural to urban informal settlements and post-industrial, we capture population diversity that represents a far greater breadth of the world's population. Using shotgun metagenomic sequencing, we find that study site explains substantially more microbial variation than disease status. We identify taxa with strong geographic and lifestyle associations, including loss of Treponema and Cryptobacteroides species and gain of Bifidobacterium species in urban populations. We uncover a wealth of prokaryotic and viral novelty, including 1,005 new bacterial metagenome-assembled genomes, and identify phylogeography signatures in Treponema succinifaciens. Finally, we find a microbiome signature of HIV infection that is defined by several taxa not previously associated with HIV, including Dysosmobacter welbionis and Enterocloster sp. This study represents the largest population-representative survey of gut metagenomes of African individuals to date, and paired with extensive clinical biomarkers, demographic data, and lifestyle information, provides extensive opportunity for microbiome-related discovery and research.
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Affiliation(s)
- Dylan G Maghini
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- Department of Medicine (Hematology), Stanford University, Stanford, CA, USA
| | - Ovokeraye H Oduaran
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Jakob Wirbel
- Department of Medicine (Hematology), Stanford University, Stanford, CA, USA
| | - Luicer A Ingasia Olubayo
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Natalie Smyth
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Theophilous Mathema
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Carl W Belger
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Godfred Agongo
- Department of Biochemistry and Forensic Sciences, C. K. Tedam University of Technology and Applied Sciences, Navrongo, Ghana
| | - Palwendé R Boua
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Burkina Faso
| | - Solomon SR Choma
- DIMAMO Population Health Research Centre, University of Limpopo, South Africa
| | - F Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Given R Mashaba
- DIMAMO Population Health Research Centre, University of Limpopo, South Africa
| | - Lisa Micklesfield
- SAMRC/Wits Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | - Shane Norris
- SAMRC/Wits Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Human Development and Health, University of Southampton, Southampton, United Kingdom
| | - Hermann Sorgho
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Burkina Faso
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Floidy Wafawanaka
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Furahini Tluway
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Ami S Bhatt
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
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10
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Biggs PJ, Moinet M, Rogers LE, Devane M, Muirhead R, Stott R, Marshall JC, Cookson AL. Draft genome sequences of Escherichia spp. isolates from New Zealand environmental sources. Microbiol Resour Announc 2024; 13:e0100723. [PMID: 38376223 DOI: 10.1128/mra.01007-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/07/2024] [Indexed: 02/21/2024] Open
Abstract
Escherichia coli is often used as a fecal indicator bacterium for water quality monitoring. We report the draft genome sequences of 500 Escherichia isolates including newly described Escherichia species, namely Escherichia marmotae, Escherichia ruysiae, and Escherichia whittamii, obtained from diverse environmental sources to assist with improved public health risk assessments.
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Affiliation(s)
- Patrick J Biggs
- mEpiLab, Hopkirk Research Institute, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- New Zealand Food Science and Safety Research Centre, Massey University, Palmerston North, New Zealand
| | - Marie Moinet
- AgResearch, Hopkirk Research Institute, Palmerston North, New Zealand
| | - Lynn E Rogers
- AgResearch, Hopkirk Research Institute, Palmerston North, New Zealand
| | - Megan Devane
- Water and Health, Institute of Environmental Science and Research Ltd. (ESR), Christchurch, New Zealand
| | | | - Rebecca Stott
- Environmental Health, National Institute of Water and Atmospheric Research (NIWA), Hamilton, New Zealand
| | - Jonathann C Marshall
- School of Mathematical and Computational Sciences, Massey University, Palmerston North, New Zealand
| | - Adrian L Cookson
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- AgResearch, Hopkirk Research Institute, Palmerston North, New Zealand
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11
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Scicchitano D, Babbi G, Palladino G, Turroni S, Mekonnen YT, Laczny C, Wilmes P, Leekitcharoenphon P, Castagnetti A, D'Amico F, Brigidi P, Savojardo C, Manfreda G, Martelli P, De Cesare A, Aarestrup FM, Candela M, Rampelli S. Routes of dispersion of antibiotic resistance genes from the poultry farm system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169086. [PMID: 38056648 DOI: 10.1016/j.scitotenv.2023.169086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/01/2023] [Accepted: 12/01/2023] [Indexed: 12/08/2023]
Abstract
Poultry farms are hotspots for the development and spread of antibiotic resistance genes (ARGs), due to high stocking densities and extensive use of antibiotics, posing a threat of spread and contagion to workers and the external environment. Here, we applied shotgun metagenome sequencing to characterize the gut microbiome and resistome of poultry, workers and their households - also including microbiomes from the internal and external farm environment - in three different farms in Italy during a complete rearing cycle. Our results highlighted a relevant overlap among the microbiomes of poultry, workers, and their families (gut and skin), with clinically relevant ARGs and associated mobile elements shared in both poultry and human samples. On a finer scale, the reconstruction of species-level genome bins (SGBs) allowed us to delineate the dynamics of microorganism and ARGs dispersion from farm systems. We found the associations with worker microbiomes representing the main route of ARGs dispersion from poultry to human populations. Collectively, our findings clearly demonstrate the urgent need to implement more effective procedures to counteract ARGs dispersion from poultry food systems and the relevance of metagenomics-based metacommunity approaches to monitor the ARGs dispersion process for the safety of the working environment on farms.
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12
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Shen H, Wang T, Dong W, Sun G, Liu J, Peng N, Zhao S. Metagenome-assembled genome reveals species and functional composition of Jianghan chicken gut microbiota and isolation of Pediococcus acidilactic with probiotic properties. MICROBIOME 2024; 12:25. [PMID: 38347598 PMCID: PMC10860329 DOI: 10.1186/s40168-023-01745-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/20/2023] [Indexed: 02/15/2024]
Abstract
BACKGROUND Chickens are one of the most widely farmed animals worldwide and play a crucial role in meat and egg production. Gut microbiota is essential for chickens' health, disease, growth, and egg production. However, native chickens such as Jianghan chickens have better meat and egg production quality than centralized chickens, their intestinal microbial diversity is richer, and the potential gut microbial resources may bring health benefits to the host. RESULTS The bacterial species composition in the gut microbiota of Jianghan chickens is similar to that of other chicken breeds, with Phocaeicola and Bacteroides being the most abundant bacterial genera. The LEfSe analysis revealed significant differences in species composition and functional profiles between samples from Jingzhou and the other three groups. Functional annotation indicated that the gut microbiota of Jianghan chickens were dominated by metabolic genes, with the highest number of genes related to carbohydrate metabolism. Several antibiotic resistance genes (ARGs) were found, and the composition of ARGs was similar to that of factory-farmed chickens, suggesting that antibiotics were widely present in the gut microbiota of Jianghan chickens. The resistance genes of Jianghan chickens are mainly carried by microorganisms of the Bacteroidota and Bacillota phylum. In addition, more than 829 isolates were selected from the microbiota of Jianghan chickens. Following three rounds of acid and bile tolerance experiments performed on all the isolated strains, it was determined that six strains of Pediococcus acidilactici exhibited consistent tolerance. Further experiments confirmed that three of these strains (A4, B9, and C2) held substantial probiotic potential, with P. acidilactici B9 displaying the highest probiotic potential. CONCLUSIONS This study elucidates the composition of the intestinal microbiota and functional gene repertoire in Jianghan chickens. Despite the absence of antibiotic supplementation, the intestinal microbial community of Jianghan chickens still demonstrates a profile of antibiotic resistance genes similar to that of intensively reared chickens, suggesting resistance genes are prevalent in free-ranging poultry. Moreover, Jianghan and intensively reared chickens host major resistance genes differently, an aspect seldom explored between free-range and pastured chickens. Furthermore, among the 829 isolates, three strains of P. acidilatici exhibited strong probiotic potential. These findings provide insights into the unique gut microbiota of Jianghan chickens and highlight potential probiotic strains offering benefits to the host. Video Abstract.
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Affiliation(s)
- Hongye Shen
- National Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tinghui Wang
- National Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Weiwei Dong
- National Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- College of Life Sciences, Hubei Normal University, Huangshi, 435000, China
| | - Guoping Sun
- Hubei Poder Biotechnology Co., Ltd, Huangshi, 435000, China
| | - Jun Liu
- Hubei Poder Biotechnology Co., Ltd, Huangshi, 435000, China
| | - Nan Peng
- National Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shumiao Zhao
- National Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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13
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Al Hakeem WG, Cason EE, Adams D, Fathima S, Shanmugasundaram R, Lourenco J, Selvaraj RK. Characterizing the Effect of Campylobacter jejuni Challenge on Growth Performance, Cecal Microbiota, and Cecal Short-Chain Fatty Acid Concentrations in Broilers. Animals (Basel) 2024; 14:473. [PMID: 38338116 PMCID: PMC10854649 DOI: 10.3390/ani14030473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/20/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
This study aimed to understand the effect of C. jejuni challenge on the cecal microbiota and short-chain fatty acid (SCFA) concentration to form a better understanding of the host-pathogen interaction. Sixty broilers were randomly allocated into two treatments: control and challenge. Each treatment was replicated in six pens with five birds per pen. On day 21, birds in the challenge group were orally gavaged with 1 × 108C. jejuni/mL, while the control group was mock challenged with PBS. The C. jejuni challenge had no effect on body weight, feed intake, and feed conversion ratio compared to the control group. On day 28, the C. jejuni challenge decreased the observed features and Shannon index compared to the control group. On the species level, the C. jejuni challenge decreased (p = 0.02) the relative abundance of Sellimonas intestinalis on day 28 and increased (p = 0.04) the relative abundance of Faecalibacterium sp002160895 on day 35 compared to the control group. The C. jejuni challenge did not change the microbial function and the cecal concentrations of SCFA on days 28 and 35 compared to the control group. In conclusion, C. jejuni might alter the gut microbiota's composition and diversity without significantly compromising broilers' growth.
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Affiliation(s)
- Walid G. Al Hakeem
- Department of Poultry Science, The University of Georgia, Athens, GA 3060, USA; (W.G.A.H.); (E.E.C.); (D.A.); (S.F.)
| | - Emily E. Cason
- Department of Poultry Science, The University of Georgia, Athens, GA 3060, USA; (W.G.A.H.); (E.E.C.); (D.A.); (S.F.)
| | - Daniel Adams
- Department of Poultry Science, The University of Georgia, Athens, GA 3060, USA; (W.G.A.H.); (E.E.C.); (D.A.); (S.F.)
| | - Shahna Fathima
- Department of Poultry Science, The University of Georgia, Athens, GA 3060, USA; (W.G.A.H.); (E.E.C.); (D.A.); (S.F.)
| | - Revathi Shanmugasundaram
- Toxicology and Mycotoxin Research Unit, US National Poultry Research Center, Athens, GA 30605, USA;
| | - Jeferson Lourenco
- Department of Animal and Dairy Science, The University of Georgia, Athens, GA 30602, USA
| | - Ramesh K. Selvaraj
- Department of Poultry Science, The University of Georgia, Athens, GA 3060, USA; (W.G.A.H.); (E.E.C.); (D.A.); (S.F.)
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14
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Moinet M, Rogers L, Biggs P, Marshall J, Muirhead R, Devane M, Stott R, Cookson A. High-resolution genomic analysis to investigate the impact of the invasive brushtail possum (Trichosurus vulpecula) and other wildlife on microbial water quality assessments. PLoS One 2024; 19:e0295529. [PMID: 38236841 PMCID: PMC10796070 DOI: 10.1371/journal.pone.0295529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/21/2023] [Indexed: 01/22/2024] Open
Abstract
Escherichia coli are routine indicators of fecal contamination in water quality assessments. Contrary to livestock and human activities, brushtail possums (Trichosurus vulpecula), common invasive marsupials in Aotearoa/New Zealand, have not been thoroughly studied as a source of fecal contamination in freshwater. To investigate their potential role, Escherichia spp. isolates (n = 420) were recovered from possum gut contents and feces and were compared to those from water, soil, sediment, and periphyton samples, and from birds and other introduced mammals collected within the Mākirikiri Reserve, Dannevirke. Isolates were characterized using E. coli-specific real-time PCR targeting the uidA gene, Sanger sequencing of a partial gnd PCR product to generate a gnd sequence type (gST), and for 101 isolates, whole genome sequencing. Escherichia populations from 106 animal and environmental sample enrichments were analyzed using gnd metabarcoding. The alpha diversity of Escherichia gSTs was significantly lower in possums and animals compared with aquatic environmental samples, and some gSTs were shared between sample types, e.g., gST535 (in 85% of samples) and gST258 (71%). Forty percent of isolates gnd-typed and 75% of reads obtained by metabarcoding had gSTs shared between possums, other animals, and the environment. Core-genome single nucleotide polymorphism (SNP) analysis showed limited variation between several animal and environmental isolates (<10 SNPs). Our data show at an unprecedented scale that Escherichia clones are shared between possums, other wildlife, water, and the wider environment. These findings support the potential role of possums as contributors to fecal contamination in Aotearoa/New Zealand freshwater. Our study deepens the current knowledge of Escherichia populations in under-sampled wildlife. It presents a successful application of high-resolution genomic methods for fecal source tracking, thereby broadening the analytical toolbox available to water quality managers. Phylogenetic analysis of isolates and profiling of Escherichia populations provided useful information on the source(s) of fecal contamination and suggest that comprehensive invasive species management strategies may assist in restoring not only ecosystem health but also water health where microbial water quality is compromised.
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Affiliation(s)
- Marie Moinet
- Hopkirk Research Institute, AgResearch, Palmerston North, New Zealand
| | - Lynn Rogers
- Hopkirk Research Institute, AgResearch, Palmerston North, New Zealand
| | - Patrick Biggs
- mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Jonathan Marshall
- School of Mathematical and Computational Sciences, Massey University, Palmerston North, New Zealand
| | | | - Megan Devane
- Institute of Environmental Science and Research Ltd. (ESR), Christchurch, New Zealand
| | - Rebecca Stott
- National Institute of Water and Atmospheric Research (NIWA), Hamilton, New Zealand
| | - Adrian Cookson
- Hopkirk Research Institute, AgResearch, Palmerston North, New Zealand
- mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
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15
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Rudra B, Gupta RS. Phylogenomics studies and molecular markers reliably demarcate genus Pseudomonas sensu stricto and twelve other Pseudomonadaceae species clades representing novel and emended genera. Front Microbiol 2024; 14:1273665. [PMID: 38249459 PMCID: PMC10797017 DOI: 10.3389/fmicb.2023.1273665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/17/2023] [Indexed: 01/23/2024] Open
Abstract
Genus Pseudomonas is a large assemblage of diverse microorganisms, not sharing a common evolutionary history. To clarify their evolutionary relationships and classification, we have conducted comprehensive phylogenomic and comparative analyses on 388 Pseudomonadaceae genomes. In phylogenomic trees, Pseudomonas species formed 12 main clusters, apart from the "Aeruginosa clade" containing its type species, P. aeruginosa. In parallel, our detailed analyses on protein sequences from Pseudomonadaceae genomes have identified 98 novel conserved signature indels (CSIs), which are uniquely shared by the species from different observed clades/groups. Six CSIs, which are exclusively shared by species from the "Aeruginosa clade," provide reliable demarcation of this clade corresponding to the genus Pseudomonas sensu stricto in molecular terms. The remaining 92 identified CSIs are specific for nine other Pseudomonas species clades and the genera Azomonas and Azotobacter which branch in between them. The identified CSIs provide strong independent evidence of the genetic cohesiveness of these species clades and offer reliable means for their demarcation/circumscription. Based on the robust phylogenetic and molecular evidence presented here supporting the distinctness of the observed Pseudomonas species clades, we are proposing the transfer of species from the following clades into the indicated novel genera: Alcaligenes clade - Aquipseudomonas gen. nov.; Fluvialis clade - Caenipseudomonas gen. nov.; Linyingensis clade - Geopseudomonas gen. nov.; Oleovorans clade - Ectopseudomonas gen. nov.; Resinovorans clade - Metapseudomonas gen. nov.; Straminea clade - Phytopseudomonas gen. nov.; and Thermotolerans clade - Zestomonas gen. nov. In addition, descriptions of the genera Azomonas, Azotobacter, Chryseomonas, Serpens, and Stutzerimonas are emended to include information for the CSIs specific for them. The results presented here should aid in the development of a more reliable classification scheme for Pseudomonas species.
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Affiliation(s)
| | - Radhey S. Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
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16
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Rios-Galicia B, Sáenz JS, Yergaliyev T, Roth C, Camarinha-Silva A, Seifert J. Novel taxonomic and functional diversity of eight bacteria from the upper digestive tract of chicken. Int J Syst Evol Microbiol 2024; 74. [PMID: 38231200 DOI: 10.1099/ijsem.0.006210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024] Open
Abstract
Eight anaerobic strains obtained from crop, jejunum and ileum of chicken were isolated, characterized and genome analysed to observe their metabolic profiles, adaptive strategies and to serve as novel future references. The novel species Ligilactobacillus hohenheimensis sp. nov. (DSM 113870T=LMG 32876T), Limosilactobacillus galli sp. nov. (DSM 113833T=LMG 32623T), Limosilactobacillus avium sp. nov. (DSM 113849T=LMG 32671T), Limosilactobacillus pulli sp. nov. (DSM 115077T=LMG 32877T), Limosilactobacillus viscerum sp. nov. (DSM 113835T=LMG 32625T), Limosilactobacillus difficilis sp. nov. (DSM 114195T=LMG 32875T) and Clostridium butanoliproducens (DSM 115076T=LMG 32878T) are found in the upper gastrointestinal tract and present consistent adaptations that enable us to predict their ecological role. Molecular characterization using 16S rRNA gene analysis and long-read whole genome sequencing, confirmed the description of the novel genus Faecalispora gen. nov. with Faecalispora anaeroviscerum gen. nov. sp. nov. (DSM 113860T=LMG 32675T) as genus type species. After phylogenetic and taxonomic analysis, we recommend the reclassification of the species
Clostridium jeddahense
and
Clostridium sporosphaeroides
to the genus Faecalispora. Exploration of the microbiome from crop and small intestine of chicken expands our knowledge on the taxonomic diversity and adaptive functions of the inhabiting bacteria. The novel species identified in this project are part of a wider cultivation effort that represents the first repository of bacteria obtained from the crop and small intestine of chicken using culturomics, improving the potential handling of chicken microorganisms with biotechnological applications.
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Affiliation(s)
- Bibiana Rios-Galicia
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen Weg 3, 70593 Stuttgart, Germany
| | - Johan S Sáenz
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen Weg 3, 70593 Stuttgart, Germany
| | - Timur Yergaliyev
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen Weg 3, 70593 Stuttgart, Germany
| | - Christoph Roth
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen Weg 3, 70593 Stuttgart, Germany
| | - Amélia Camarinha-Silva
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen Weg 3, 70593 Stuttgart, Germany
| | - Jana Seifert
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen Weg 3, 70593 Stuttgart, Germany
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17
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Yan D, Li G, Zhang H, Xue Q, Zhou C, Jiang Y, Yin J, Wang Z, Zhao W, Han W. Metagenomic Sequencing Revealed Differences in the Composition of Cecal Microbes in Different Breeds of Chickens. Animals (Basel) 2023; 14:28. [PMID: 38200759 PMCID: PMC10778133 DOI: 10.3390/ani14010028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 12/16/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024] Open
Abstract
Intestinal microorganisms are closely related to the health, development, and production performance of animals and can also provide basic information for us to fully understand and explore the germplasm characteristics and traits of local chicken breeds. In this experiment, we used five local Chinese chicken breeds as research materials; metagenomic sequencing technology was used to explore the differences in the composition of intestinal microorganisms in different breeds, and it was found that each local chicken breed had unique unigenes, of which Silkies had the most, with a total of 12,948. GO and KEGG analyses found that the biological processes most enriched by differential functional genes include genetic coding, macromolecular transport, protein synthesis, and molecular functions such as glycoprotein binding, protein hydrolysis, etc. Each breed is enriched with specific pathways, such as Anyi tile-like gray chickens, which are enriched with pathways related to disease resistance, while Gamecocks' enrichment is related to amino acid metabolism. Random Forest and LEfSe analyses revealed specific species of intestinal microorganisms in the cecum of different breeds, such as Exiguobacterium, which is associated with melanin deposition in Silkies. Therefore, we infer that gut microorganisms are closely related to the formation of chicken breed characteristics, and the results of this experiment can provide a theoretical basis for the discovery of high-quality traits and the improvement of feeding conditions in the future.
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Affiliation(s)
- Dan Yan
- Jiangsu Institute of Poultry Science, National Chickens Genetic Resources, Yangzhou 225125, China; (D.Y.); (G.L.)
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
| | - Guohui Li
- Jiangsu Institute of Poultry Science, National Chickens Genetic Resources, Yangzhou 225125, China; (D.Y.); (G.L.)
| | - Huiyong Zhang
- Jiangsu Institute of Poultry Science, National Chickens Genetic Resources, Yangzhou 225125, China; (D.Y.); (G.L.)
| | - Qian Xue
- Jiangsu Institute of Poultry Science, National Chickens Genetic Resources, Yangzhou 225125, China; (D.Y.); (G.L.)
| | - Chenghao Zhou
- Jiangsu Institute of Poultry Science, National Chickens Genetic Resources, Yangzhou 225125, China; (D.Y.); (G.L.)
| | - Yixiu Jiang
- Jiangsu Institute of Poultry Science, National Chickens Genetic Resources, Yangzhou 225125, China; (D.Y.); (G.L.)
| | - Jianmei Yin
- Jiangsu Institute of Poultry Science, National Chickens Genetic Resources, Yangzhou 225125, China; (D.Y.); (G.L.)
| | - Zhixiu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
| | - Wenming Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
| | - Wei Han
- Jiangsu Institute of Poultry Science, National Chickens Genetic Resources, Yangzhou 225125, China; (D.Y.); (G.L.)
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18
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Campodónico VL, Tekle T, Bergman Y, Lu J, Gisriel E, Romagnoli M, Bourdas D, Hanlon A, Manuel C, Humphries R, Simner PJ, Carroll KC. Clinical significance of Nosocomiicoccus ampullae isolated from blood cultures. Microbiol Spectr 2023; 11:e0217923. [PMID: 37855460 PMCID: PMC10715106 DOI: 10.1128/spectrum.02179-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/31/2023] [Indexed: 10/20/2023] Open
Abstract
IMPORTANCE Nosocomiicoccus species are recently described as members of the Staphylococcaceae family. With their inclusion in commercial matrix-assisted laser desorption/ionization-time of flight mass spectrometry databases, Nosocomiicoccus species can now be identified when Gram-positive cocci in clusters are detected in positive blood cultures. However, their clinical significance is not known, making it difficult for the clinical microbiology laboratory to decide the extent of work-up. Based on our study, Nosocomiicoccus species demonstrate low pathogenicity and opportunistic potential. If isolated from a single blood culture set, limited work-up should be performed to an extent similar to other possible blood culture contaminants.
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Affiliation(s)
- Victoria L. Campodónico
- Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Tsigereda Tekle
- Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yehudit Bergman
- Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jennifer Lu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Emily Gisriel
- Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mark Romagnoli
- Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Dimitrios Bourdas
- Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ann Hanlon
- Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Carmila Manuel
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Romney Humphries
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Patricia J. Simner
- Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Division of Infectious Diseases, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Karen C. Carroll
- Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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19
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Afonso CL, Afonso AM. Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples. Vet Sci 2023; 10:690. [PMID: 38133241 PMCID: PMC10747646 DOI: 10.3390/vetsci10120690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/24/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023] Open
Abstract
Direct-targeted next-generation sequencing (tNGS), with its undoubtedly superior diagnostic capacity over real-time PCR (RT-PCR), and direct-non-targeted NGS (ntNGS), with its higher capacity to identify and characterize multiple agents, are both likely to become diagnostic methods of choice in the future. tNGS is a rapid and sensitive method for precise characterization of suspected agents. ntNGS, also known as agnostic diagnosis, does not require a hypothesis and has been used to identify unsuspected infections in clinical samples. Implemented in the form of multiplexed total DNA metagenomics or as total RNA sequencing, the approach produces comprehensive and actionable reports that allow semi-quantitative identification of most of the agents present in respiratory, cloacal, and tissue samples. The diagnostic benefits of the use of direct tNGS and ntNGS are high specificity, compatibility with different types of clinical samples (fresh, frozen, FTA cards, and paraffin-embedded), production of nearly complete infection profiles (viruses, bacteria, fungus, and parasites), production of "semi-quantitative" information, direct agent genotyping, and infectious agent mutational information. The achievements of NGS in terms of diagnosing poultry problems are described here, along with future applications. Multiplexing, development of standard operating procedures, robotics, sequencing kits, automated bioinformatics, cloud computing, and artificial intelligence (AI) are disciplines converging toward the use of this technology for active surveillance in poultry farms. Other advances in human and veterinary NGS sequencing are likely to be adaptable to avian species in the future.
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Protasov E, Nonoh JO, Kästle Silva JM, Mies US, Hervé V, Dietrich C, Lang K, Mikulski L, Platt K, Poehlein A, Köhler-Ramm T, Miambi E, Boga HI, Feldewert C, Ngugi DK, Plarre R, Sillam-Dussès D, Šobotník J, Daniel R, Brune A. Diversity and taxonomic revision of methanogens and other archaea in the intestinal tract of terrestrial arthropods. Front Microbiol 2023; 14:1281628. [PMID: 38033561 PMCID: PMC10684969 DOI: 10.3389/fmicb.2023.1281628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/13/2023] [Indexed: 12/02/2023] Open
Abstract
Methane emission by terrestrial invertebrates is restricted to millipedes, termites, cockroaches, and scarab beetles. The arthropod-associated archaea known to date belong to the orders Methanobacteriales, Methanomassiliicoccales, Methanomicrobiales, and Methanosarcinales, and in a few cases also to non-methanogenic Nitrososphaerales and Bathyarchaeales. However, all major host groups are severely undersampled, and the taxonomy of existing lineages is not well developed. Full-length 16S rRNA gene sequences and genomes of arthropod-associated archaea are scarce, reference databases lack resolution, and the names of many taxa are either not validly published or under-classified and require revision. Here, we investigated the diversity of archaea in a wide range of methane-emitting arthropods, combining phylogenomic analysis of isolates and metagenome-assembled genomes (MAGs) with amplicon sequencing of full-length 16S rRNA genes. Our results allowed us to describe numerous new species in hitherto undescribed taxa among the orders Methanobacteriales (Methanacia, Methanarmilla, Methanobaculum, Methanobinarius, Methanocatella, Methanoflexus, Methanorudis, and Methanovirga, all gen. nova), Methanomicrobiales (Methanofilum and Methanorbis, both gen. nova), Methanosarcinales (Methanofrustulum and Methanolapillus, both gen. nova), Methanomassiliicoccales (Methanomethylophilaceae fam. nov., Methanarcanum, Methanogranum, Methanomethylophilus, Methanomicula, Methanoplasma, Methanoprimaticola, all gen. nova), and the new family Bathycorpusculaceae (Bathycorpusculum gen. nov.). Reclassification of amplicon libraries from this and previous studies using this new taxonomic framework revealed that arthropods harbor only CO2 and methyl-reducing hydrogenotrophic methanogens. Numerous genus-level lineages appear to be present exclusively in arthropods, suggesting long evolutionary trajectories with their termite, cockroach, and millipede hosts, and a radiation into various microhabitats and ecological niches provided by their digestive tracts (e.g., hindgut compartments, gut wall, or anaerobic protists). The distribution patterns among the different host groups are often complex, indicating a mixed mode of transmission and a parallel evolution of invertebrate and vertebrate-associated lineages.
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Affiliation(s)
- Evgenii Protasov
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - James O. Nonoh
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Joana M. Kästle Silva
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Undine S. Mies
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Vincent Hervé
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Carsten Dietrich
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Kristina Lang
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Lena Mikulski
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Katja Platt
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg August University of Göttingen, Göttingen, Germany
| | - Tim Köhler-Ramm
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Edouard Miambi
- Evolutionary Ecology Department, Institute of Ecology and Environmental Sciences of Paris (iEES-Paris), University of Paris-Est Créteil (UPEC), Créteil, France
| | - Hamadi I. Boga
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Christopher Feldewert
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - David K. Ngugi
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Rudy Plarre
- Bundesanstalt für Materialforschung und -prüfung, Berlin, Germany
| | - David Sillam-Dussès
- Laboratory of Experimental and Comparative Ethology (LEEC), UR 4443, Université Sorbonne Paris Nord, Villetaneuse, France
| | - Jan Šobotník
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czechia
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg August University of Göttingen, Göttingen, Germany
| | - Andreas Brune
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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Ren Q, Wang D, Han J, Wang J, Liu Z, Wu Z. Ligilactobacillus cholophilus sp. nov., isolated from pickled potherb mustard ( Brassica juncea Coss.). Int J Syst Evol Microbiol 2023; 73. [PMID: 37947349 DOI: 10.1099/ijsem.0.006160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023] Open
Abstract
Strain BD7642T was isolated from Chinese pickled potherb mustard (Brassica juncea Coss.) purchased from a local market in Shanghai, PR China. A polyphasic approach, including 16S rRNA gene sequence, housekeeping gene, average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), G+C content and phenotypic analyses, was employed to characterize strain BD7642T. Cells of the bacterium were short round rods, Gram-stain-positive, non-spore-forming and catalase-negative. The strain grew at 30-45 °C and pH 4.0-8.0. Optimum growth occurred at 35-40 °C and pH 6.0-7.0. The strain exhibited growth with salt (NaCl) concentrations of up to 5 % (w/v). The G+C content of the strain's genomic DNA was 31.37 mol%. The major fatty acids were C16 : 0, C18 : 1 c9 and summed feature 10 (C18 : 1 c11/t9/t6). 16S rRNA gene sequencing revealed that strain BD7642T represents a member of the genus Ligilactobacillus and it had high sequence similarity to Ligilactobacillus aviarius NBRC 102162T (96.73 %), Ligilactobacillus araffinosus LGM 23560 (96.66 %) and Ligilactobacillus salivarius JCM 1231T (95.82 %). The dDDH values between strain BD7642T and its phylogenetically related species within the genus Ligilactobacillus ranged from 12.6 to 25.4 %. The ANI values between strain BD7642T and its closely related taxa were far lower than the threshold (95 %-96 %) used for species differentiation. Results of phylogenetic, physiological and phenotypic characterization confirmed that strain BD7642T represents a novel species within the genus Ligilactobacillus, for which the name Ligilactobacillus cholophilus sp. nov. is proposed. The type strain is BD7642T (=CCTCC AB 2022398T=JCM 36074T).
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Affiliation(s)
- Quanlu Ren
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd, Shanghai 200436, PR China
| | - Danqi Wang
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd, Shanghai 200436, PR China
| | - Jin Han
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd, Shanghai 200436, PR China
| | - Jing Wang
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd, Shanghai 200436, PR China
| | - Zhenmin Liu
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd, Shanghai 200436, PR China
| | - Zhengjun Wu
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd, Shanghai 200436, PR China
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da Silva MBF, da Mota FF, Cypriano J, Abreu F, Seldin L. Psychrobacillus antarcticus sp. nov., a psychrotolerant bioemulsifier producer isolated from King George Island, Antarctica. Int J Syst Evol Microbiol 2023; 73. [PMID: 38009904 DOI: 10.1099/ijsem.0.006181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Abstract
A Gram-stain-positive rod, psychrotolerant, aerobic and bioemulsifier-producing strain, denoted as Val9T, was isolated from soil sampled at Vale Ulman, King George Island, Antarctica. The strain grew at up to 30 °C (optimum, 15 °C), at pH 6-9 (optimum, pH 8) and with up to 5 % w/v NaCl (optimum, 3 %). The strain was motile and positive for catalase, oxidase and H2S. It did not hydrolyse starch, casein or gelatin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Val9T belonged to the genus Psychrobacillus and was closely related to Psychrobacillus psychrotolerans DSM 11706T (99.9 % similarity), Psychrobacillus psychrodurans DSM 11713T (99.8 %) and Psychrobacillus glaciei PB01T (99.2 %). Digital DNA-DNA hybridization and average nucleotide identity values were lower than 37.3 and 85.5 %, respectively, with the closest phylogenetic neighbours. The DNA G+C content of strain Val9T calculated from the complete genome sequence was 36.6 mol%. The predominant cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 1ω11c. Menaquinone-8 was the major respiratory quinone. The peptidoglycan type was A4β l-Orn-d-glu. The novel strain contained diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol as predominant polar lipids. Based on 16S rRNA phylogenetic and multilocus sequence analyses (recA, rpoB and gyrB), as well as phylogenomic, chemotaxonomic and phenotypic tests, we demonstrate that strain Val9T represents a novel species of the genus Psychrobacillus, for which the name Psychrobacillus antarcticus sp. nov. is proposed. The type strain is Val9T (=DSM 115096T=CCGB 1952T=NRRL B-65674T).
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Affiliation(s)
| | - Fabio Faria da Mota
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Jefferson Cypriano
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Fernanda Abreu
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Lucy Seldin
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Lorenzo-Rebenaque L, Casto-Rebollo C, Diretto G, Frusciante S, Rodríguez JC, Ventero MP, Molina-Pardines C, Vega S, Marin C, Marco-Jiménez F. Modulation of Caecal Microbiota and Metabolome Profile in Salmonella-Infected Broilers by Phage Therapy. Int J Mol Sci 2023; 24:15201. [PMID: 37894882 PMCID: PMC10607084 DOI: 10.3390/ijms242015201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Bacteriophage therapy is considered one of the most promising tools to control zoonotic bacteria, such as Salmonella, in broiler production. Phages exhibit high specificity for their targeted bacterial hosts, causing minimal disruption to the niche microbiota. However, data on the gut environment's response to phage therapy in poultry are limited. This study investigated the influence of Salmonella phage on host physiology through caecal microbiota and metabolome modulation using high-throughput 16S rRNA gene sequencing and an untargeted metabolomics approach. We employed 24 caecum content samples and 24 blood serum samples from 4-, 5- and 6-week-old broilers from a previous study where Salmonella phages were administered via feed in Salmonella-infected broilers, which were individually weighed weekly. Phage therapy did not affect the alpha or beta diversity of the microbiota. Specifically, we observed changes in the relative abundance of 14 out of the 110 genera using the PLS-DA and Bayes approaches. On the other hand, we noted changes in the caecal metabolites (63 up-accumulated and 37 down-accumulated out of the 1113 caecal metabolites). Nevertheless, the minimal changes in blood serum suggest a non-significant physiological response. The application of Salmonella phages under production conditions modulates the caecal microbiome and metabolome profiles in broilers without impacting the host physiology in terms of growth performance.
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Affiliation(s)
- Laura Lorenzo-Rebenaque
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology, Biomedical Research Institute, Faculty of Veterinary Medicine, Cardenal Herrera-CEU University, CEU Universities, Calle Santiago Ramón y Cajal 20, Alfara del Patriarca, 45115 Valencia, Spain; (L.L.-R.); (S.V.); (C.M.)
| | - Cristina Casto-Rebollo
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain;
| | - Gianfranco Diretto
- Italian Agency for New Technologies, Energy and Sustainable Development (ENEA), Biotechnology Laboratory, Centro Ricerche Casaccia, Via Anguillarese, 301, Santa Maria di Galeria, 00123 Rome, Italy; (G.D.); (S.F.)
| | - Sarah Frusciante
- Italian Agency for New Technologies, Energy and Sustainable Development (ENEA), Biotechnology Laboratory, Centro Ricerche Casaccia, Via Anguillarese, 301, Santa Maria di Galeria, 00123 Rome, Italy; (G.D.); (S.F.)
| | - Juan Carlos Rodríguez
- Microbiology Department, Dr. Balmis University General Hospital, Microbiology Division, Miguel Hernández University, ISABIAL, 03010 Alicante, Spain;
| | - María-Paz Ventero
- Microbiology Department, Dr. Balmis University General Hospital, ISABIAL, 03010 Alicante, Spain; (M.-P.V.); (C.M.-P.)
| | - Carmen Molina-Pardines
- Microbiology Department, Dr. Balmis University General Hospital, ISABIAL, 03010 Alicante, Spain; (M.-P.V.); (C.M.-P.)
| | - Santiago Vega
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology, Biomedical Research Institute, Faculty of Veterinary Medicine, Cardenal Herrera-CEU University, CEU Universities, Calle Santiago Ramón y Cajal 20, Alfara del Patriarca, 45115 Valencia, Spain; (L.L.-R.); (S.V.); (C.M.)
| | - Clara Marin
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology, Biomedical Research Institute, Faculty of Veterinary Medicine, Cardenal Herrera-CEU University, CEU Universities, Calle Santiago Ramón y Cajal 20, Alfara del Patriarca, 45115 Valencia, Spain; (L.L.-R.); (S.V.); (C.M.)
| | - Francisco Marco-Jiménez
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain;
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Mills M, Lee S, Piperata BA, Garabed R, Choi B, Lee J. Household environment and animal fecal contamination are critical modifiers of the gut microbiome and resistome in young children from rural Nicaragua. MICROBIOME 2023; 11:207. [PMID: 37715296 PMCID: PMC10503196 DOI: 10.1186/s40168-023-01636-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/31/2023] [Indexed: 09/17/2023]
Abstract
BACKGROUND Early life plays a vital role in the development of the gut microbiome and subsequent health. While many factors that shape the gut microbiome have been described, including delivery mode, breastfeeding, and antibiotic use, the role of household environments is still unclear. Furthermore, the development of the gut antimicrobial resistome and its role in health and disease is not well characterized, particularly in settings with water insecurity and less sanitation infrastructure. RESULTS This study investigated the gut microbiome and resistome of infants and young children (ages 4 days-6 years) in rural Nicaragua using Oxford Nanopore Technology's MinION long-read sequencing. Differences in gut microbiome diversity and antibiotic resistance gene (ARG) abundance were examined for associations with host factors (age, sex, height for age z-score, weight for height z-score, delivery mode, breastfeeding habits) and household environmental factors (animals inside the home, coliforms in drinking water, enteric pathogens in household floors, fecal microbial source tracking markers in household floors). We identified anticipated associations of higher gut microbiome diversity with participant age and vaginal delivery. However, novel to this study were the significant, positive associations between ruminant and dog fecal contamination of household floors and gut microbiome diversity. We also identified greater abundance of potential pathogens in the gut microbiomes of participants with higher fecal contamination on their household floors. Path analysis revealed that water quality and household floor contamination independently and significantly influenced gut microbiome diversity when controlling for age. These gut microbiome contained diverse resistome, dominated by multidrug, tetracycline, macrolide/lincosamide/streptogramin, and beta-lactam resistance. We found that the abundance of ARGs in the gut decreased with age. The bacterial hosts of ARGs were mainly from the family Enterobacteriaceae, particularly Escherichia coli. CONCLUSIONS This study identified the role of household environmental contamination in the developing gut microbiome and resistome of young children and infants with a One Health perspective. We found significant relationships between host age, gut microbiome diversity, and the resistome. Understanding the impact of the household environment on the development of the resistome and microbiome in early life is essential to optimize the relationship between environmental exposure and human health. Video Abstract.
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Affiliation(s)
- Molly Mills
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA
- Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Seungjun Lee
- Department of Food Science and Nutrition, College of Fisheries Science, Pukyong National University, Busan, Republic of Korea
| | - Barbara A Piperata
- Department of Anthropology, The Ohio State University, Columbus, OH, USA
| | - Rebecca Garabed
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, USA
| | - Boseung Choi
- Division of Big Data Science, Korea University, Sejong, Republic of Korea
| | - Jiyoung Lee
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, USA.
- Environmental Sciences Graduate Program, The Ohio State University, Columbus, OH, USA.
- Department of Food Science & Technology, The Ohio State University, Columbus, OH, USA.
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Feehan B, Ran Q, Dorman V, Rumback K, Pogranichniy S, Ward K, Goodband R, Niederwerder MC, Lee STM. Novel complete methanogenic pathways in longitudinal genomic study of monogastric age-associated archaea. Anim Microbiome 2023; 5:35. [PMID: 37461084 DOI: 10.1186/s42523-023-00256-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/11/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Archaea perform critical roles in the microbiome system, including utilizing hydrogen to allow for enhanced microbiome member growth and influencing overall host health. With the majority of microbiome research focusing on bacteria, the functions of archaea are largely still under investigation. Understanding methanogenic functions during the host lifetime will add to the limited knowledge on archaeal influence on gut and host health. In our study, we determined lifelong archaea dynamics, including detection and methanogenic functions, while assessing global, temporal and host distribution of our novel archaeal metagenome-assembled genomes (MAGs). We followed 7 monogastric swine throughout their life, from birth to adult (1-156 days of age), and collected feces at 22 time points. The samples underwent gDNA extraction, Illumina sequencing, bioinformatic quality and assembly processes, MAG taxonomic assignment and functional annotation. MAGs were utilized in downstream phylogenetic analysis for global, temporal and host distribution in addition to methanogenic functional potential determination. RESULTS We generated 1130 non-redundant MAGs, representing 588 unique taxa at the species level, with 8 classified as methanogenic archaea. The taxonomic classifications were as follows: orders Methanomassiliicoccales (5) and Methanobacteriales (3); genera UBA71 (3), Methanomethylophilus (1), MX-02 (1), and Methanobrevibacter (3). We recovered the first US swine Methanobrevibacter UBA71 sp006954425 and Methanobrevibacter gottschalkii MAGs. The Methanobacteriales MAGs were identified primarily during the young, preweaned host whereas Methanomassiliicoccales primarily in the adult host. Moreover, we identified our methanogens in metagenomic sequences from Chinese swine, US adult humans, Mexican adult humans, Swedish adult humans, and paleontological humans, indicating that methanogens span different hosts, geography and time. We determined complete metabolic pathways for all three methanogenic pathways: hydrogenotrophic, methylotrophic, and acetoclastic. This study provided the first evidence of acetoclastic methanogenesis in archaea of monogastric hosts which indicated a previously unknown capability for acetate utilization in methanogenesis for monogastric methanogens. Overall, we hypothesized that the age-associated detection patterns were due to differential substrate availability via the host diet and microbial metabolism, and that these methanogenic functions are likely crucial to methanogens across hosts. This study provided a comprehensive, genome-centric investigation of monogastric-associated methanogens which will further improve our understanding of microbiome development and functions.
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Affiliation(s)
- Brandi Feehan
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Qinghong Ran
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Victoria Dorman
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Kourtney Rumback
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Sophia Pogranichniy
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Kaitlyn Ward
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Robert Goodband
- Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS, 66506, USA
| | | | - Sonny T M Lee
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA.
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Harrison J, Hussain RMF, Greer SF, Ntoukakis V, Aspin A, Vicente JG, Grant M, Studholme DJ. Draft genome sequences for ten strains of Xanthomonas species that have phylogenomic importance. Access Microbiol 2023; 5:acmi000532.v3. [PMID: 37601434 PMCID: PMC10436009 DOI: 10.1099/acmi.0.000532.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 06/25/2023] [Indexed: 08/22/2023] Open
Abstract
Here we report draft-quality genome sequences for pathotype strains of eight plant-pathogenic bacterial pathovars: Xanthomonas campestris pv. asclepiadis, X. campestris pv. cannae, X. campestris pv. esculenti, X. campestris pv. nigromaculans, X. campestris pv. parthenii, X. campestris pv. phormiicola, X. campestris pv. zinniae and X. dyei pv. eucalypti (= X. campestris pv. eucalypti). We also sequenced the type strain of species X. melonis and the unclassified Xanthomonas strain NCPPB 1067. These data will be useful for phylogenomic and taxonomic studies, filling some important gaps in sequence coverage of Xanthomonas phylogenetic diversity. We include representatives of previously under-sequenced pathovars and species-level clades. Furthermore, these genome sequences may be useful in elucidating the molecular basis for important phenotypes, such as biosynthesis of coronatine-related toxins and degradation of fungal toxin cercosporin.
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Affiliation(s)
| | - Rana Muhammad Fraz Hussain
- Gibbet Hill Campus, School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Wellesbourne Campus, School of Life Sciences, University of Warwick, Coventry, CV35 9EF, UK
| | - Shannon F. Greer
- Gibbet Hill Campus, School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Wellesbourne Campus, School of Life Sciences, University of Warwick, Coventry, CV35 9EF, UK
| | - Vardis Ntoukakis
- Gibbet Hill Campus, School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Andrew Aspin
- Fera Science Ltd., York Biotech Campus, Sand Hutton, York, YO41 1LZ, UK
| | - Joana G. Vicente
- Wellesbourne Campus, School of Life Sciences, University of Warwick, Coventry, CV35 9EF, UK
- Fera Science Ltd., York Biotech Campus, Sand Hutton, York, YO41 1LZ, UK
| | - Murray Grant
- Gibbet Hill Campus, School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
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Gilroy R, Adam ME, Kumar B, Pallen MJ. An initial genomic blueprint of the healthy human oesophageal microbiome. Access Microbiol 2023; 5:acmi000558.v3. [PMID: 37424544 PMCID: PMC10323806 DOI: 10.1099/acmi.0.000558.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/15/2023] [Indexed: 07/11/2023] Open
Abstract
Background The oesophageal microbiome is thought to contribute to the pathogenesis of oesophageal cancer. However, investigations using culture and molecular barcodes have provided only a low-resolution view of this important microbial community. We therefore explored the potential of culturomics and metagenomic binning to generate a catalogue of reference genomes from the healthy human oesophageal microbiome, alongside a comparison set from saliva. Results Twenty-two distinct colonial morphotypes from healthy oesophageal samples were genome-sequenced. These fell into twelve species clusters, eleven of which represented previously defined species. Two isolates belonged to a novel species, which we have named Rothia gullae. We performed metagenomic binning of reads generated from UK samples from this study alongside reads generated from Australian samples in a recent study. Metagenomic binning generated 136 medium or high-quality metagenome-assembled genomes (MAGs). MAGs were assigned to 56 species clusters, eight representing novel Candidatus species, which we have named Ca. Granulicatella gullae, Ca. Streptococcus gullae, Ca. Nanosynbacter quadramensis, Ca. Nanosynbacter gullae, Ca. Nanosynbacter colneyensis, Ca. Nanosynbacter norwichensis, Ca. Nanosynococcus oralis and Ca. Haemophilus gullae. Five of these novel species belong to the recently described phylum Patescibacteria . Although members of the Patescibacteria are known to inhabit the oral cavity, this is the first report of their presence in the oesophagus. Eighteen of the metagenomic species were, until recently, identified only by hard-to-remember alphanumeric placeholder designations. Here we illustrate the utility of a set of recently published arbitrary Latinate species names in providing user-friendly taxonomic labels for microbiome analyses.Our non-redundant species catalogue contained 63 species derived from cultured isolates or MAGs. Mapping revealed that these species account for around half of the sequences in the oesophageal and saliva metagenomes. Although no species was present in all oesophageal samples, 60 species occurred in at least one oesophageal metagenome from either study, with 50 identified in both cohorts. Conclusions Recovery of genomes and discovery of new species represents an important step forward in our understanding of the oesophageal microbiome. The genes and genomes that we have released into the public domain will provide a base line for future comparative, mechanistic and intervention studies.
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Affiliation(s)
- Rachel Gilroy
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Mina E. Adam
- Norfolk & Norwich University Hospitals NHS Foundation Trust, Norwich, UK
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
| | - Bhaskar Kumar
- Norfolk & Norwich University Hospitals NHS Foundation Trust, Norwich, UK
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
| | - Mark J. Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
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Okuno M, Arimizu Y, Miyahara S, Wakabayashi Y, Gotoh Y, Yoshino S, Harada T, Seto K, Yamamoto T, Nakamura K, Hayashi T, Ogura Y. Escherichia cryptic clade I is an emerging source of human intestinal pathogens. BMC Biol 2023; 21:81. [PMID: 37055811 PMCID: PMC10100065 DOI: 10.1186/s12915-023-01584-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/30/2023] [Indexed: 04/15/2023] Open
Abstract
BACKGROUND Within the genus Escherichia, several monophyletic clades other than the traditionally defined species have been identified. Of these, cryptic clade I (C-I) appears to represent a subspecies of E. coli, but due to the difficulty in distinguishing it from E. coli sensu stricto, the population structure and virulence potential of C-I are unclear. RESULTS We defined a set of true C-I strains (n = 465), including a Shiga toxin 2a (Stx2a)-producing isolate from a patient with bloody diarrhoea identified by the retrospective analyses using a C-I-specific detection system. Through genomic analysis of 804 isolates from the cryptic clades, including these C-I strains, we revealed their global population structures and the marked accumulation of virulence genes and antimicrobial resistance genes in C-I. In particular, half of the C-I strains contained hallmark virulence genes of Stx-producing E. coli (STEC) and/or enterotoxigenic E. coli (ETEC). We also found the host-specific distributions of virulence genes, which suggests bovines as the potential source of human infections caused by STEC- and STEC/ETEC hybrid-type C-I strains, as is known in STEC. CONCLUSIONS Our findings demonstrate the emergence of human intestinal pathogens in C-I lineage. To better understand the features of C-I strains and their infections, extensive surveillance and larger population studies of C-I strains are needed. The C-I-specific detection system developed in this study will be a powerful tool for screening and identifying C-I strains.
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Affiliation(s)
- Miki Okuno
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka, 830-0011, Japan
| | - Yoko Arimizu
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
- Department of Infectious Disease, National Hospital Organization Kyushu Medical Center, Fukuoka, 810-0065, Japan
| | - Seina Miyahara
- Department of Microbiology, Miyazaki Prefectural Institute for Public Health and Environment, Miyazaki, 889-2155, Japan
| | - Yuki Wakabayashi
- Division of Microbiology, Osaka Institute of Public Health, Osaka, 537-0025, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Shuji Yoshino
- Department of Microbiology, Miyazaki Prefectural Institute for Public Health and Environment, Miyazaki, 889-2155, Japan
| | - Tetsuya Harada
- Division of Microbiology, Osaka Institute of Public Health, Osaka, 537-0025, Japan
| | - Kazuko Seto
- Division of Planning, Osaka Institute of Public Health, Osaka, 537-0025, Japan
| | - Takeshi Yamamoto
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka, 830-0011, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka, 830-0011, Japan.
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Cisek AA, Dolka B, Bąk I, Cukrowska B. Microorganisms Involved in Hydrogen Sink in the Gastrointestinal Tract of Chickens. Int J Mol Sci 2023; 24:ijms24076674. [PMID: 37047647 PMCID: PMC10095559 DOI: 10.3390/ijms24076674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/17/2023] [Accepted: 03/31/2023] [Indexed: 04/14/2023] Open
Abstract
Hydrogen sink is a beneficial process, which has never been properly examined in chickens. Therefore, the aim of this study was to assess the quantity and quality of microbiota involved in hydrogen uptake with the use of real-time PCR and metagenome sequencing. Analyses were carried out in 50 free-range chickens, 50 commercial broilers, and 54 experimental chickens isolated from external factors. The median values of acetogens, methanogens, sulfate-reducing bacteria (SRB), and [NiFe]-hydrogenase utilizers measured in the cecum were approx. 7.6, 0, 0, and 3.2 log10/gram of wet weight, respectively. For the excreta samples, these values were 5.9, 4.8, 4, and 3 log10/gram of wet weight, respectively. Our results showed that the acetogens were dominant over the other tested groups of hydrogen consumers. The quantities of methanogens, SRB, and the [NiFe]-hydrogenase utilizers were dependent on the overall rearing conditions, being the result of diet, environment, agrotechnical measures, and other factors combined. By sequencing of the 16S rRNA gene, archaea of the genus Methanomassiliicoccus (Candidatus Methanomassiliicoccus) were discovered in chickens for the first time. This study provides some indication that in chickens, acetogenesis may be the main metabolic pathway responsible for hydrogen sink.
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Affiliation(s)
- Agata Anna Cisek
- Department of Pathology, The Children's Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland
| | - Beata Dolka
- Department of Pathology and Veterinary Diagnostics, Institute of Veterinary Medicine, Warsaw University of Life Sciences, St. Ciszewskiego 8, 02-786 Warsaw, Poland
| | - Iwona Bąk
- Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences, St. Ciszewskiego 8, 02-786 Warsaw, Poland
| | - Bożena Cukrowska
- Department of Pathology, The Children's Memorial Health Institute, Av. Dzieci Polskich 20, 04-730 Warsaw, Poland
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Hisatomi A, Ohkuma M, Sakamoto M. Sellimonas catena sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2023; 73. [PMID: 37185104 DOI: 10.1099/ijsem.0.005853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Obligately anaerobic, Gram-stain-positive, small-chain coccobacilli, strains 12EGH17T and 18CBH55, were isolated from faecal samples of healthy Japanese humans. Strain 12EGH17T showed the highest 16S rRNA gene sequence similarity to Sellimonas intestinalis BR72T (95.5 %), Coprococcus comes ATCC 27758T (94.4 %) and Clostridium nexile DSM 1787T (93.7 %). The percentage of conserved proteins values between the genome of strain 12EGH17T and that of the members of the genus Sellimonas were >54 %, suggesting that strain 12EGH17T belongs to the genus Sellimonas. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strains 12EGH17T and 18CBH55 were higher than the cut-off values of species demarcation (90 % dDDH and 99 % ANI), indicating these two strains are the same species. However, the dDDH and ANI values of these strains were lower than the cut-off values of species demarcation against other strains (<30 % dDDH and <79 % ANI). These results indicate that the isolates should be considered to represent a new species of the genus Sellimonas. The isolates were differentiated from the type species, S. intestinalis, by the ability of aesculin hydrolysis. Based on the collected data, strains 12EGH17T and 18CBH55 represent a novel species in the genus Sellimonas, for which the name Sellimonas catena sp. nov. is proposed. The type strain of S. catena is 12EGH17T (=JCM 35622T=DSM 114916T).
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Affiliation(s)
- Atsushi Hisatomi
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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31
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Volmer JG, Soo RM, Evans PN, Hoedt EC, Astorga Alsina AL, Woodcroft BJ, Tyson GW, Hugenholtz P, Morrison M. Isolation and characterisation of novel Methanocorpusculum species indicates the genus is ancestrally host-associated. BMC Biol 2023; 21:59. [PMID: 36949471 PMCID: PMC10035134 DOI: 10.1186/s12915-023-01524-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/20/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND With an increasing interest in the manipulation of methane produced from livestock cultivation, the microbiome of Australian marsupials provides a unique ecological and evolutionary comparison with 'low-methane' emitters. Previously, marsupial species were shown to be enriched for novel lineages of Methanocorpusculum, as well as Methanobrevibacter, Methanosphaera, and Methanomassiliicoccales. Despite sporadic reports of Methanocorpusculum from stool samples of various animal species, there remains little information on the impacts of these methanogens on their hosts. RESULTS Here, we characterise novel host-associated species of Methanocorpusculum, to explore unique host-specific genetic factors and their associated metabolic potential. We performed comparative analyses on 176 Methanocorpusculum genomes comprising 130 metagenome-assembled genomes (MAGs) recovered from 20 public animal metagenome datasets and 35 other publicly available Methanocorpusculum MAGs and isolate genomes of host-associated and environmental origin. Nine MAGs were also produced from faecal metagenomes of the common wombat (Vombatus ursinus) and mahogany glider (Petaurus gracilis), along with the cultivation of one axenic isolate from each respective animal; M. vombati (sp. nov.) and M. petauri (sp. nov.). CONCLUSIONS Through our analyses, we substantially expand the available genetic information for this genus by describing the phenotypic and genetic characteristics of 23 host-associated species of Methanocorpusculum. These lineages display differential enrichment of genes associated with methanogenesis, amino acid biosynthesis, transport system proteins, phosphonate metabolism, and carbohydrate-active enzymes. These results provide insights into the differential genetic and functional adaptations of these novel host-associated species of Methanocorpusculum and suggest that this genus is ancestrally host-associated.
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Affiliation(s)
- James G Volmer
- Faculty of Medicine, University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, 4102, Australia
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, 4102, Australia
| | - Rochelle M Soo
- School of Chemistry and Molecular Biosciences and Australian Centre for Ecogenomics, University of Queensland, Saint Lucia, 4072, Australia
| | - Paul N Evans
- School of Chemistry and Molecular Biosciences and Australian Centre for Ecogenomics, University of Queensland, Saint Lucia, 4072, Australia
| | - Emily C Hoedt
- Faculty of Medicine, University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, 4102, Australia
- Current Address: NHMRC Centre of Research Excellence (CRE) in Digestive Health, Hunter Medical Research Institute (HMRI), Newcastle, NSW, Australia
| | - Ana L Astorga Alsina
- Faculty of Medicine, University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, 4102, Australia
| | - Benjamin J Woodcroft
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, 4102, Australia
| | - Gene W Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, 4102, Australia
| | - Philip Hugenholtz
- School of Chemistry and Molecular Biosciences and Australian Centre for Ecogenomics, University of Queensland, Saint Lucia, 4072, Australia
| | - Mark Morrison
- Faculty of Medicine, University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, 4102, Australia.
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32
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Oren A. Naming new taxa of prokaryotes in the 21st century. Can J Microbiol 2023; 69:151-157. [PMID: 36852830 DOI: 10.1139/cjm-2022-0266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
The nomenclature of prokaryotes is regulated by the rules of the International Code of Nomenclature of Prokaryotes (ICNP) and is based on the Linnaean binomial system. The current rules of the Code only cover the nomenclature of the cultivated minority. Proposals to incorporate the uncultivated majority of bacteria and archaea under the rules of the Code were recently rejected by the International Committee on Systematics of Prokaryotes. The provisional rank of Candidatus can be used to name uncultivated prokaryotes whose names cannot be validly published under the rules of the ICNP, but their names can now be validated under the Code of Nomenclature of Prokaryotes Described from Sequence Data (the SeqCode), which was recently established to cover the nomenclature of the uncultivated majority. Metagenomics, single-cell genomics, and high-throughput cultivation techniques have led to a flood of new organisms currently waiting to be named. Automated programs such as GAN and Protologger can assist researchers in naming and describing newly discovered prokaryotes, cultivated as well as uncultivated. However, Latin and Greek skills remain indispensable for proper quality control of names that must meet the standards set by the codes of nomenclature.
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Affiliation(s)
- Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
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33
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Albright S, Louca S. Trait biases in microbial reference genomes. Sci Data 2023; 10:84. [PMID: 36759614 PMCID: PMC9911409 DOI: 10.1038/s41597-023-01994-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 01/31/2023] [Indexed: 02/11/2023] Open
Abstract
Common culturing techniques and priorities bias our discovery towards specific traits that may not be representative of microbial diversity in nature. So far, these biases have not been systematically examined. To address this gap, here we use 116,884 publicly available metagenome-assembled genomes (MAGs, completeness ≥80%) from 203 surveys worldwide as a culture-independent sample of bacterial and archaeal diversity, and compare these MAGs to the popular RefSeq genome database, which heavily relies on cultures. We compare the distribution of 12,454 KEGG gene orthologs (used as trait proxies) in the MAGs and RefSeq genomes, while controlling for environment type (ocean, soil, lake, bioreactor, human, and other animals). Using statistical modeling, we then determine the conditional probabilities that a species is represented in RefSeq depending on its genetic repertoire. We find that the majority of examined genes are significantly biased for or against in RefSeq. Our systematic estimates of gene prevalences across bacteria and archaea in nature and gene-specific biases in reference genomes constitutes a resource for addressing these issues in the future.
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Affiliation(s)
- Sage Albright
- Department of Biology, University of Oregon, Eugene, USA
| | - Stilianos Louca
- Department of Biology, University of Oregon, Eugene, USA. .,Institute of Ecology and Evolution, University of Oregon, Eugene, USA.
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34
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Phylogenomic Analysis Supports the Transfer of 20 Pathovars from Xanthomonas campestris into Xanthomonas euvesicatoria. TAXONOMY 2023. [DOI: 10.3390/taxonomy3010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The Gram-negative bacterial genus Xanthomonas includes numerous infra-specific taxa known as pathovars, which are defined primarily on host range and disease symptoms. With the advent of molecular sequence data, many pathovars have been transferred from X. campestris into other Xanthomonas species to better harmonise taxonomy and phylogeny. We performed whole-genome shotgun sequencing on pathotype strains of the following X. campestris pathovars: blepharidis, carissae, clerodendri, convolvuli, coriandri, daturae, euphorbiae, fici, heliotropii, ionidii, lawsoniae, mirabilis, obscurae, paulliniae, pennamericanum, spermacoces, uppalii, vernoniae, viegasii and zingibericola. These genomes showed more than 98% average nucleotide identity with the type-strain of X. euvesicatoria and less than 88% with the type-strain of X. campestris. We propose the transfer of these pathovars into X. euvesicatoria and present an emended species description for X. euvesicatoria.
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Zhang XX, Lv QB, Yan QL, Zhang Y, Guo RC, Meng JX, Ma H, Qin SY, Zhu QH, Li CQ, Liu R, Liu G, Li SH, Sun DB, Ni HB. A Catalog of over 5,000 Metagenome-Assembled Microbial Genomes from the Caprinae Gut Microbiota. Microbiol Spectr 2022; 10:e0221122. [PMID: 36321901 PMCID: PMC9769736 DOI: 10.1128/spectrum.02211-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/10/2022] [Indexed: 12/24/2022] Open
Abstract
Most microbiome studies regarding the ruminant digestive tract have focused on the rumen microbiota, whereas only a few studies were performed on investigating the gut microbiota of ruminants, which limits our understanding of this important component. Herein, the gut microbiota of 30 Caprinae animals (sheep and goats) from six provinces in China was characterized using ultradeep (>100 Gbp per sample) metagenome shotgun sequencing. An inventory of Caprinae gut microbial species containing 5,046 metagenomic assembly genomes (MAGs) was constructed. Particularly, 2,530 of the genomes belonged to uncultured candidate species. These genomes largely expanded the genomic repository of the current microbes in the Caprinae gut. Several enzymes and biosynthetic gene clusters encoded by these Caprinae gut species were identified. In summary, our study extends the gut microbiota characteristics of Caprinae and provides a basis for future studies on animal production and animal health. IMPORTANCE We constructed a microbiota catalog containing 5,046 MAGs from Caprinae gut from six regions of China. Most of the MAGs do not overlap known databases and appear to be potentially new species. We also characterized the functional spectrum of these MAGs and analyzed the differences between different regions. Our study enriches the understanding of taxonomic, functional, and metabolic diversity of Caprinae gut microbiota. We are confident that the manuscript will be of utmost interest to a wide range of readers and be widely applied in future research.
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Affiliation(s)
- Xiao-Xuan Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, China
- Heilongjiang Provincial Key Laboratory of the Prevention and Control of Bovine Diseases, College of Animal Science, Heilongjiang Bayi Agriculture University, Daqing, Heilongjiang Province, China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Qing-Bo Lv
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, China
- Heilongjiang Provincial Key Laboratory of the Prevention and Control of Bovine Diseases, College of Animal Science, Heilongjiang Bayi Agriculture University, Daqing, Heilongjiang Province, China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Qiu-Long Yan
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, Liaoning Province, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan, Hubei Province, China
| | - Ruo-Chun Guo
- Puensum Genetech Institute, Wuhan, Hubei Province, China
| | - Jin-Xin Meng
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - He Ma
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Si-Yuan Qin
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, Jilin Province, China
- Center for Biological Disaster Prevention and Control, National Forestry and Grassland Administration, Shenyang, Liaoning Province, China
| | - Qing-He Zhu
- Heilongjiang Provincial Key Laboratory of the Prevention and Control of Bovine Diseases, College of Animal Science, Heilongjiang Bayi Agriculture University, Daqing, Heilongjiang Province, China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Chun-Qiu Li
- Heilongjiang Provincial Key Laboratory of the Prevention and Control of Bovine Diseases, College of Animal Science, Heilongjiang Bayi Agriculture University, Daqing, Heilongjiang Province, China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Rui Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Gang Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Sheng-Hui Li
- Puensum Genetech Institute, Wuhan, Hubei Province, China
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Dong-Bo Sun
- Heilongjiang Provincial Key Laboratory of the Prevention and Control of Bovine Diseases, College of Animal Science, Heilongjiang Bayi Agriculture University, Daqing, Heilongjiang Province, China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Hong-Bo Ni
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, China
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People's Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
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Reclassification of eight Akkermansia muciniphila strains and description of Akkermansia massiliensis sp. nov. and Candidatus Akkermansia timonensis, isolated from human feces. Sci Rep 2022; 12:21747. [PMID: 36526682 PMCID: PMC9758162 DOI: 10.1038/s41598-022-25873-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
Akkermansia muciniphila is a human intestinal tract bacterium that plays an important role in the mucus layer renewal. Several studies have demonstrated that it is a modulator for gut homeostasis and a probiotic for human health. The Akkermansia genus contains two species with standing in nomenclature but their genomic diversity remains unclear. In this study, eight new Akkermansia sp. strains were isolated from the human gut. Using the digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI) and core genome-based phylogenetic analysis applied to 104 A. muciniphila whole genomes sequences, strains were reclassified into three clusters. Cluster I groups A. muciniphila strains (including strain ATCC BAA-835T as type strain), whereas clusters II and III represent two new species. A member of cluster II, strain Marseille-P6666 differed from A. muciniphila strain ATCC BAA-835T and from A. glycaniphila strain PytT in its ability to grow in microaerophilic atmosphere up to 42 °C, to assimilate various carbon sources and to produce acids from a several compounds. The major fatty acids of strain Marseille-P6666 were 12-methyl-tetradecanoic and pentadecanoic acids. The DNA G + C content of strain Marseille-P6666 was 57.8%. On the basis of these properties, we propose the name A. massiliensis sp. nov. for members of cluster II, with strain Marseille-P6666T (= CSUR P6666 = CECT 30548) as type strain. We also propose the name "Candidatus Akkermansia timonensis" sp. nov. for the members of cluster III, which contains only uncultivated strains, strain Akk0196 being the type strain.
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Gut Microbiome Studies in Livestock: Achievements, Challenges, and Perspectives. Animals (Basel) 2022; 12:ani12233375. [PMID: 36496896 PMCID: PMC9736591 DOI: 10.3390/ani12233375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/16/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
The variety and makeup of the gut microbiome are frequently regarded as the primary determinants of health and production performances in domestic animals. High-throughput DNA/RNA sequencing techniques (NGS) have recently gained popularity and permitted previously unheard-of advancements in the study of gut microbiota, particularly for determining the taxonomic composition of such complex communities. Here, we summarize the existing body of knowledge on livestock gut microbiome, discuss the state-of-the-art in sequencing techniques, and offer predictions for next research. We found that the enormous volumes of available data are biased toward a small number of globally distributed and carefully chosen varieties, while local breeds (or populations) are frequently overlooked despite their demonstrated resistance to harsh environmental circumstances. Furthermore, the bulk of this research has mostly focused on bacteria, whereas other microbial components such as protists, fungi, and viruses have received far less attention. The majority of these data were gathered utilizing traditional metabarcoding techniques that taxonomically identify the gut microbiota by analyzing small portions of their genome (less than 1000 base pairs). However, to extend the coverage of microbial genomes for a more precise and thorough characterization of microbial communities, a variety of increasingly practical and economical shotgun techniques are currently available.
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Zhang Y, Jiang F, Yang B, Wang S, Wang H, Wang A, Xu D, Fan W. Improved microbial genomes and gene catalog of the chicken gut from metagenomic sequencing of high-fidelity long reads. Gigascience 2022; 11:6833030. [PMID: 36399059 PMCID: PMC9673493 DOI: 10.1093/gigascience/giac116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 09/27/2022] [Accepted: 10/30/2022] [Indexed: 11/19/2022] Open
Abstract
Background Due to the importance of chicken production and the remarkable influence of the gut microbiota on host health and growth, tens of thousands of metagenome-assembled genomes (MAGs) have been constructed for the chicken gut microbiome. However, due to the limitations of short-read sequencing and assembly technologies, most of these MAGs are far from complete, are of lower quality, and include contaminant reads. Results We generated 332 Gb of high-fidelity (HiFi) long reads from the 5 chicken intestinal compartments and assembled 461 and 337 microbial genomes, of which 53% and 55% are circular, at the species and strain levels, respectively. For the assembled microbial genomes, approximately 95% were regarded as complete according to the “RNA complete” criteria, which requires at least 1 full-length ribosomal RNA (rRNA) operon encoding all 3 types of rRNA (16S, 23S, and 5S) and at least 18 copies of full-length transfer RNA genes. In comparison with the short-read-derived chicken MAGs, 384 (83% of 461) and 89 (26% of 337) strain-level and species-level genomes in this study are novel, with no matches to previously reported sequences. At the gene level, one-third of the 2.5 million genes in the HiFi-derived gene catalog are novel and cannot be matched to the short-read-derived gene catalog. Moreover, the HiFi-derived genomes have much higher continuity and completeness, as well as lower contamination; the HiFi-derived gene catalog has a much higher ratio of complete gene structures. The dominant phylum in our HiFi-assembled genomes was Firmicutes (82.5%), and the foregut was highly enriched in 5 genera: Ligilactobacillus, Limosilactobacillus, Lactobacillus, Weissella, and Enterococcus, all of which belong to the order Lactobacillales. Using GTDB-Tk, all 337 species-level genomes were successfully classified at the order level; however, 2, 35, and 189 genomes could not be classified into any known family, genus, and species, respectively. Among these incompletely classified genomes, 9 and 49 may belong to novel genera and species, respectively, because their 16S rRNA genes have identities lower than 95% and 97% to any known 16S rRNA genes. Conclusions HiFi sequencing not only produced metagenome assemblies and gene structures with markedly improved quality but also recovered a substantial portion of novel genomes and genes that were missed in previous short-read-based metagenome studies. The novel genomes and species obtained in this study will facilitate gut microbiome and host–microbiota interaction studies, thereby contributing to the sustainable development of poultry resources.
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Affiliation(s)
- Yan Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, Guangdong, 518120, China
| | - Fan Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, Guangdong, 518120, China
| | - Boyuan Yang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, Guangdong, 518120, China
| | - Sen Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, Guangdong, 518120, China
| | - Hengchao Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, Guangdong, 518120, China
| | - Anqi Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, Guangdong, 518120, China
| | - Dong Xu
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, Guangdong, 518120, China
| | - Wei Fan
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, Guangdong, 518120, China
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Yang F, Shen S, Gao W, Ma Y, Han B, Ding Y, Wang X, Zhang K. Deciphering discriminative antibiotic resistance genes and pathogens in agricultural soil following chemical and organic fertilizer. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 322:116110. [PMID: 36049303 DOI: 10.1016/j.jenvman.2022.116110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/17/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
Fertilizers containing rich nutrients can change the profiles of antibiotic resistant pathogens (ARPs) and antibiotic resistance genes (ARGs) in receiving soils; however, the discriminative ARGs and ARPs in agricultural soil following different fertilizer applications remain unknown. Using metagenomic sequencing combined with binning approach, the present study investigated the discriminative ARGs and ARPs under various fertilizer applications (chemical and organic fertilizer) in a 8-year field experiment. VanR, multidrug ARG transporter, vanS, ermA, and arnA were the discriminative ARGs in the chemical fertilizer group, whereas rosB, multidrug transporter, mexW, and aac(3)-I were enhanced in the organic fertilizer group. The metagenomic binning approach revealed that both fertilizer applications caused pathogen proliferation. Chemical fertilizer caused the increase in the pathogenic genus Luteimonas, and organic fertilizer facilitated the proliferation of the pathogenic genera Dokdonella and Pseudomonas. The pathogenic species Pseudomonas_H sp014836765, carrying mexW and multidrug transporter, was enriched only in the organic fertilizer group, indicating that it was a discriminative ARP in the organic fertilizer group. Our results demonstrated that fertilizer application, particularly organic fertilizer application, can facilitate the proliferation of ARGs and ARPs in the receiving soil, posing the risk of the development and spread of soil-borne ARPs.
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Affiliation(s)
- Fengxia Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China; Dali, Yunnan, Agro-Ecosystem, National Observation and Research Station, 671004, China
| | - Shizhou Shen
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China; Dali, Yunnan, Agro-Ecosystem, National Observation and Research Station, 671004, China
| | - Wenxuan Gao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China; Dali, Yunnan, Agro-Ecosystem, National Observation and Research Station, 671004, China
| | - Yingjun Ma
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Bingjun Han
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Yongzhen Ding
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Xiaolong Wang
- School of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China.
| | - Keqiang Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China; Dali, Yunnan, Agro-Ecosystem, National Observation and Research Station, 671004, China.
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Oren A. Candidatus List No. 4: Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748458 DOI: 10.1099/ijsem.0.005545] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
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Mach N, Midoux C, Leclercq S, Pennarun S, Le Moyec L, Rué O, Robert C, Sallé G, Barrey E. Mining the equine gut metagenome: poorly-characterized taxa associated with cardiovascular fitness in endurance athletes. Commun Biol 2022; 5:1032. [PMID: 36192523 PMCID: PMC9529974 DOI: 10.1038/s42003-022-03977-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 09/12/2022] [Indexed: 12/01/2022] Open
Abstract
Emerging evidence indicates that the gut microbiome contributes to endurance exercise performance. Still, the extent of its functional and metabolic potential remains unknown. Using elite endurance horses as a model system for exercise responsiveness, we built an integrated horse gut gene catalog comprising ~25 million unique genes and 372 metagenome-assembled genomes. This catalog represents 4179 genera spanning 95 phyla and functional capacities primed to exploit energy from dietary, microbial, and host resources. The holo-omics approach shows that gut microbiomes enriched in Lachnospiraceae taxa are negatively associated with cardiovascular capacity. Conversely, more complex and functionally diverse microbiomes are associated with higher glucose concentrations and reduced accumulation of long-chain acylcarnitines and non-esterified fatty acids in plasma, suggesting increased ß-oxidation capacity in the mitochondria. In line with this hypothesis, more fit athletes show upregulation of mitochondrial-related genes involved in energy metabolism, biogenesis, and Ca2+ cytosolic transport, all of which are necessary to improve aerobic work power, spare glycogen usage, and enhance cardiovascular capacity. The results identify an associative link between endurance performance and gut microbiome composition and gene function, laying the basis for nutritional interventions that could benefit horse athletes. An integrated gene catalog of the gut microbiome in elite endurance horses is build. The holo-omics analyses identify an associative link between endurance performance and gut microbiome composition and gene function.
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Affiliation(s)
- Núria Mach
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France. .,Université de Toulouse, INRAE, ENVT, IHAP, Toulouse, France.
| | - Cédric Midoux
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France.,Université Paris-Saclay, INRAE, BioinfOmics, MIGALE bioinformatics facility, Jouy-en-Josas, France.,Université Paris-Saclay, INRAE, PROSE, Antony, France
| | | | | | - Laurence Le Moyec
- Université d'Évry Val d'Essonne, Université Paris-Saclay, Évry, France.,Muséum National d'Histoire Naturelle, CNRS, MCAM, Paris, France
| | - Olivier Rué
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France.,Université Paris-Saclay, INRAE, BioinfOmics, MIGALE bioinformatics facility, Jouy-en-Josas, France
| | - Céline Robert
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.,École Nationale Vétérinaire d'Alfort, Maisons-Alfort, France
| | - Guillaume Sallé
- Université François Rabelais de Tours, INRAE, ISP, Nouzilly, France
| | - Eric Barrey
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
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Roth C, Sims T, Rodehutscord M, Seifert J, Camarinha-Silva A. The active core microbiota of two high-yielding laying hen breeds fed with different levels of calcium and phosphorus. Front Physiol 2022; 13:951350. [PMID: 36213242 PMCID: PMC9539745 DOI: 10.3389/fphys.2022.951350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/07/2022] [Indexed: 11/13/2022] Open
Abstract
The nutrient availability and supplementation of dietary phosphorus (P) and calcium (Ca) in avian feed, especially in laying hens, plays a vital role in phytase degradation and mineral utilization during the laying phase. The required concentration of P and Ca peaks during the laying phase, and the direct interaction between Ca and P concentration shrinks the availability of both supplements in the feed. Our goal was to characterize the active microbiota of the entire gastrointestinal tract (GIT) (crop, gizzard, duodenum, ileum, caeca), including digesta- and mucosa-associated communities of two contrasting high-yielding breeds of laying hens (Lohmann Brown Classic, LB; Lohmann LSL-Classic, LSL) under different P and Ca supplementation levels. Statistical significances were observed for breed, GIT section, Ca, and the interaction of GIT section x breed, P x Ca, Ca x breed and P x Ca x breed (p < 0.05). A core microbiota of five species was detected in more than 97% of all samples. They were represented by an uncl. Lactobacillus (average relative abundance (av. abu.) 12.1%), Lactobacillus helveticus (av. abu. 10.8%), Megamonas funiformis (av. abu. 6.8%), Ligilactobacillus salivarius (av. abu. 4.5%), and an uncl. Fusicatenibacter (av. abu. 1.1%). Our findings indicated that Ca and P supplementation levels 20% below the recommendation have a minor effect on the microbiota compared to the strong impact of the bird’s genetic background. Moreover, a core active microbiota across the GIT of two high-yielding laying hen breeds was revealed for the first time.
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Affiliation(s)
- Christoph Roth
- HoLMiR—Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Tanja Sims
- HoLMiR—Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Markus Rodehutscord
- HoLMiR—Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Jana Seifert
- HoLMiR—Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Amélia Camarinha-Silva
- HoLMiR—Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- *Correspondence: Amélia Camarinha-Silva,
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Hedlund BP, Chuvochina M, Hugenholtz P, Konstantinidis KT, Murray AE, Palmer M, Parks DH, Probst AJ, Reysenbach AL, Rodriguez-R LM, Rossello-Mora R, Sutcliffe IC, Venter SN, Whitman WB. SeqCode: a nomenclatural code for prokaryotes described from sequence data. Nat Microbiol 2022; 7:1702-1708. [PMID: 36123442 PMCID: PMC9519449 DOI: 10.1038/s41564-022-01214-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 07/25/2022] [Indexed: 01/03/2023]
Abstract
Most prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules and recommendations of the International Code of Nomenclature of Prokaryotes (ICNP). Here we summarize the development of the SeqCode, a code of nomenclature under which genome sequences serve as nomenclatural types. This code enables valid publication of names of prokaryotes based upon isolate genome, metagenome-assembled genome or single-amplified genome sequences. Otherwise, it is similar to the ICNP with regard to the formation of names and rules of priority. It operates through the SeqCode Registry ( https://seqco.de/ ), a registration portal through which names and nomenclatural types are registered, validated and linked to metadata. We describe the two paths currently available within SeqCode to register and validate names, including Candidatus names, and provide examples for both. Recommendations on minimal standards for DNA sequences are provided. Thus, the SeqCode provides a reproducible and objective framework for the nomenclature of all prokaryotes regardless of cultivability and facilitates communication across microbiological disciplines.
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Affiliation(s)
- Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, Queensland, Australia
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, Queensland, Australia
| | | | - Alison E Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Donovan H Parks
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, Queensland, Australia
| | - Alexander J Probst
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology and Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | | | - Luis M Rodriguez-R
- Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute of Advanced Studies (CSIC-UIB), Esporles, Spain
| | - Iain C Sutcliffe
- Faculty of Health & Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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Tous N, Marcos S, Goodarzi Boroojeni F, Pérez de Rozas A, Zentek J, Estonba A, Sandvang D, Gilbert MTP, Esteve-Garcia E, Finn R, Alberdi A, Tarradas J. Novel strategies to improve chicken performance and welfare by unveiling host-microbiota interactions through hologenomics. Front Physiol 2022; 13:884925. [PMID: 36148301 PMCID: PMC9485813 DOI: 10.3389/fphys.2022.884925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Fast optimisation of farming practices is essential to meet environmental sustainability challenges. Hologenomics, the joint study of the genomic features of animals and the microbial communities associated with them, opens new avenues to obtain in-depth knowledge on how host-microbiota interactions affect animal performance and welfare, and in doing so, improve the quality and sustainability of animal production. Here, we introduce the animal trials conducted with broiler chickens in the H2020 project HoloFood, and our strategy to implement hologenomic analyses in light of the initial results, which despite yielding negligible effects of tested feed additives, provide relevant information to understand how host genomic features, microbiota development dynamics and host-microbiota interactions shape animal welfare and performance. We report the most relevant results, propose hypotheses to explain the observed patterns, and outline how these questions will be addressed through the generation and analysis of animal-microbiota multi-omic data during the HoloFood project.
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Affiliation(s)
- Núria Tous
- Animal Nutrition, Institute of Agrifood Research and Technology (IRTA), Constantí, Spain
| | - Sofia Marcos
- Applied Genomics and Bioinformatics, University of the Basque Country (UPV/EHU, Bilbao, Spain
| | - Farshad Goodarzi Boroojeni
- Institute of Animal Nutrition, Department of Veterinary Medicine, Freie Universität Berlin (FUB), Berlin, Germany
| | - Ana Pérez de Rozas
- Animal Health-CReSA, Institute of Agrifood Research and Technology (IRTA), Bellaterra, Spain
| | - Jürgen Zentek
- Institute of Animal Nutrition, Department of Veterinary Medicine, Freie Universität Berlin (FUB), Berlin, Germany
| | - Andone Estonba
- Applied Genomics and Bioinformatics, University of the Basque Country (UPV/EHU, Bilbao, Spain
| | - Dorthe Sandvang
- Chr. Hansen A/S, Animal Health Innovation, Hoersholm, Denmark
| | - M. Thomas P. Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Enric Esteve-Garcia
- Animal Nutrition, Institute of Agrifood Research and Technology (IRTA), Constantí, Spain
| | - Robert Finn
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- *Correspondence: Antton Alberdi,
| | - Joan Tarradas
- Animal Nutrition, Institute of Agrifood Research and Technology (IRTA), Constantí, Spain
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Cui Y, Zhang L, Wang X, Yi Y, Shan Y, Liu B, Zhou Y, Lü X. Roles of intestinal Parabacteroides in human health and diseases. FEMS Microbiol Lett 2022; 369:6659190. [PMID: 35945336 DOI: 10.1093/femsle/fnac072] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 06/09/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
The stability of gut microbiota is essential for the host health. Parabacteroides spp., core members of the human gut microbiota, have average abundance of 1.27% in the human of 12 populations. Parabacteroides has been recently reported to have a close relationship with host health (E.g., metabolic syndrome, inflammatory bowel disease and obesity). Parabacteroides have the physiological characteristics of carbohydrate metabolism and secreting SCFAs. However, antimicrobial resistance of Parabacteroides to antibiotic (such as clindamycin, moxifloxacin and cefoxitin) should not be ignored. In this review, we primarily focused on Parabacteroides distasoniss, Parabacteroides goldsteinii, Parabacteroides johnsonii and Parabacteroides merdae and discussed their relationships with host disease, diet and the prevention or induction of diseases. P. distasonis and P. goldsteinii may be viewed as the potential next generation probiotics (NGP) candidate due to their protective effects on inflammation and obesity in mice. We also discussed the potential therapeutic application of Parabacteroides spp. in maintaining host-intestine homeostasis.
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Affiliation(s)
- Yanlong Cui
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Leshan Zhang
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Xin Wang
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Yanglei Yi
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Yuanyuan Shan
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Bianfang Liu
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Yuan Zhou
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Xin Lü
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
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Crippen TL, Singh B, Anderson RC, Sheffield CL. Management Practices Affecting Lesser Mealworm Larvae (Alphitobius diaperinus) Associated Microbial Community in a Broiler House and After Relocating With the Litter Into Pastureland. Front Microbiol 2022; 13:875930. [PMID: 35847098 PMCID: PMC9283091 DOI: 10.3389/fmicb.2022.875930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
Lesser mealworms are often found infesting production houses used to raise broiler chickens. Previous studies have investigated pathogenic microorganisms associated with the larvae, but a more thorough study relating total microbiome changes due to management procedures and flock rotations was needed. Additionally, there is a question of what microbiota are transferred into the environment when the litter, in which larvae reside, is piled in pastureland for use as fertilizer and where interactions with the soil and other fauna can occur. This study chronicled, by the 16S rRNA sequencing, the bacterial community profile of larvae in a broiler grow-out house synchronizing to when birds were added to and removed from the house over 2.5 years. The profile was found to be relatively constant despite 11 flock rotations and management disruptions, specifically litter cleanout procedures and the addition of new birds or bedding. In contrast, once removed from the controlled broiler house environment and placed into open pastureland, the substantial microbial diversity brought with the larvae showed greater fluctuation in structure with environmental conditions, one of which was rainfall. Surprisingly, these larvae survived at least 19 weeks, so the potential for moving larval-associated microbes into the environment needs further assessment to minimize the risk of relocating foodborne pathogens and also to assess those bacteria-generating metabolites that have benefits to plant growth when using the litter as a fertilizer. The characterization of their microbiome is the first step to investigating the influences of their microbes on the manmade and environmental ecosystems.
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Affiliation(s)
- Tawni L. Crippen
- Southern Plains Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, College Station, TX, United States
- *Correspondence: Tawni L. Crippen,
| | - Baneshwar Singh
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, United States
| | - Robin C. Anderson
- Southern Plains Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, College Station, TX, United States
| | - Cynthia L. Sheffield
- Southern Plains Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, College Station, TX, United States
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Xu L, Shang J, Tian J, Sun JQ, Shen B. Ruania suaedae sp. nov. and Ruania halotolerans sp. nov., two actinobacteria isolated from saline soil, and reclassification of Haloactinobacterium kanbiaonis as Occultella kanbiaonis comb. nov. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005443] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-positive, non-motile, strictly aerobic, yellow-coloured, rod-shaped bacterial strains, designated LR1S40T and M4N3S171T, were isolated from rhizosphere and bulk saline soil of Suaeda salsa collected in Inner Mongolia, China. Phylogenetic trees based on 16S rRNA gene and whole genome sequences showed that the two strains clustered tightly with strains of the genus
Ruania
. Strains LR1S40T and M4N3S171T had 95.5% 16S rRNA gene similarity to each other, and strain LR1S40T had 98.8, 98.7, 97.4 and <97.0% similarity to
Ruania alkalisoli
RN3S43T,
Ruania rhizosphaerae
LNNU 22110T,
Ruania alba
YIM 93306T and all other current type strains, while strain M4N3S171T had 98.6 and <97.0% similarity to
R. alba
YIM 93306T, and all other current type strains, respectively. The average nucleotide identity based on blast (ANIb) and digital DNA–DNA hybridization (dDDH) values of LR1S40T and M4N3S171T with each other and to the other type strains of
Ruania
were well below the threshold values (95% for ANIb, 70% for dDDH) for differentiating a species. Diphosphatidylglycerol and phosphatidylglycerol were the major polar lipids in both strains. The predominant menaquinone in both strains was both MK-8. The genome of strain LR1S40T consisted of a 3557440 bp circular chromosome, with a G+C content of 71.1 mol%, while the genome of strain M4N3S171T consisted of 4270413 bp, with a G+C content of 67.6 mol%. The phylogenetic, physiological and phenotypic characteristics allowed discrimination of the two strains from their relatives. The names Ruania suaedae sp. nov. [type strain LR1S40T (=CGMCC 1.19028T=KCTC 49726T)] and Ruania halotolerans sp. nov. [type strain M4N3S171T (=CGMCC 1. 19142T=KCTC 49727T)] are therefore proposed. During the publication of
Haloactinobacterium kanbiaonis
,
Haloactinobacterium glacieicola
(type strain T3246-1T), which was selected as the reference strain for the identification of
H. kanbiaonis
, was reclassified as
Occultella glacieicola
. The two phylogenetic trees showed that
H. kanbiaonis
HY164T tightly clustered with
Occultella aeris
F300T, and had the highest 16S rRNA gene similarity (99.8%) to
O. aeris
F300T. Based on the phylogenetic analysis and the publication record,
Haloactinobacterium kanbiaonis
should be reclassified as Occultella kanbiaonis comb. nov.
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Affiliation(s)
- Lian Xu
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Jia Shang
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Jing Tian
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Ji-Quan Sun
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Biao Shen
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
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48
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Dehau T, Ducatelle R, Immerseel FV, Goossens E. Omics technologies in poultry health and productivity - part 1: current use in poultry research. Avian Pathol 2022; 51:407-417. [PMID: 35675291 DOI: 10.1080/03079457.2022.2086447] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In biology, molecular terms with the suffix "-omics" refer to disciplines aiming at the collective characterization of pools of molecules derived from different layers (DNA, RNA, proteins, metabolites) of living organisms using high-throughput technologies. Such omics analyses have been widely implemented in poultry research in recent years. This first part of a bipartite review on omics technologies in poultry health and productivity examines the use of multiple omics and multi-omics techniques in poultry research. More specific present and future applications of omics technologies, not only for the identification of specific diagnostic biomarkers, but also for potential future integration in the daily monitoring of poultry production, are discussed in part 2. Approaches based on omics technologies are particularly used in poultry research in the hunt for genetic markers of economically important phenotypical traits in the host, and in the identification of key bacterial species or functions in the intestinal microbiome. Integrative multi-omics analyses, however, are still scarce. Host physiology is investigated via genomics together with transcriptomics, proteomics and metabolomics techniques, to understand more accurately complex production traits such as disease resistance and fertility. The gut microbiota, as a key player in chicken productivity and health, is also a main subject of such studies, investigating the association between its composition (16S rRNA gene sequencing) or function (metagenomics, metatranscriptomics, metaproteomics, metabolomics) and host phenotypes. Applications of these technologies in the study of other host-associated microbiota and other host characteristics are still in their infancy.
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Affiliation(s)
- Tessa Dehau
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Richard Ducatelle
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Filip Van Immerseel
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Evy Goossens
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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49
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Marcos S, Parejo M, Estonba A, Alberdi A. Recovering High-Quality Host Genomes from Gut Metagenomic Data through Genotype Imputation. ADVANCED GENETICS (HOBOKEN, N.J.) 2022; 3:2100065. [PMID: 36620197 PMCID: PMC9744478 DOI: 10.1002/ggn2.202100065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 03/05/2022] [Indexed: 01/11/2023]
Abstract
Metagenomic datasets of host-associated microbial communities often contain host DNA that is usually discarded because the amount of data is too low for accurate host genetic analyses. However, genotype imputation can be employed to reconstruct host genotypes if a reference panel is available. Here, the performance of a two-step strategy is tested to impute genotypes from four types of reference panels built using different strategies to low-depth host genome data (≈2× coverage) recovered from intestinal samples of two chicken genetic lines. First, imputation accuracy is evaluated in 12 samples for which both low- and high-depth sequencing data are available, obtaining high imputation accuracies for all tested panels (>0.90). Second, the impact of reference panel choice in population genetics statistics on 100 chickens is assessed, all four panels yielding comparable results. In light of the observations, the feasibility and application of the applied imputation strategy are discussed for different species with regard to the host DNA proportion, genomic diversity, and availability of a reference panel. This method enables leveraging insofar discarded host DNA to get insights into the genetic structure of host populations, and in doing so, facilitates the implementation of hologenomic approaches that jointly analyze host and microbial genomic data.
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Affiliation(s)
- Sofia Marcos
- Applied Genomics and BioinformaticsUniversity of the Basque Country (UPV/EHU)LeioaBilbao48940Spain
| | - Melanie Parejo
- Applied Genomics and BioinformaticsUniversity of the Basque Country (UPV/EHU)LeioaBilbao48940Spain
| | - Andone Estonba
- Applied Genomics and BioinformaticsUniversity of the Basque Country (UPV/EHU)LeioaBilbao48940Spain
| | - Antton Alberdi
- Center for Evolutionary HologenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen1353Denmark
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50
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Abstract
We hereby present the first descriptions of human-invasive infections caused by Escherichia marmotae, a recently described species that encompasses the former “Escherichia cryptic clade V.” We describe four cases, one acute sepsis of unknown origin, one postoperative sepsis after cholecystectomy, one spondylodiscitis, and one upper urinary tract infection. Cases were identified through unsystematic queries in a single clinical lab over 6 months. Through genome sequencing of the causative strains combined with available genomes from elsewhere, we demonstrate Es. marmotae to be a likely ubiquitous species containing genotypic virulence traits associated with Escherichia pathogenicity. The invasive isolates were scattered among isolates from a range of nonhuman sources in the phylogenetic analyses, thus indicating inherent virulence in multiple lineages. Pan genome analyses indicate that Es. marmotae has a large accessory genome and is likely to obtain ecologically advantageous traits, such as genes encoding antimicrobial resistance. Reliable identification might be possible by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS), but relevant spectra are missing in commercial databases. It can be identified through 16S rRNA gene sequencing. Escherichia marmotae could represent a relatively common human pathogen, and improved diagnostics will provide a better understanding of its clinical importance. IMPORTANCEEscherichia coli is the most common pathogen found in blood cultures and urine and among the most important pathogenic species in the realm of human health. The notion that some of these isolates are not Es. coli but rather another species within the same genus may have implications for what Es. coli constitutes. We only recently have obtained methods to separate the two species, which means that possible differences in important clinical aspects, such as antimicrobial resistance rates, virulence, and phylogenetic structure, may exist. We believe that Es. marmotae as a common pathogen is new merely because we have not looked or bothered to distinguish between the thousands of invasive Escherichia passing through microbiological laboratories each day.
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