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Meier SA, Furrer M, Nowak N, Zenobi R, Sundset MA, Huber R, Brown SA, Wagner G. Uncoupling of behavioral and metabolic 24-h rhythms in reindeer. Curr Biol 2024; 34:1596-1603.e4. [PMID: 38503287 DOI: 10.1016/j.cub.2024.02.072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 01/04/2024] [Accepted: 02/28/2024] [Indexed: 03/21/2024]
Abstract
Reindeer in the Arctic seasonally suppress daily circadian patterns of behavior present in most animals.1 In humans and mice, even when all daily behavioral and environmental influences are artificially suppressed, robust endogenous rhythms of metabolism governed by the circadian clock persist and are essential to health.2,3 Disrupted rhythms foster metabolic disorders and weight gain.4 To understand circadian metabolic organization in reindeer, we performed behavioral measurements and untargeted metabolomics from blood plasma samples taken from Eurasian tundra reindeer (Rangifer tarandus tarandus) across 24 h at 2-h intervals in four seasons. Our study confirmed the absence of circadian rhythms of behavior under constant darkness in the Arctic winter and constant daylight in the Arctic summer, as reported by others.1 We detected and measured the intensity of 893 metabolic features in all plasma samples using untargeted ultra-high-performance liquid chromatography-mass spectrometry (UPLC-MS). A core group of metabolites (66/893 metabolic features) consistently displayed 24-h rhythmicity. Most metabolites displayed a robust 24-h rhythm in winter and spring but were arrhythmic in summer and fall. Half of all measured metabolites displayed ultradian sleep-wake dependence in summer. Irrespective of the arrhythmic behavior, metabolism is rhythmic (24 h) in seasons of low food availability, potentially favoring energy efficiency. In seasons of food abundance, 24-h rhythmicity in metabolism is drastically reduced, again irrespective of behavioral rhythms, potentially fostering weight gain.
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Affiliation(s)
- Sara A Meier
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland
| | - Melanie Furrer
- Child Development Center and Children's Research Center, University Children's Hospital Zurich, University of Zurich, 8032 Zurich, Switzerland
| | - Nora Nowak
- Department of Chemistry and Applied Biosciences, Swiss National Technical University (ETH), 8093 Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, Swiss National Technical University (ETH), 8093 Zurich, Switzerland
| | - Monica A Sundset
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, 9019 Tromsø, Norway
| | - Reto Huber
- Child Development Center and Children's Research Center, University Children's Hospital Zurich, University of Zurich, 8032 Zurich, Switzerland; Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric Hospital Zurich, University of Zurich, 8032 Zurich, Switzerland.
| | - Steven A Brown
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland
| | - Gabriela Wagner
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, 9019 Tromsø, Norway; Division of Forest and Forest Resources, Norwegian Institute of Bioeconomy Research, 9016 Tromsø, Norway.
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Furrer M, Meier SA, Jan M, Franken P, Sundset MA, Brown SA, Wagner GC, Huber R. Reindeer in the Arctic reduce sleep need during rumination. Curr Biol 2024; 34:427-433.e5. [PMID: 38141616 DOI: 10.1016/j.cub.2023.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 11/24/2023] [Accepted: 12/06/2023] [Indexed: 12/25/2023]
Abstract
Timing and quantity of sleep depend on a circadian (∼24-h) rhythm and a specific sleep requirement.1 Sleep curtailment results in a homeostatic rebound of more and deeper sleep, the latter reflected in increased electroencephalographic (EEG) slow-wave activity (SWA) during non-rapid eye movement (NREM) sleep.2 Circadian rhythms are synchronized by the light-dark cycle but persist under constant conditions.3,4,5 Strikingly, arctic reindeer behavior is arrhythmic during the solstices.6 Moreover, the Arctic's extreme seasonal environmental changes cause large variations in overall activity and food intake.7 We hypothesized that the maintenance of optimal functioning under these extremely fluctuating conditions would require adaptations not only in daily activity patterns but also in the homeostatic regulation of sleep. We studied sleep using non-invasive EEG in four Eurasian tundra reindeer (Rangifer tarandus tarandus) in Tromsø, Norway (69°N) during the fall equinox and both solstices. As expected, sleep-wake rhythms paralleled daily activity distribution, and sleep deprivation resulted in a homeostatic rebound in all seasons. Yet, these sleep rebounds were smaller in summer and fall than in winter. Surprisingly, SWA decreased not only during NREM sleep but also during rumination. Quantitative modeling revealed that sleep pressure decayed at similar rates during the two behavioral states. Finally, reindeer spent less time in NREM sleep the more they ruminated. These results suggest that they can sleep during rumination. The ability to reduce sleep need during rumination-undisturbed phases for both sleep recovery and digestion-might allow for near-constant feeding in the arctic summer.
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Affiliation(s)
- Melanie Furrer
- Child Development Center and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Steinwiesstrasse 75, 8032 Zurich, Switzerland
| | - Sara A Meier
- Institute of Pharmacology and Toxicology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Maxime Jan
- Center for Integrative Genomics, University of Lausanne, Génopode building, 1015 Lausanne, Switzerland; Bioinformatics Competence Center, University of Lausanne, Génopode building, 1015 Lausanne, Switzerland
| | - Paul Franken
- Center for Integrative Genomics, University of Lausanne, Génopode building, 1015 Lausanne, Switzerland
| | - Monica A Sundset
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
| | - Steven A Brown
- Institute of Pharmacology and Toxicology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Gabriela C Wagner
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway; Division of Forest and Forest Resources, Norwegian Institute of Bioeconomy Research, Holtvegen 66, 9016 Tromsø, Norway.
| | - Reto Huber
- Child Development Center and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Steinwiesstrasse 75, 8032 Zurich, Switzerland; Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric Hospital Zurich, University of Zurich, Lenggstrasse 31, 8032 Zurich, Switzerland.
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Abstract
Smoking reindeer meat in a traditional Sámi lávvu (tent) is a knowledgeable and long tradition for food preservation among Sámi reindeer herders. However, due to the formation of polycyclic aromatic hydrocarbons (PAH) during smoking, scientists associate smoked meat with human health risks. PAH contamination of smoked food depends on the smoking method, the temperature and the wood species. The smoking temperature and the PAH contaminations of Sámi traditional lávvu-smoked reindeer products yet remain uninvestigated. To remedy this knowledge gap, we developed a unique co-produced lávvu-laboratory pilot study for temperature measurements and PAH analysis of smoked reindeer meat with different Arctic wood species (willow, birch and juniper) and plant parts (logs and twigs). Our study confirms reindeer herders understanding, that birch wood, and especially birch twigs, generate higher smoking temperatures than willow. Except reindeer meat smoked with birch twigs, PAH levels of analysed reindeer meat cuts were lower than EU recommended maximum levels. However, all smoked reindeer fat samples showed much elevated PAH contaminations. Our results demonstrate the importance of co-production including both scientific and traditional knowledge in research for increased understanding of Indigenous peoples' traditional food smoking and to insure healthy traditional smoked Arctic products.
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Affiliation(s)
- Kia Krarup Hansen
- Department of Social Sciences, UiT - the Arctic University of Norway, Tromsø, Norway.,UArctic EALÀT Institute at International Centre for Reindeer Husbandry, Kautokeino, Norway
| | - Issat Turi
- UArctic EALÀT Institute at International Centre for Reindeer Husbandry, Kautokeino, Norway
| | - Monica A Sundset
- Department of Arctic and Marine Biology, UiT - the Arctic University of Norway, Tromsø, Norway
| | - Svein D Mathiesen
- UArctic EALÀT Institute at International Centre for Reindeer Husbandry, Kautokeino, Norway.,Department of Languages, Duodji and Social Sciences, Sámi University of Applied Sciences, Kautokeino, Norway
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Salgado-Flores A, Tveit AT, Wright AD, Pope PB, Sundset MA. Characterization of the cecum microbiome from wild and captive rock ptarmigans indigenous to Arctic Norway. PLoS One 2019; 14:e0213503. [PMID: 30856229 PMCID: PMC6411164 DOI: 10.1371/journal.pone.0213503] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 02/24/2019] [Indexed: 01/17/2023] Open
Abstract
Rock ptarmigans (Lagopus muta) are gallinaceous birds inhabiting arctic and sub-arctic environments. Their diet varies by season, including plants or plant parts of high nutritional value, but also toxic plant secondary metabolites (PSMs). Little is known about the microbes driving organic matter decomposition in the cecum of ptarmigans, especially the last steps leading to methanogenesis. The cecum microbiome in wild rock ptarmigans from Arctic Norway was characterized to unveil their functional potential for PSM detoxification, methanogenesis and polysaccharides degradation. Cecal samples were collected from wild ptarmigans from Svalbard (L. m. hyperborea) and northern Norway (L. m. muta) during autumn/winter (Sept-Dec). Samples from captive Svalbard ptarmigans fed commercial pelleted feed were included to investigate the effect of diet on microbial composition and function. Abundances of methanogens and bacteria were determined by qRT-PCR, while microbial community composition and functional potential were studied using 16S rRNA gene sequencing and shotgun metagenomics. Abundances of bacteria and methanogenic Archaea were higher in wild ptarmigans compared to captive birds. The ceca of wild ptarmigans housed bacterial groups involved in PSM-degradation, and genes mediating the conversion of phenol compounds to pyruvate. Methanomassiliicoccaceae was the major archaeal family in wild ptarmigans, carrying the genes for methanogenesis from methanol. It might be related to increased methanol production from pectin degradation in wild birds due to a diet consisting of primarily fresh pectin-rich plants. Both wild and captive ptarmigans possessed a broad suite of genes for the depolymerization of hemicellulose and non-cellulosic polysaccharides (e.g. starch). In conclusion, there were no physiological and phenotypical dissimilarities in the microbiota found in the cecum of wild ptarmigans on mainland Norway and Svalbard. While substantial differences in the functional potential for PSM degradation and methanogenesis in wild and captive birds seem to be a direct consequence of their dissimilar diets.
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Affiliation(s)
- Alejandro Salgado-Flores
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Langnes, Tromsø, Norway
- * E-mail: (AS); (MS)
| | - Alexander T. Tveit
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Langnes, Tromsø, Norway
| | - Andre-Denis Wright
- College of Agricultural, Human, and Natural Resource Sciences, Washington State University, Pullman, Washington, United States of America
| | - Phil B. Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Monica A. Sundset
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Langnes, Tromsø, Norway
- * E-mail: (AS); (MS)
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Salgado-Flores A, Bockwoldt M, Hagen LH, Pope PB, Sundset MA. First insight into the faecal microbiota of the high Arctic muskoxen ( Ovibos moschatus). Microb Genom 2016; 2:e000066. [PMID: 28348861 PMCID: PMC5343138 DOI: 10.1099/mgen.0.000066] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/29/2016] [Indexed: 12/21/2022] Open
Abstract
The faecal microbiota of muskoxen (n=3) pasturing on Ryøya (69° 33′ N 18° 43′ E), Norway, in late September was characterized using high-throughput sequencing of partial 16S rRNA gene regions. A total of 16 209 high-quality sequence reads from bacterial domains and 19 462 from archaea were generated. Preliminary taxonomic classifications of 806 bacterial operational taxonomic units (OTUs) resulted in 53.7–59.3 % of the total sequences being without designations beyond the family level. Firmicutes (70.7–81.1 % of the total sequences) and Bacteroidetes (16.8–25.3 %) constituted the two major bacterial phyla, with uncharacterized members within the family Ruminococcaceae (28.9–40.9 %) as the major phylotype. Multiple-library comparisons between muskoxen and other ruminants indicated a higher similarity for muskoxen faeces and reindeer caecum (P>0.05) and some samples from cattle faeces. The archaeal sequences clustered into 37 OTUs, with dominating phylotypes affiliated to the methane-producing genus Methanobrevibacter (80–92 % of the total sequences). UniFrac analysis demonstrated heterogeneity between muskoxen archaeal libraries and those from reindeer and roe deer (P=1.0e-02, Bonferroni corrected), but not with foregut fermenters. The high proportion of cellulose-degrading Ruminococcus-affiliated bacteria agrees with the ingestion of a highly fibrous diet. Further experiments are required to elucidate the role played by these novel bacteria in the digestion of this fibrous Artic diet eaten by muskoxen.
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Affiliation(s)
| | - Mathias Bockwoldt
- 2Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Live H Hagen
- 3Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Phillip B Pope
- 3Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Monica A Sundset
- 2Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, Tromsø, Norway
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Salgado-Flores A, Hagen LH, Ishaq SL, Zamanzadeh M, Wright ADG, Pope PB, Sundset MA. Rumen and Cecum Microbiomes in Reindeer (Rangifer tarandus tarandus) Are Changed in Response to a Lichen Diet and May Affect Enteric Methane Emissions. PLoS One 2016; 11:e0155213. [PMID: 27159387 PMCID: PMC4861291 DOI: 10.1371/journal.pone.0155213] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 04/26/2016] [Indexed: 02/01/2023] Open
Abstract
Reindeer (Rangifer tarandus tarandus) are large Holarctic herbivores whose heterogeneous diet has led to the development of a unique gastrointestinal microbiota, essential for the digestion of arctic flora, which may include a large proportion of lichens during winter. Lichens are rich in plant secondary metabolites, which may affect members of the gut microbial consortium, such as the methane-producing methanogenic archaea. Little is known about the effect of lichen consumption on the rumen and cecum microbiotas and how this may affect methanogenesis in reindeer. Here, we examined the effects of dietary lichens on the reindeer gut microbiota, especially methanogens. Samples from the rumen and cecum were collected from two groups of reindeer, fed either lichens (Ld: n = 4), or a standard pelleted feed (Pd: n = 3). Microbial densities (methanogens, bacteria and protozoa) were quantified using quantitative real-time PCR and methanogen and bacterial diversities were determined by 454 pyrosequencing of the 16S rRNA genes. In general, the density of methanogens were not significantly affected (p>0.05) by the intake of lichens. Methanobrevibacter constituted the main archaeal genus (>95% of reads), with Mbr. thaueri CW as the dominant species in both groups of reindeer. Bacteria belonging to the uncharacterized Ruminococcaceae and the genus Prevotella were the dominant phylotypes in the rumen and cecum, in both diets (ranging between 16–38% total sequences). Bacteria belonging to the genus Ruminococcus (3.5% to 0.6%; p = 0.001) and uncharacterized phylotypes within the order Bacteroidales (8.4% to 1.3%; p = 0.027), were significantly decreased in the rumen of lichen-fed reindeer, but not in the cecum (p = 0.2 and p = 0.087, respectively). UniFrac-based analyses showed archaeal and bacterial libraries were significantly different between diets, in both the cecum and the rumen (vegan::Adonis: pseudo-F<0.05). Based upon previous literature, we suggest that the altered methanogen and bacterial profiles may account for expected lower methane emissions from lichen-fed reindeer.
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Affiliation(s)
- Alejandro Salgado-Flores
- Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, Tromsø, Norway
- * E-mail:
| | - Live H. Hagen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Suzanne L. Ishaq
- Department of Animal and Range Sciences, Montana State University, Bozeman, Montana, United States of America
| | | | - André-Denis G. Wright
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Phillip B. Pope
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Monica A. Sundset
- Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, Tromsø, Norway
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7
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Ishaq SL, Sundset MA, Crouse J, Wright ADG. High-throughput DNA sequencing of the moose rumen from different geographical locations reveals a core ruminal methanogenic archaeal diversity and a differential ciliate protozoal diversity. Microb Genom 2015; 1:e000034. [PMID: 28348818 PMCID: PMC5320624 DOI: 10.1099/mgen.0.000034] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 09/05/2015] [Accepted: 09/15/2015] [Indexed: 12/13/2022] Open
Abstract
Moose rumen samples from Vermont, Alaska and Norway were investigated for methanogenic archaeal and protozoal density using real-time PCR, and diversity using high-throughput sequencing of the 16S and 18S rRNA genes. Vermont moose showed the highest protozoal and methanogen densities. Alaskan samples had the highest percentages of Methanobrevibacter smithii, followed by the Norwegian samples. One Norwegian sample contained 43 % Methanobrevibacter thaueri, whilst all other samples contained < 10 %. Vermont samples had large percentages of Methanobrevibacter ruminantium, as did two Norwegian samples. Methanosphaera stadtmanae represented one-third of sequences in three samples. Samples were heterogeneous based on gender, geographical location and weight class using analysis of molecular variance (AMOVA). Two Alaskan moose contained >70 % Polyplastron multivesiculatum and one contained >75 % Entodinium spp. Protozoa from Norwegian moose belonged predominantly (>50 %) to the genus Entodinium, especially Entodinium caudatum. Norwegian moose contained a large proportion of sequences (25–97 %) which could not be classified beyond family. Protozoa from Vermont samples were predominantly Eudiplodinium rostratum (>75 %), with up to 7 % Diploplastron affine. Four of the eight Vermont samples also contained 5–12 % Entodinium spp. Samples were heterogeneous based on AMOVA, principal coordinate analysis and UniFrac. This study gives the first insight into the methanogenic archaeal diversity in the moose rumen. The high percentage of rumen archaeal species associated with high starch diets found in Alaskan moose corresponds well to previous data suggesting that they feed on plants high in starch. Similarly, the higher percentage of species related to forage diets in Vermont moose also relates well to their higher intake of fibre.
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Affiliation(s)
- Suzanne L Ishaq
- Department of Animal Science, University of Vermont, Burlington, Vermont, USA.,Department of Animal and Range Science, Montana State University, Bozeman, Montana, USA
| | - Monica A Sundset
- Department of Arctic and Marine Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway, USA
| | - John Crouse
- Alaska Department of Fish and Game, Soldotna, Alaska, USA
| | - André-Denis G Wright
- Department of Animal Science, University of Vermont, Burlington, Vermont, USA.,School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, USA
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Præsteng KE, Pope PB, Cann IKO, Mackie RI, Mathiesen SD, Folkow LP, Eijsink VGH, Sundset MA. Probiotic dosing of Ruminococcus flavefaciens affects rumen microbiome structure and function in reindeer. Microb Ecol 2013; 66:840-849. [PMID: 23959114 DOI: 10.1007/s00248-013-0279-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 08/06/2013] [Indexed: 06/02/2023]
Abstract
Highly cellulolytic bacterial species such as Ruminococcus flavefaciens are regarded essential for the microbial breakdown of cellulose in the rumen. We have investigated the effect of ruminal dosing of R. flavefaciens strain 8/94-32 during realimentation of starved reindeer (males, n = 3). Microbiome function measured as in situ digestion of cellulose and food pellets (percent DMD; dry matter disappearance) decreased after probiotic dosing. Microbial community analyses (>100,000 16S rDNA gene sequences for 27 samples) demonstrated that ruminal dosing influenced the microbiome structure; reflected by increased phylogenetic distances from background samples (unweighted UniFrac analysis) and reduced species diversity and evenness. Despite the inability to detect strain 8/94-32 post-dosing, the relative abundance of its affiliate family Ruminococcaceae remained consistent throughout the trial, whilst a dominant peak in the genus Prevotella and decline in uncharacterized Bacteroidetes (uBacNR) were observed in treatment samples. No clear relationships were observed between the relative abundance of Ruminococcaceae, Prevotella and uBacNR with cellulose DMD; however, Prevotella (negative) and uBacNR (positive) exhibited relationships with pellet DMD. These unexpected effects of ruminal dosing of a cellulolytic bacterium on digestibility are relevant for other studies on rumen manipulation.
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Pope PB, Mackenzie AK, Gregor I, Smith W, Sundset MA, McHardy AC, Morrison M, Eijsink VGH. Metagenomics of the Svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci. PLoS One 2012; 7:e38571. [PMID: 22701672 PMCID: PMC3368933 DOI: 10.1371/journal.pone.0038571] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 05/07/2012] [Indexed: 02/01/2023] Open
Abstract
Lignocellulosic biomass remains a largely untapped source of renewable energy predominantly due to its recalcitrance and an incomplete understanding of how this is overcome in nature. We present here a compositional and comparative analysis of metagenomic data pertaining to a natural biomass-converting ecosystem adapted to austere arctic nutritional conditions, namely the rumen microbiome of Svalbard reindeer (Rangifer tarandus platyrhynchus). Community analysis showed that deeply-branched cellulolytic lineages affiliated to the Bacteroidetes and Firmicutes are dominant, whilst sequence binning methods facilitated the assemblage of metagenomic sequence for a dominant and novel Bacteroidales clade (SRM-1). Analysis of unassembled metagenomic sequence as well as metabolic reconstruction of SRM-1 revealed the presence of multiple polysaccharide utilization loci-like systems (PULs) as well as members of more than 20 glycoside hydrolase and other carbohydrate-active enzyme families targeting various polysaccharides including cellulose, xylan and pectin. Functional screening of cloned metagenome fragments revealed high cellulolytic activity and an abundance of PULs that are rich in endoglucanases (GH5) but devoid of other common enzymes thought to be involved in cellulose degradation. Combining these results with known and partly re-evaluated metagenomic data strongly indicates that much like the human distal gut, the digestive system of herbivores harbours high numbers of deeply branched and as-yet uncultured members of the Bacteroidetes that depend on PUL-like systems for plant biomass degradation.
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Affiliation(s)
- Phillip B Pope
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
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Præsteng KE, Mackie RI, Cann IKO, Mathiesen SD, Sundset MA. Development of a signature probe targeting the 16S-23S rRNA internal transcribed spacer of a ruminal Ruminococcus flavefaciens isolate from reindeer. Benef Microbes 2012; 2:47-55. [PMID: 21831789 DOI: 10.3920/bm2010.0044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The cellulolytic Ruminococcus flavefaciens has previously been introduced into the ruminant rumen to increase microbial degradation of plant cell wall carbohydrates. The functional effect of an introduced bacterium depends on its ability to establish in the digestive tract, and signature probes can be used as a tool to track and quantify introduced strains. The purpose of this current study was to develop an oligonucleotide signature probe targeting the 16S-23S rRNA internal transcribed spacer (ITS) of a putative probiotic cellulolytic isolate (R. flavefaciens strain 8/94-32) from the rumen of reindeer (Rangifer tarandus tarandus). The 16S-23S rRNA gene ITS of three Ruminococcus strains; R. flavefaciens strain 8/94-32, R. flavefaciens FD-1 and Ruminococcus albus Ra-8, was investigated. The ITS region has been reported to vary more between closely related bacteria compared to the widely used 16S rRNA gene, and a high degree of sequence polymorphism was indeed detected between the three Ruminococcus strains studied. Based on observed sequence differences, two oligonucloetide probes, ITSRumi1 and ITSRumi2, targeting the ITS region of the R. flavefaciens isolate 8/94-32 were developed. Probe specificity was evaluated in dot blot hybridisations with R. flavefaciens isolate 8/94-32 and four other Ruminococcus-strains tested. The probe ITSRumi1 gave positive signals for the R. flavefaciens isolate 8/94-32 only, while probe ITSRumi2 gave positive signals for R. flavefaciens isolate 8/94-32 as well as for R. albus Ra-8. The result of hybridisations with the probe ITSRumi1 indicates that the probe is specific for the R. flavefaciens strain 8/94-32 amongst the four Ruminococcus-strains tested, and is promising for further studies using it as a signature probe for tracking this strain when re-introduced to the reindeer rumen.
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Affiliation(s)
- K E Præsteng
- Department of Arctic and Marine Biology, University of Tromsø, Norway
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11
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Præsteng KE, Mackie RI, Cann IKO, Mathiesen SD, Sundset MA. Variations in the 16S-23S rRNA internal transcribed spacer of fibrolytic Butyrivibrio isolates from the reindeer rumen. Can J Microbiol 2011; 57:617-21. [PMID: 21774627 DOI: 10.1139/w11-038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Strains of Butyrivibrio are principal cellulytic bacteria in the rumen of the High Arctic Svalbard reindeer ( Rangifer tarandus platyrhynchus ). According to phylogenetic analysis based on 16S rRNA gene sequencing, Butyrivibrio can be divided into three subgroups within the Clostridia class of the phylum Firmicutes, but the current phenotypic and genotypic differentiation within the family Lachnospiraceae is insufficient. This current study describes the sequence diversity of the 16S-23S rRNA intergenic transcribed spacer (ITS) region of Butyrivibrio isolates from reindeer. A total of 17 different ITS sequences with sizes between 449 and 784 nt were obtained. Genes encoding tRNA(Ile) and tRNA(Ala) were identified in four of the sequences. Phylogenetic neighbor-joining trees were constructed based on the ITS sequence and compared with a phylogenetic neighbor-joining tree based on 16S rRNA gene sequences previously obtained for the same isolates. These comparisons indicated a better differentiation between strains in the ITS sequence than the 16S rRNA gene based tree. Through this study, a better means for identifying and tracking fibrolytic and potentially probiotic Butyrivibrio strains in reindeer and other ruminants has been provided.
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Affiliation(s)
- Kirsti E Præsteng
- Department of Arctic and Marine Biology, University of Tromsø, Norway
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Barboza PS, Bennett A, Lignot JH, Mackie RI, McWhorter TJ, Secor SM, Skovgaard N, Sundset MA, Wang T. Digestive challenges for vertebrate animals: microbial diversity, cardiorespiratory coupling, and dietary specialization. Physiol Biochem Zool 2010; 83:764-74. [PMID: 20578844 DOI: 10.1086/650472] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The digestive system is the interface between the supply of food for an animal and the demand for energy and nutrients to maintain the body, to grow, and to reproduce. Digestive systems are not morphologically static but rather dynamically respond to changes in the physical and chemical characteristics of the diet and the level of food intake. In this article, we discuss three themes that affect the ability of an animal to alter digestive function in relation to novel substrates and changing food supply: (1) the fermentative digestion in herbivores, (2) the integration of cardiopulmonary and digestive functions, and (3) the evolution of dietary specialization. Herbivores consume, digest, and detoxify complex diets by using a wide variety of enzymes expressed by bacteria, predominantly in the phyla Firmicutes and Bacteroidetes. Carnivores, such as snakes that feed intermittently, sometimes process very large meals that require compensatory adjustments in blood flow, acid secretion, and regulation of acid-base homeostasis. Snakes and birds that specialize in simple diets of prey or nectar retain their ability to digest a wider selection of prey. The digestive system continues to be of interest to comparative physiologists because of its plasticity, both phenotypic and evolutionary, and because of its widespread integration with other physiological systems, including thermoregulation, circulation, ventilation, homeostasis, immunity, and reproduction.
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Affiliation(s)
- P S Barboza
- Department of Biology and Wildlife, University of Alaska, Fairbanks, AK 99775, USA.
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Glad T, Kristiansen VF, Nielsen KM, Brusetti L, Wright ADG, Sundset MA. Ecological characterisation of the colonic microbiota in arctic and sub-arctic seals. Microb Ecol 2010; 60:320-330. [PMID: 20523986 DOI: 10.1007/s00248-010-9690-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Accepted: 05/16/2010] [Indexed: 05/29/2023]
Abstract
Dominant colonic bacteria in wild hooded (n = 9), harbour (n = 1) and grey (n = 1) seals were identified using 16S rRNA gene clone libraries (313 clones), revealing 52.7% Bacteroidetes, 41.5% Firmicutes, 4.5% Proteobacteria and 1.0% Fusobacteria. Thirty (77%) of the 39 phylotypes identified were novel, showing <97% sequence similarity to their nearest cultivated relatives. Mean colonic bacterial cell density, determined by real-time PCR, was high (12.8 log(10) cells/g wet wt) for the hooded seals, while the number of methanogenic Archea was low (4.0 log(10) cells/g wet wt). The level of ampicillin (amp(r)) and tetracycline-resistant (tet(r)) isolates was investigated by cultivation. Aerobic amp(r) isolates were only detected in colon contents from four hooded seals, whereas aerobic tet(r) isolates were found in seven of the nine hooded seals. These data provide novel insight to the gut microbiota of Arctic and sub-Arctic seals living in the wild.
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Affiliation(s)
- Trine Glad
- Department of Pharmacy, University of Tromsø, 9037 Tromsø, Norway.
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Glad T, Bernhardsen P, Nielsen KM, Brusetti L, Andersen M, Aars J, Sundset MA. Bacterial diversity in faeces from polar bear (Ursus maritimus) in Arctic Svalbard. BMC Microbiol 2010; 10:10. [PMID: 20074323 PMCID: PMC2822771 DOI: 10.1186/1471-2180-10-10] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 01/14/2010] [Indexed: 11/29/2022] Open
Abstract
Background Polar bears (Ursus maritimus) are major predators in the Arctic marine ecosystem, feeding mainly on seals, and living closely associated with sea ice. Little is known of their gut microbial ecology and the main purpose of this study was to investigate the microbial diversity in faeces of polar bears in Svalbard, Norway (74-81°N, 10-33°E). In addition the level of blaTEM alleles, encoding ampicillin resistance (ampr) were determined. In total, ten samples were collected from ten individual bears, rectum swabs from five individuals in 2004 and faeces samples from five individuals in 2006. Results A 16S rRNA gene clone library was constructed, and all sequences obtained from 161 clones showed affiliation with the phylum Firmicutes, with 160 sequences identified as Clostridiales and one sequence identified as unclassified Firmicutes. The majority of the sequences (70%) were affiliated with the genus Clostridium. Aerobic heterotrophic cell counts on chocolate agar ranged between 5.0 × 104 to 1.6 × 106 colony forming units (cfu)/ml for the rectum swabs and 4.0 × 103 to 1.0 × 105 cfu/g for the faeces samples. The proportion of ampr bacteria ranged from 0% to 44%. All of 144 randomly selected ampr isolates tested positive for enzymatic β-lactamase activity. Three % of the ampr isolates from the rectal samples yielded positive results when screened for the presence of blaTEM genes by PCR. BlaTEM alleles were also detected by PCR in two out of three total faecal DNA samples from polar bears. Conclusion The bacterial diversity in faeces from polar bears in their natural environment in Svalbard is low compared to other animal species, with all obtained clones affiliating to Firmicutes. Furthermore, only low levels of blaTEM alleles were detected in contrast to their increasing prevalence in some clinical and commensal bacterial populations.
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Affiliation(s)
- Trine Glad
- Department of Pharmacy, University of Tromsø, 9037 Tromsø, Norway.
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Sundset MA, Edwards JE, Cheng YF, Senosiain RS, Fraile MN, Northwood KS, Praesteng KE, Glad T, Mathiesen SD, Wright ADG. Rumen microbial diversity in Svalbard reindeer, with particular emphasis on methanogenic archaea. FEMS Microbiol Ecol 2009; 70:553-62. [DOI: 10.1111/j.1574-6941.2009.00750.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Sundset MA, Edwards JE, Cheng YF, Senosiain RS, Fraile MN, Northwood KS, Praesteng KE, Glad T, Mathiesen SD, Wright ADG. Molecular diversity of the rumen microbiome of Norwegian reindeer on natural summer pasture. Microb Ecol 2009; 57:335-348. [PMID: 18604648 DOI: 10.1007/s00248-008-9414-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2008] [Accepted: 05/21/2008] [Indexed: 05/26/2023]
Abstract
The molecular diversity of the rumen microbiome was investigated in five semi-domesticated adult female Norwegian reindeer (Rangifer tarandus tarandus) grazing on natural summer pastures on the coast of northern Norway (71.00 degrees N, 25.30 degrees E). Mean population densities (numbers per gram wet weight) of methanogenic archaea, rumen bacteria and ciliate protozoa, estimated using quantitative real-time polymerase chain reaction (PCR), were 3.17x10(9), 5.17x10(11) and 4.02x10(7), respectively. Molecular diversity of rumen methanogens was revealed using a 16S rRNA gene library (54 clones) constructed using pooled PCR products from the whole rumen contents of the five individual reindeer. Based upon a similarity criterion of <97%, a total of 19 distinct operational taxonomic units (OTUs) were identified, nine of which are potential new species. The 16S rRNA sequences generated from the reindeer rumen exhibited a high degree of sequence similarity to methanogens affiliated with the families Methanobacteriaceae (14 OTUs) and Methanosarcinaceae (one OTU). Four of the OTUs detected belonged to a group of uncultivated archaea previously found in domestic ruminants and thought to be dominant in the rumen together with Methanobrevibacter spp. Denaturing gradient gel electrophoresis profiling of the rumen bacterial 16S rRNA gene and the protozoal 18S rRNA gene indicated a high degree of animal variation, although some bands were common to all individuals. Automated ribosomal intergenic spacer analysis (ARISA) profiling of the ruminal Neocallimastigales population indicated that the reindeer are likely to contain more than one type of anaerobic fungus. The ARISA profile from one animal was distinct from the other four. This is the first molecular investigation of the ruminal methanogenic archaea in reindeer, revealing higher numbers than expected based on methane emission data available. Also, many of the reindeer archaeal 16S rRNA gene sequences were similar to those reported in domesticated ruminants in Australia, Canada, China, New Zealand and Venezuela, supporting previous findings that there seems to be no host type or geographical effect on the methanogenic archaea community structure in ruminants.
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Affiliation(s)
- Monica A Sundset
- Department of Arctic Biology and Institute of Medical Biology, University of Tromsø, 9037, Tromsø, Norway.
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Sundset MA, Kohn A, Mathiesen SD, Praesteng KE. Eubacterium rangiferina, a novel usnic acid-resistant bacterium from the reindeer rumen. Naturwissenschaften 2008; 95:741-9. [PMID: 18421431 DOI: 10.1007/s00114-008-0381-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2007] [Revised: 03/17/2008] [Accepted: 03/19/2008] [Indexed: 11/24/2022]
Abstract
Reindeer are able to eat and utilize lichens as an important source of energy and nutrients. In the current study, the activities of antibiotic secondary metabolites including usnic, antranoric, fumarprotocetraric, and lobaric acid commonly found in lichens were tested against a collection of 26 anaerobic rumen bacterial isolates from reindeer (Rangifer tarandus tarandus) using the agar diffusion method. The isolates were identified based on their 16S ribosomal ribonucleic acid (rRNA) gene sequences. Usnic acid had a potent antimicrobial effect against 25 of the isolates, belonging to Clostridiales, Enterococci, and Streptococci. Isolates of Clostridia and Streptococci were also susceptible to atranoric and lobaric acid. However, one isolate (R3_91_1) was found to be resistant to usnic, antranoric, fumarprotocetraric, and lobaric acid. R3_91_1 was also seen invading and adhering to lichen particles when grown in a liquid anaerobic culture as demonstrated by transmission electron microscopy. This was a Gram-negative, nonmotile rod (0.2-0.7 x 2.0-3.5 microm) with a deoxyribonucleic acid G + C content of 47.0 mol% and main cellular fatty acids including 15:0 anteiso-dimethyl acetal (DMA), 16:0 iso-fatty acid methyl ester (FAME), 13:0 iso-3OH FAME, and 17:0 anteiso-FAME, not matching any of the presently known profiles in the MIDI database. Combined, the phenotypic and genotypic traits including the 16S rRNA gene sequence show that R3_91_1 is a novel species inside the order Clostridiales within the family Lachnospiraceae, for which we propose the name Eubacterium rangiferina. This is the first record of a rumen bacterium able to tolerate and grow in the presence of usnic acid, indicating that the rumen microorganisms in these animals have adapted mechanisms to deal with lichen secondary metabolites, well known for their antimicrobial and toxic effects.
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Affiliation(s)
- Monica A Sundset
- Department of Arctic Biology and Institute of Medical Biology, University of Tromsø, 9037 Tromsø, Norway.
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Sundset MA, Praesteng KE, Cann IKO, Mathiesen SD, Mackie RI. Novel rumen bacterial diversity in two geographically separated sub-species of reindeer. Microb Ecol 2007; 54:424-38. [PMID: 17473904 DOI: 10.1007/s00248-007-9254-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Revised: 03/21/2007] [Accepted: 03/27/2007] [Indexed: 05/15/2023]
Abstract
Svalbard reindeer (Rangifer tarandus platyrhynchus) live under austere nutritional conditions on the high-arctic archipelago of Svalbard, while semi-domesticated Norwegian reindeer (R. tarandus tarandus) migrate between lush coastal summer pastures and inland winter pastures with lichens on mainland Norway. Svalbard reindeer are known to have high rumen concentrations of cellulolytic bacteria, ranging from 15% of the viable population in summer to 35% in winter, compared to only 2.5% in Norwegian reindeer. Their rumen bacterial diversity was investigated through comparative analyses of 16S rRNA gene sequences ( approximately 1.5 kb in length) generated from clone libraries (n = 121) and bacterial isolates (n = 51). LIBSHUFF comparisons of the composition of the two 16S rRNA libraries from Norwegian reindeer showed a significant effect of artificial feeding compared to natural pasture, but failed to yield significant differences between libraries from Norwegian reindeer and Svalbard reindeer. The combined sequences from reindeer were not significantly different from those reported in wild Thompson's gazelle in Kenya but did differ from those reported in domestic cattle in Japan. A total of 90 distinct operational taxonomic units (OTUs) were identified by employing a criterion of 97% similarity, while the Chao1 index estimated the reindeer bacterial rumen population richness at 698 OTUs. The majority of the clone library sequences (92.5%) represented novel strains with <97% identity to any known sequence in the public database, most of them affiliated with the bacterial phylum Firmicutes (low G+C Gram-positives) related to the order Clostridiales (76.7%), while Gram-negative bacteria in the Bacteriodales (Prevotella-Bacteroides group) contributed to 22.5%. Also, six of the isolates were putatively novel strains, possibly representing new species in the Clostridium subphylum (cluster XIVa), Actinomyces and Butyrivibrio.
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Affiliation(s)
- Monica A Sundset
- Department of Arctic Biology and Institute of Medical Biology, University of Tromsø, 9037, Tromsø, Norway.
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Mackie RI, Aminov RI, Hu W, Klieve AV, Ouwerkerk D, Sundset MA, Kamagata Y. Ecology of uncultivated Oscillospira species in the rumen of cattle, sheep, and reindeer as assessed by microscopy and molecular approaches. Appl Environ Microbiol 2004; 69:6808-15. [PMID: 14602644 PMCID: PMC262257 DOI: 10.1128/aem.69.11.6808-6815.2003] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ecology of the uncultured, but large and morphologically conspicuous, rumen bacterium Oscillospira spp. was studied. Oscillospira-specific 16S rRNA gene sequences were detected in North American domestic cattle, sheep from Australia and Japan, and Norwegian reindeer. Phylogenetic analysis of the sequences obtained allowed definition of three operational taxonomic units within the Oscillospira clade. Consistent with this genetic diversity, we observed atypical smaller morphotypes by using an Oscillospira-specific fluorescence in situ hybridization probe. Despite the visual disappearance of typical large Oscillospira morphotypes, the presence of Oscillospira spp. was still detected by Oscillospira-specific PCR in the rumen of cattle and sheep. These observations suggest the broad presence of Oscillospira species in various rumen ecosystems with the level, and most likely the morphological form, dependent on diet. An ecological analysis based on enumeration of the morphologically conspicuous, large-septate form confirms that the highest counts are associated with the feeding of fresh forage diets to cattle and sheep and in two different subspecies of reindeer investigated.
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Affiliation(s)
- Roderick I Mackie
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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Storeheier PV, Sehested J, Diernaes L, Sundset MA, Mathiesen SD. Effects of seasonal changes in food quality and food intake on the transport of sodium and butyrate across ruminal epithelium of reindeer. J Comp Physiol B 2003; 173:391-9. [PMID: 12759766 DOI: 10.1007/s00360-003-0345-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2003] [Indexed: 12/01/2022]
Abstract
Transport of 22Na and 14C-butyrate across the ruminal epithelium of captive reindeer fed a concentrate diet in summer (n=5) and in winter (n=5) and from free-ranging reindeer taken from summer (n=3) and winter pasture (n=5) was measured in vitro in Ussing chambers. Significant amounts of both Na+ and butyrate were transported across the isolated epithelium without any external driving force. The ruminal transport of Na+ and butyrate were interacting, as evidenced by both the observed amiloride-induced reduction of net butyrate-transport and by the positive correlation between net transport of butyrate and Na+. Amiloride also reduced the net transport of Na+ without significantly affecting the short-circuit current, indicating the presence of an apical Na+/H+ exchanger in the ruminal epithelium of reindeer. The captive reindeer increased the dry matter intake of a constant quality concentrate from winter to summer, but this neither affected their ruminal transport capacity nor their ruminal surface enlargement factor (SEF). Free-ranging reindeer increased their ruminal transport capacity for Na+ and butyrate from summer to winter but simultaneously reduced their ruminal SEF. The present data indicate that this food-induced increase in transport capacity was attributed to changes in the nutrient composition of the diet.
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Affiliation(s)
- P V Storeheier
- Department of Arctic Biology and Institute of Medical Biology, University of Tromsø, 9037 Tromsø, Norway.
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