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Wiull K, Hagen LH, Rončević J, Westereng B, Boysen P, Eijsink VGH, Mathiesen G. Antigen surface display in two novel whole genome sequenced food grade strains, Lactiplantibacillus pentosus KW1 and KW2. Microb Cell Fact 2024; 23:19. [PMID: 38212746 PMCID: PMC10782763 DOI: 10.1186/s12934-024-02296-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/04/2024] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Utilization of commensal bacteria for delivery of medicinal proteins, such as vaccine antigens, is an emerging strategy. Here, we describe two novel food-grade strains of lactic acid bacteria, Lactiplantibacillus pentosus KW1 and KW2, as well as newly developed tools for using this relatively unexplored but promising bacterial species for production and surface-display of heterologous proteins. RESULTS Whole genome sequencing was performed to investigate genomic features of both strains and to identify native proteins enabling surface display of heterologous proteins. Basic characterization of the strains revealed the optimum growth temperatures for both strains to be 35-37 °C, with peak heterologous protein production at 33 °C (KW1) and 37 °C (KW2). Negative staining revealed that only KW1 produces closely bound exopolysaccharides. Production of heterologous proteins with the inducible pSIP-expression system enabled high expression in both strains. Exposure to KW1 and KW2 skewed macrophages toward the antigen presenting state, indicating potential adjuvant properties. To develop these strains as delivery vehicles, expression of the mycobacterial H56 antigen was fused to four different strain-specific surface-anchoring sequences. CONCLUSION All experiments that enabled comparison of heterologous protein production revealed KW1 to be the better recombinant protein production host. Use of the pSIP expression system enabled successful construction of L. pentosus strains for production and surface display of an antigen, underpinning the potential of these strains as novel delivery vehicles.
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Affiliation(s)
- Kamilla Wiull
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway.
| | - Live Heldal Hagen
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Jelena Rončević
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Bjørge Westereng
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Preben Boysen
- Faculty of Veterinary Medicine, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Geir Mathiesen
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway.
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Nyløy E, Prestløkken E, Eknæs M, Eikanger KS, Heldal Hagen L, Kidane A. Inclusion of Red Macroalgae ( Asparagopsis taxiformis) in Dairy Cow Diets Modulates Feed Intake, Chewing Activity and Estimated Saliva Secretion. Animals (Basel) 2023; 13:ani13030489. [PMID: 36766377 PMCID: PMC9913350 DOI: 10.3390/ani13030489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
The current study assessed the effects of red macroalgae Asparagopsis taxiformis (AT)-included as an enteric methane inhibitor-in dairy cow diets on feed intake and eating-rumination behaviour. Fifteen early lactating Norwegian Red dairy cows were offered ad libitum access to drinking water and a total mixed ration (TMR) composed of 35% concentrate feed and 65% grass silage on a dry matter (DM) basis. The experiment lasted for 74 days with the first 22 days on a common diet used as the covariate period. At the end of the covariate period, the cows were randomly allocated into one of three dietary treatments: namely, 0% AT (control), 0.125% AT and 0.25% AT in the TMR. The TMR was offered in individual feed troughs with AT blended in a 400 g (w/w) water-molasses mixture. Eating-rumination behaviour was recorded for 11 days using RumiWatchSystem after feeding the experimental diets for 30 days. The 0.25% AT inclusion significantly reduced the DM intake (DMI). Time (min/d) spent on eating and eating in a head-down position increased with the increasing AT level in the diet, whereas rumination time was not affected. The greater time spent on eating head-down with the 0.25% AT group resulted in a significantly higher chewing index (min/kg DMI). Estimated saliva production per unit DMI (L/kg DMI, SE) increased from 10.9 (0.4) in the control to 11.3 (0.3) and 13.0 (0.3) in the 0.125% and 0.25% AT groups, respectively. This aligned with the measured ruminal fluid pH (6.09, 6.14, and 6.37 in the control, 0.125% AT and 0.25% AT groups, respectively). In conclusion, either the level of the water-molasses mixture used was not sufficient to mask the taste of AT, or the cows used it as a cue to sort out the AT. Studies with relatively larger numbers of animals and longer adaptation periods than what we used here, with varied modes of delivery of the seaweed may provide novel strategies for administering the additive in ruminant diets.
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Affiliation(s)
- Emma Nyløy
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1430 Ås, Norway
| | - Egil Prestløkken
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1430 Ås, Norway
| | - Margrete Eknæs
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1430 Ås, Norway
| | - Katrine Sømliøy Eikanger
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1430 Ås, Norway
| | - Live Heldal Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway
| | - Alemayehu Kidane
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1430 Ås, Norway
- Correspondence: ; Tel.: +47-67232727
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Ferrillo A, Kobel CM, Vera-Ponce de León A, La Rosa SL, Kunath BJ, Pope PB, Hagen LH. Long-Read Metagenomics and CAZyme Discovery. Methods Mol Biol 2023; 2657:253-284. [PMID: 37149537 DOI: 10.1007/978-1-0716-3151-5_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Microorganisms play a primary role in regulating biogeochemical cycles and are a valuable source of enzymes that have biotechnological applications, such as carbohydrate-active enzymes (CAZymes). However, the inability to culture the majority of microorganisms that exist in natural ecosystems restricts access to potentially novel bacteria and beneficial CAZymes. While commonplace molecular-based culture-independent methods such as metagenomics enable researchers to study microbial communities directly from environmental samples, recent progress in long-read sequencing technologies are advancing the field. We outline key methodological stages that are required as well as describe specific protocols that are currently used for long-read metagenomic projects dedicated to CAZyme discovery.
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Affiliation(s)
- Alessandra Ferrillo
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Carl Mathias Kobel
- Faculty of Bioscience, Norwegian University of Life Sciences, Aas, Norway
| | - Arturo Vera-Ponce de León
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
- Faculty of Bioscience, Norwegian University of Life Sciences, Aas, Norway
| | - Sabina Leanti La Rosa
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | | | - Phillip Byron Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
- Faculty of Bioscience, Norwegian University of Life Sciences, Aas, Norway
| | - Live Heldal Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway.
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Alvarez C, Os Andersen T, Sømliøy Eikanger K, Wøyen Hamfjord I, Niu P, Weiby KV, Årvik L, Dörsch P, Hagen LH, Pope PB, Forberg DK, Kolsrud Hustoft H, Schwarm A, Kidane A. Methane inhibition by Asparagopsis taxiformis with rumen fluid collected from ventral and central location – a pilot study. ACTA AGR SCAND A-AN 2022. [DOI: 10.1080/09064702.2022.2152196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Clementina Alvarez
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
- TineSA, Oslo, Norway
| | - Thea Os Andersen
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | | | - Ida Wøyen Hamfjord
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Puchun Niu
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Kim Viggo Weiby
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
- TineSA, Oslo, Norway
| | - Linda Årvik
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Peter Dörsch
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - Live Heldal Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Phillip B. Pope
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | | | | | - Angela Schwarm
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Alemayehu Kidane
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
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Nilsen M, Madelen Saunders C, Leena Angell I, Arntzen MØ, Lødrup Carlsen KC, Carlsen KH, Haugen G, Heldal Hagen L, Carlsen MH, Hedlin G, Monceyron Jonassen C, Nordlund B, Maria Rehbinder E, Skjerven HO, Snipen L, Cathrine Staff A, Vettukattil R, Rudi K. Butyrate Levels in the Transition from an Infant- to an Adult-Like Gut Microbiota Correlate with Bacterial Networks Associated with Eubacterium Rectale and Ruminococcus Gnavus. Genes (Basel) 2020; 11:genes11111245. [PMID: 33105702 PMCID: PMC7690385 DOI: 10.3390/genes11111245] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/18/2020] [Accepted: 10/19/2020] [Indexed: 01/14/2023] Open
Abstract
Relatively little is known about the ecological forces shaping the gut microbiota composition during infancy. Therefore, the objective of the present study was to identify the nutrient utilization- and short-chain fatty acid (SCFA) production potential of gut microbes in infants during the first year of life. Stool samples were obtained from mothers at 18 weeks of pregnancy and from infants at birth (first stool) at 3, 6, and 12-months of age from the general population-based PreventADALL cohort. We identified the taxonomic and SCFA composition in 100 mother-child pairs. The SCFA production and substrate utilization potential of gut microbes were observed by multiomics (shotgun sequencing and proteomics) on six infants. We found a four-fold increase in relative butyrate levels from 6 to 12 months of infant age. The increase was correlated to Eubacterium rectale and its bacterial network, and Faecalibacterium prausnitzii relative abundance, while low butyrate at 12 months was correlated to Ruminococcus gnavus and its associated network of bacteria. Both E. rectale and F. prausnitzii expressed enzymes needed for butyrate production and enzymes related to dietary fiber degradation, while R. gnavus expressed mucus-, fucose, and human milk oligosaccharides (HMO)-related degradation enzymes. Therefore, we believe that the presence of E. rectale, its network, and F. prausnitzii are key bacteria in the transition from an infant- to an adult-like gut microbiota with respect to butyrate production. Our results indicate that the transition from an infant- to an adult-like gut microbiota with respect to butyrate producing bacteria, occurs between 6 and 12 months of infant age. The bacteria associated with the increased butyrate ratio/levels were E. rectale and F. prausnitzii, which potentially utilize a variety of dietary fibers based on the glycoside hydrolases (GHs) expressed. R. gnavus with a negative association to butyrate potentially utilizes mucin, fucose, and HMO components. This knowledge could have future importance in understanding how microbial metabolites can impact infant health and development.
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Affiliation(s)
- Morten Nilsen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway; (I.L.A.); (M.Ø.A.); (L.H.H.); (C.M.J.); (L.S.); (K.R.)
- Correspondence: (M.N.); (C.M.S.)
| | - Carina Madelen Saunders
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0450 Oslo, Norway; (K.C.L.C.); (K.-H.C.); (H.O.S.); (R.V.)
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway; (G.H.); (E.M.R.); (A.C.S.)
- Correspondence: (M.N.); (C.M.S.)
| | - Inga Leena Angell
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway; (I.L.A.); (M.Ø.A.); (L.H.H.); (C.M.J.); (L.S.); (K.R.)
| | - Magnus Ø. Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway; (I.L.A.); (M.Ø.A.); (L.H.H.); (C.M.J.); (L.S.); (K.R.)
| | - Karin C. Lødrup Carlsen
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0450 Oslo, Norway; (K.C.L.C.); (K.-H.C.); (H.O.S.); (R.V.)
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway; (G.H.); (E.M.R.); (A.C.S.)
| | - Kai-Håkon Carlsen
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0450 Oslo, Norway; (K.C.L.C.); (K.-H.C.); (H.O.S.); (R.V.)
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway; (G.H.); (E.M.R.); (A.C.S.)
| | - Guttorm Haugen
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway; (G.H.); (E.M.R.); (A.C.S.)
- Division of Obstetrics and Gynaecology, Oslo University Hospital, 0450 Oslo, Norway
| | - Live Heldal Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway; (I.L.A.); (M.Ø.A.); (L.H.H.); (C.M.J.); (L.S.); (K.R.)
| | - Monica H. Carlsen
- Department of Nutrition, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, 0405 Oslo, Norway;
| | - Gunilla Hedlin
- Astrid Lindgren Children’s Hospital, Karolinska University Hospital, 17176 Stockholm, Sweden; (G.H.); (B.N.)
- Department of Women’s and Children’s Health, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Christine Monceyron Jonassen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway; (I.L.A.); (M.Ø.A.); (L.H.H.); (C.M.J.); (L.S.); (K.R.)
- Genetic Unit, Centre for Laboratory Medicine, Østfold Hospital Trust, 1714 Kalnes, Norway
| | - Björn Nordlund
- Astrid Lindgren Children’s Hospital, Karolinska University Hospital, 17176 Stockholm, Sweden; (G.H.); (B.N.)
- Department of Women’s and Children’s Health, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Eva Maria Rehbinder
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway; (G.H.); (E.M.R.); (A.C.S.)
- Department of Dermatology, Oslo University Hospital, 0424 Oslo, Norway
| | - Håvard O. Skjerven
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0450 Oslo, Norway; (K.C.L.C.); (K.-H.C.); (H.O.S.); (R.V.)
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway; (G.H.); (E.M.R.); (A.C.S.)
| | - Lars Snipen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway; (I.L.A.); (M.Ø.A.); (L.H.H.); (C.M.J.); (L.S.); (K.R.)
| | - Anne Cathrine Staff
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway; (G.H.); (E.M.R.); (A.C.S.)
- Division of Obstetrics and Gynaecology, Oslo University Hospital, 0450 Oslo, Norway
| | - Riyas Vettukattil
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, 0450 Oslo, Norway; (K.C.L.C.); (K.-H.C.); (H.O.S.); (R.V.)
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway; (G.H.); (E.M.R.); (A.C.S.)
| | - Knut Rudi
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway; (I.L.A.); (M.Ø.A.); (L.H.H.); (C.M.J.); (L.S.); (K.R.)
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Minniti G, Rød Sandve S, Padra JT, Heldal Hagen L, Lindén S, Pope PB, Ø Arntzen M, Vaaje-Kolstad G. The Farmed Atlantic Salmon ( Salmo salar) Skin-Mucus Proteome and Its Nutrient Potential for the Resident Bacterial Community. Genes (Basel) 2019; 10:genes10070515. [PMID: 31284681 PMCID: PMC6678340 DOI: 10.3390/genes10070515] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/01/2019] [Accepted: 07/04/2019] [Indexed: 12/29/2022] Open
Abstract
Norway is the largest producer and exporter of farmed Atlantic salmon (Salmo salar) worldwide. Skin disorders correlated with bacterial infections represent an important challenge for fish farmers due to the economic losses caused. Little is known about this topic, thus studying the skin-mucus of Salmo salar and its bacterial community depict a step forward in understanding fish welfare in aquaculture. In this study, we used label free quantitative mass spectrometry to investigate the skin-mucus proteins associated with both Atlantic salmon and bacteria. In particular, the microbial temporal proteome dynamics during nine days of mucus incubation with sterilized seawater was investigated, in order to evaluate their capacity to utilize mucus components for growth in this environment. At the start of the incubation period, the largest proportion of proteins (~99%) belonged to the salmon and many of these proteins were assigned to protecting functions, confirming the defensive role of mucus. On the contrary, after nine days of incubation, most of the proteins detected were assigned to bacteria, mainly to the genera Vibrio and Pseudoalteromonas. Most of the predicted secreted proteins were affiliated with transport and metabolic processes. In particular, a large abundance and variety of bacterial proteases were observed, highlighting the capacity of bacteria to degrade the skin-mucus proteins of Atlantic salmon.
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Affiliation(s)
- Giusi Minniti
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), NO-1432 Ås, Norway
| | - Simen Rød Sandve
- Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), NO-1432 Ås, Norway
| | - János Tamás Padra
- Department of Medical Biochemistry and Cell Biology, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Live Heldal Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), NO-1432 Ås, Norway
| | - Sara Lindén
- Department of Medical Biochemistry and Cell Biology, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Phillip B Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), NO-1432 Ås, Norway
| | - Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), NO-1432 Ås, Norway.
| | - Gustav Vaaje-Kolstad
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), NO-1432 Ås, Norway.
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Naas AE, Solden LM, Norbeck AD, Brewer H, Hagen LH, Heggenes IM, McHardy AC, Mackie RI, Paša-Tolić L, Arntzen MØ, Eijsink VGH, Koropatkin NM, Hess M, Wrighton KC, Pope PB. "Candidatus Paraporphyromonas polyenzymogenes" encodes multi-modular cellulases linked to the type IX secretion system. Microbiome 2018; 6:44. [PMID: 29490697 PMCID: PMC5831590 DOI: 10.1186/s40168-018-0421-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 02/07/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND In nature, obligate herbivorous ruminants have a close symbiotic relationship with their gastrointestinal microbiome, which proficiently deconstructs plant biomass. Despite decades of research, lignocellulose degradation in the rumen has thus far been attributed to a limited number of culturable microorganisms. Here, we combine meta-omics and enzymology to identify and describe a novel Bacteroidetes family ("Candidatus MH11") composed entirely of uncultivated strains that are predominant in ruminants and only distantly related to previously characterized taxa. RESULTS The first metabolic reconstruction of Ca. MH11-affiliated genome bins, with a particular focus on the provisionally named "Candidatus Paraporphyromonas polyenzymogenes", illustrated their capacity to degrade various lignocellulosic substrates via comprehensive inventories of singular and multi-modular carbohydrate active enzymes (CAZymes). Closer examination revealed an absence of archetypical polysaccharide utilization loci found in human gut microbiota. Instead, we identified many multi-modular CAZymes putatively secreted via the Bacteroidetes-specific type IX secretion system (T9SS). This included cellulases with two or more catalytic domains, which are modular arrangements that are unique to Bacteroidetes species studied to date. Core metabolic proteins from Ca. P. polyenzymogenes were detected in metaproteomic data and were enriched in rumen-incubated plant biomass, indicating that active saccharification and fermentation of complex carbohydrates could be assigned to members of this novel family. Biochemical analysis of selected Ca. P. polyenzymogenes CAZymes further iterated the cellulolytic activity of this hitherto uncultured bacterium towards linear polymers, such as amorphous and crystalline cellulose as well as mixed linkage β-glucans. CONCLUSION We propose that Ca. P. polyenzymogene genotypes and other Ca. MH11 members actively degrade plant biomass in the rumen of cows, sheep and most likely other ruminants, utilizing singular and multi-domain catalytic CAZymes secreted through the T9SS. The discovery of a prominent role of multi-modular cellulases in the Gram-negative Bacteroidetes, together with similar findings for Gram-positive cellulosomal bacteria (Ruminococcus flavefaciens) and anaerobic fungi (Orpinomyces sp.), suggests that complex enzymes are essential and have evolved within all major cellulolytic dominions inherent to the rumen.
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Affiliation(s)
- A E Naas
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Post Office Box 5003, 1432, Ås, Norway
| | - L M Solden
- Department of Microbiology, The Ohio State University, Columbus, OH, 43201, USA
| | - A D Norbeck
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - H Brewer
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - L H Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Post Office Box 5003, 1432, Ås, Norway
| | - I M Heggenes
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Post Office Box 5003, 1432, Ås, Norway
| | - A C McHardy
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraβe 7, 38124, Braunschweig, Germany
| | - R I Mackie
- Institute for Genomic Biology and Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - L Paša-Tolić
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - M Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Post Office Box 5003, 1432, Ås, Norway
| | - V G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Post Office Box 5003, 1432, Ås, Norway
| | - N M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - M Hess
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - K C Wrighton
- Department of Microbiology, The Ohio State University, Columbus, OH, 43201, USA
| | - P B Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Post Office Box 5003, 1432, Ås, Norway.
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Zamanzadeh M, Hagen LH, Svensson K, Linjordet R, Horn SJ. Biogas production from food waste via co-digestion and digestion- effects on performance and microbial ecology. Sci Rep 2017; 7:17664. [PMID: 29247239 PMCID: PMC5732306 DOI: 10.1038/s41598-017-15784-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [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: 08/14/2017] [Accepted: 11/02/2017] [Indexed: 12/13/2022] Open
Abstract
In this work, performance and microbial structure of a digestion (food waste-only) and a co-digestion process (mixture of cow manure and food waste) were studied at mesophilic (37 °C) and thermophilic (55 °C) temperatures. The highest methane yield (480 mL/g VS) was observed in the mesophilic digester (MDi) fed with food waste alone. The mesophilic co-digestion of food waste and manure (McoDi) yielded 26% more methane than the sum of individual digestions of manure and food waste. The main volatile fatty acid (VFA) in the mesophilic systems was acetate, averaging 93 and 172 mg/L for McoDi and MDi, respectively. Acetate (2150 mg/L) and propionate (833 mg/L) were the main VFAs in the thermophilic digester (TDi), while propionate (163 mg/L) was the major VFA in the thermophilic co-digester (TcoDi). The dominant bacteria in MDi was Chloroflexi (54%), while Firmicutes was dominant in McoDi (60%). For the mesophilic reactors, the dominant archaea was Methanosaeta in MDi, while Methanobacterium and Methanosaeta had similar abundance in McoDi. In the thermophilic systems, the dominant bacteria were Thermotogae, Firmicutes and Synergistetes in both digesters, however, the relative abundance of these phyla were different. For archaea, the genus Methanothermobacter were entirely dominant in both TDi and TcoDi.
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Affiliation(s)
- Mirzaman Zamanzadeh
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P. O. Box 5003, N-1432, Ås, Norway
- Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Sciences, P.O. Box 14155-6446, Tehran, Iran
- Department of Civil and Environmental Engineering, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Live Heldal Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P. O. Box 5003, N-1432, Ås, Norway
| | - Kine Svensson
- Nibio, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Roar Linjordet
- Nibio, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Svein Jarle Horn
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P. O. Box 5003, N-1432, Ås, Norway.
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Minniti G, Hagen LH, Porcellato D, Jørgensen SM, Pope PB, Vaaje-Kolstad G. The Skin-Mucus Microbial Community of Farmed Atlantic Salmon ( Salmo salar). Front Microbiol 2017; 8:2043. [PMID: 29104567 PMCID: PMC5655796 DOI: 10.3389/fmicb.2017.02043] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 10/06/2017] [Indexed: 01/07/2023] Open
Abstract
The skin of the teleost is a flexible and scaled structure that protects the fish toward the external environment. The outermost surface of the skin is coated with mucus, which is believed to be colonized by a diverse bacterial community (commensal and/or opportunistic). Little is known about such communities and their role in fish welfare. In aquaculture, fish seem to be more susceptible to pathogens compared to wild fish. Indeed common fish farming practices may play important roles in promoting their vulnerability, possibly by causing changes to their microbiomes. In the present study, 16S rRNA gene amplicon sequencing was employed to analyze the composition of the farmed Salmo salar skin-mucus microbiome before and after netting and transfer. The composition of the bacterial community present in the rearing water was also investigated in order to evaluate its correlation with the community present on the fish skin. Our results reveal variability of the skin-mucus microbiome among the biological replicates before fish handling. On the contrary, after fish handling, the skin-mucus community exhibited structural similarity among the biological replicates and significant changes were observed in the bacterial composition compared to the fish analyzed prior to netting and transfer. Limited correlation was revealed between the skin-mucus microbiome and the bacterial community present in the rearing water. Finally, analysis of skin-mucus bacterial biomasses indicated low abundance for some samples, highlighting the need of caution when interpreting community data due to the possible contamination of water-residing bacteria.
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Affiliation(s)
- Giusi Minniti
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Live Heldal Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Davide Porcellato
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Sven Martin Jørgensen
- Nofima AS, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Phillip B. Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Gustav Vaaje-Kolstad
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
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Hagen LH, Vivekanand V, Pope PB, Eijsink VGH, Horn SJ. The effect of storage conditions on microbial community composition and biomethane potential in a biogas starter culture. Appl Microbiol Biotechnol 2015; 99:5749-61. [DOI: 10.1007/s00253-015-6623-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 04/14/2015] [Accepted: 04/18/2015] [Indexed: 10/23/2022]
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Hagen LH, Vivekanand V, Linjordet R, Pope PB, Eijsink VGH, Horn SJ. Microbial community structure and dynamics during co-digestion of whey permeate and cow manure in continuous stirred tank reactor systems. Bioresour Technol 2014; 171:350-9. [PMID: 25222739 DOI: 10.1016/j.biortech.2014.08.095] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 08/21/2014] [Accepted: 08/22/2014] [Indexed: 05/19/2023]
Abstract
Microbial community profiles in two parallel CSTR biogas reactors fed with whey permeate and cow manure were investigated. The operating conditions for these two reactors were identical, yet only one of them (R1) showed stable performance, whereas the other (R2) showed a decrease in methane production accompanied by accumulation of propionic acid and, later, acetic acid. This gave a unique opportunity to study the dynamics of the microbial communities in two biogas reactors apparently operating close to the edge of stability. The microbial community was dominated by Bacteroidetes and Firmicutes, and the methanogens Methanobacteriales and Methanomicrobiales in both reactors, but with larger fluctuations in R2. Correlation analyses showed that the depletion of propionic acid in R1 and the late increase of acetic acid in R2 was related to several bacterial groups. The biogas production in R1 shows that stable co-digestion of manure and whey can be achieved with reasonable yields.
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Affiliation(s)
- Live Heldal Hagen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Ås, Norway
| | - Vivekanand Vivekanand
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Ås, Norway
| | - Roar Linjordet
- Bioforsk, Norwegian Institute for Agricultural and Environmental Research, Frederik A. Dahls vei 20, 1432 Ås, Norway
| | - Phillip B Pope
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Ås, Norway
| | - Vincent G H Eijsink
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Ås, Norway
| | - Svein J Horn
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Ås, Norway.
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