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Alahdal H, Almuneef G, Alkhulaifi MM, Aldibasi O, Aljouie A, Alharbi O, Almohawes ZN, Basingab F, Rejili M. Gut microbiota composition in patients with Crohn's disease in Saudi Arabia. PLoS One 2024; 19:e0299749. [PMID: 38656971 PMCID: PMC11042705 DOI: 10.1371/journal.pone.0299749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 02/14/2024] [Indexed: 04/26/2024] Open
Abstract
Crohn's disease (CD) entails intricate interactions with gut microbiome diversity, richness, and composition. The relationship between CD and gut microbiome is not clearly understood and has not been previously characterized in Saudi Arabia. We performed statistical analysis about various factors influencing CD activity and microbiota dysbiosis, including diagnosis, treatment, and its impact on their quality of life as well as high-throughput metagenomic V3-V4 16S rRNA encoding gene hypervariable region of a total of eighty patients with CD, both in its active and inactive state with healthy controls. The results were correlated with the demographic and lifestyle information, which the participants provided via a questionnaire. α-diversity measures indicated lower bacterial diversity and richness in the active and inactive CD groups compared to the control group. Greater dysbiosis was observed in the active CD patients compared to the inactive form of the disease, showed by a reduction in microbial diversity. Specific pathogenic bacteria such as Filifactor, Peptoniphilus, and Sellimonas were identified as characteristic of CD groups. In contrast, anti-inflammatory bacteria like Defluviitalea, Papillibacter, and Petroclostridium were associated with the control group. Among the various factors influencing disease activity and microbiota dysbiosis, smoking emerged as the most significant, with reduced α-diversity and richness for the smokers in all groups, and proinflammatory Fusobacteria was more present (p<0.05). Opposite to the control group, microbial diversity and richness were lower in CD participants of older age compared to younger ones, and male CD participants showed less diversity compared to women participants from the same groups. Our results describe the first report on the relationship between microbiota and Crohn's disease progress in Saudi Arabia, which may provide a theoretical basis for the application of therapeutic methods to regulate gut microbes in CD.
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Affiliation(s)
- Hadil Alahdal
- Department of Biology, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Ghaida Almuneef
- Department of Biology, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Manal Muhammed Alkhulaifi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Omar Aldibasi
- Biostatistics Section, King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Abdulrahman Aljouie
- Artificial Intelligence and Bioinformatics Department, King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
- Department of Health Informatics, College of Public Health and Health Informatics, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Othman Alharbi
- Department of Medicine, College of Medicine, King Khalid University Hospital, King Saud University, Riyadh, Saudi Arabia
| | - Zakiah Naser Almohawes
- Department of Biology, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Fatemah Basingab
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Immunology Unit, King Fahad Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mokhtar Rejili
- Department of Life Sciences, College of Sciences, Al Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
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Gállego-Bravo AK, García-Mena J, Piña-Escobedo A, López-Jiménez G, Gutiérrez-Castillo ME, Tovar-Gálvez LR. Monitoring of a microbial community during bioaugmentation with hydrogenotrophic methanogens to improve methane yield of an anaerobic digestion process. Biotechnol Lett 2023; 45:1339-1353. [PMID: 37535136 PMCID: PMC10460350 DOI: 10.1007/s10529-023-03414-7] [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: 12/14/2022] [Revised: 06/12/2023] [Accepted: 06/26/2023] [Indexed: 08/04/2023]
Abstract
Methane production by microbial fermentation of municipal waste is a challenge for better yield processes. This work describes the characterization of a hydrogenotrophic methanogen microbial community used in a bioaugmentation procedure to improve the methane yield in a thermophilic anaerobic process, digesting the organic fraction of municipal solid waste. The performance of the bioaugmentation was assessed in terms of methane production and changes in the microbial community structure. The results showed that bioaugmentation slightly improved the cumulative methane yield (+ 4%) in comparison to the control, and its use led to an acceleration of the methanogenesis stage. We observed associated significant changes in the relative abundance of taxa and their interactions, using high throughput DNA sequencing of V3-16S rRNA gene libraries, where the abundance of the archaeal hydrogenotrophic genus Methanoculleus (class Methanomicrobia, phylum Euryarchaeota) and the bacterial order MBA08 (class Clostridia, phylum Firmicutes) were dominant. The relevant predicted metabolic pathways agreed with substrate degradation and the anaerobic methanogenic process. The purpose of the study was to evaluate the effect of the addition of hydrogenotrophic methanogens in the generation of methane, while treating organic waste through anaerobic digestion.
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Affiliation(s)
- Aixa Kari Gállego-Bravo
- Instituto Politécnico Nacional, Centro Mexicano Para la Producción más Limpia, Av. Acueducto s/n, 07340 Ciudad de Mexico, Mexico
| | - Jaime García-Mena
- Departamento de Genética y Biología Molecular, Cinvestav, Av. Instituto Politécnico Nacional 2508, 07360 Ciudad de México, Mexico
| | - Alberto Piña-Escobedo
- Departamento de Genética y Biología Molecular, Cinvestav, Av. Instituto Politécnico Nacional 2508, 07360 Ciudad de México, Mexico
| | - Gloria López-Jiménez
- Departamento de Ciencias Básicas, Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología, Av. Acueducto s/n, 07340 Ciudad de Mexico, Mexico
| | - María Eugenia Gutiérrez-Castillo
- Instituto Politécnico Nacional, Centro Interdisciplinario de Investigaciones y Estudios Sobre Medio Ambiente y Desarrollo, Calle 30 de Junio de 1520 s/n, 07340 Ciudad de Mexico, Mexico
| | - Luis Raúl Tovar-Gálvez
- Instituto Politécnico Nacional, Centro Interdisciplinario de Investigaciones y Estudios Sobre Medio Ambiente y Desarrollo, Calle 30 de Junio de 1520 s/n, 07340 Ciudad de Mexico, Mexico
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Bai L, Paek J, Kim H, Kim SH, Shin JH, Kook JK, Chang YH. Limosilactobacillus kribbianus sp. nov., isolated from pig faeces. Int J Syst Evol Microbiol 2023; 73. [PMID: 37486340 DOI: 10.1099/ijsem.0.005988] [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: 07/25/2023] Open
Abstract
A rod-shaped, aerotolerant, Gram-stain-positive bacterium isolated from pig faeces was designated as strain YH-lim2214T. Analysis of the 16S rRNA gene sequence revealed that the isolate was most closely related to Limosilactobacillus pontis KCTC 25258T with 98.0 % similarity. The average nucleotide identity and average amino acid identity values between YH-lim2214T and the most closely related strain Lm. pontis KCTC 25258T were 81.4 and 81.3 %, respectively. The major fatty acids were C18 : 1 ω9c, summed feature 7 and C16 : 0. The cell-wall peptidoglycan type was A4α l-Lys-d-Asp. The genomic DNA G+C content was 51.1 mol%. The chemotaxonomic, phenotypic and phylogenetic properties of YH-lim2214T (=KCTC 25572T=JCM 35701T) suggest that it represents a novel taxon, for which the name Limosilactobacillus kribbianus sp. nov. is proposed.
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Affiliation(s)
- Lu Bai
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jayoung Paek
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hongik Kim
- Vitabio, Inc., Daejeon, 305-500, Republic of Korea
| | - Si Hyun Kim
- Department of Clinical Laboratory Science, Semyung University, Jecheon, Republic of Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University College of Medicine, Busan 614-735, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, 501-759, Republic of Korea
| | - Young Hyo Chang
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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Prem EM, Schwarzenberger A, Markt R, Wagner AO. Effects of phenyl acids on different degradation phases during thermophilic anaerobic digestion. Front Microbiol 2023; 14:1087043. [PMID: 37089573 PMCID: PMC10113666 DOI: 10.3389/fmicb.2023.1087043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 03/06/2023] [Indexed: 04/08/2023] Open
Abstract
Aromatic compounds like phenyl acids (PA) can accumulate during anaerobic digestion (AD) of organic wastes due to an increased entry of lignocellulose, secondary plant metabolites or proteins, and thermodynamic challenges in degrading the benzene ring. The effects of aromatic compounds can be various – from being highly toxic to be stimulating for methanogenesis – depending on many parameters like inoculum or molecular characteristics of the aromatic compound. To contribute to a better understanding of the consequences of PA exposure during AD, the aim was to evaluate the effects of 10 mM PA on microbial communities degrading different, degradation phase–specific substrates in thermophilic batch reactors within 28 days: Microcrystalline cellulose (MCC, promoting hydrolytic to methanogenic microorganisms), butyrate or propionate (promoting syntrophic volatile fatty acid (VFA) oxidisers to methanogens), or acetate (promoting syntrophic acetate oxidisers to methanogens). Methane production, VFA concentrations and pH were evaluated, and microbial communities and extracellular polymeric substances (EPS) were assessed. The toxicity of PA depended on the type of substrate which in turn determined the (i) microbial diversity and composition and (ii) EPS quantity and quality. Compared with the respective controls, methane production in MCC reactors was less impaired by PA than in butyrate, propionate and acetate reactors which showed reductions in methane production of up to 93%. In contrast to the controls, acetate concentrations were high in all PA reactors at the end of incubation thus acetate was a bottle-neck intermediate in those reactors. Considerable differences in EPS quantity and quality could be found among substrates but not among PA variants of each substrate. Methanosarcina spp. was the dominant methanogen in VFA reactors without PA exposure and was inhibited when PA were present. VFA oxidisers and Methanothermobacter spp. were abundant in VFA assays with PA exposure as well as in all MCC reactors. As MCC assays showed higher methane yields, a higher microbial diversity and a higher EPS quantity and quality than VFA reactors when exposed to PA, we conclude that EPS in MCC reactors might have been beneficial for absorbing/neutralising phenyl acids and keeping (more susceptible) microorganisms shielded in granules or biofilms.
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Affiliation(s)
- Eva Maria Prem
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | | | - Rudolf Markt
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
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Almeida PDS, de Menezes CA, Camargo FP, Sakamoto IK, Lovato G, Rodrigues JAD, Varesche MBA, Silva EL. Biomethane recovery through co-digestion of cheese whey and glycerol in a two-stage anaerobic fluidized bed reactor: Effect of temperature and organic loading rate on methanogenesis. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 330:117117. [PMID: 36584460 DOI: 10.1016/j.jenvman.2022.117117] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/07/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Anaerobic digestion for CH4 recovery in wastewater treatment has been carried out with different strategies to increase process efficiency, among which co-digestion and the two-stage process can be highlighted. In this context, this study aimed at evaluating the co-digestion of cheese whey and glycerol in a two-stage process using fluidized bed reactors, verifying the effect of increasing the organic loading rate (OLR) (2-20 g-COD.L-1.d-1) and temperature (thermophilic and mesophilic) in the second stage methanogenic reactor. The mesophilic methanogenic reactor (R-Meso) (mean temperature of 22 °C) was more tolerant to high OLR and its best performance was at 20 g-COD.L-1.d-1, resulting in methane yield (MY) and methane production (MPR) of 273 mL-CH4.g-COD-1 and 5.8 L-CH4.L-1.d-1 (with 67% of CH4), respectively. Through 16S rRNA gene massive sequencing analysis, a greater diversity of microorganisms was identified in R-Meso than in R-Thermo (second stage methanogenic reactor, 55 °C). Firmicutes was the phyla with higher relative abundance in R-Thermo, while in R-Meso the most abundant ones were Proteobacteria and Bacteroidetes. Regarding the Archaea domain, a predominance of hydrogenotrophic microorganisms could be observed, being the genera Methanothermobacter and Methanobacterium the most abundant in R-Thermo and R-Meso, respectively. The two-stage system composed with a thermophilic acidogenic reactor + R-Meso was more adequate for the co-digestion of cheese whey and glycerol than the single-stage process, promoting increases of up to 47% in the energetic yield (10.3 kJ.kg-COD-1) and 14% in organic matter removal (90.5%).
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Affiliation(s)
- Priscilla de Souza Almeida
- Department of Chemical Engineering, Federal University of São Carlos, Rod. Washington Luis, Km 235, Zip Code 13.565-905, São Carlos, SP, Brazil
| | - Camila Aparecida de Menezes
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo, Av. João Dagnone, 1100 - Jd. Santa Angelina, Zip Code 13.563-120, São Carlos, SP, Brazil
| | - Franciele Pereira Camargo
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo, Av. João Dagnone, 1100 - Jd. Santa Angelina, Zip Code 13.563-120, São Carlos, SP, Brazil
| | - Isabel Kimiko Sakamoto
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo, Av. João Dagnone, 1100 - Jd. Santa Angelina, Zip Code 13.563-120, São Carlos, SP, Brazil
| | - Giovanna Lovato
- Department of Chemical Engineering, Mauá School of Engineering, Mauá Institute of Technology, Praça Mauá 1, Zip Code 09.580-900, São Caetano Do Sul, SP, Brazil
| | - José Alberto Domingues Rodrigues
- Department of Chemical Engineering, Mauá School of Engineering, Mauá Institute of Technology, Praça Mauá 1, Zip Code 09.580-900, São Caetano Do Sul, SP, Brazil
| | - Maria Bernadete Amâncio Varesche
- Department of Hydraulics and Sanitation, School of Engineering of São Carlos, University of São Paulo, Av. João Dagnone, 1100 - Jd. Santa Angelina, Zip Code 13.563-120, São Carlos, SP, Brazil
| | - Edson Luiz Silva
- Department of Chemical Engineering, Federal University of São Carlos, Rod. Washington Luis, Km 235, Zip Code 13.565-905, São Carlos, SP, Brazil.
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Hominibacterium faecale gen. nov., sp. nov., an anaerobic l-arginine-degrading bacterium isolated from human feces. Arch Microbiol 2023; 205:33. [DOI: 10.1007/s00203-022-03365-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022]
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Description of a moderately acidotolerant and aerotolerant anaerobic bacterium Acidilutibacter cellobiosedens gen. nov., sp. nov. within the family Acidilutibacteraceae fam. nov., and proposal of Sporanaerobacteraceae fam. nov. and Tepidimicrobiaceae fam. nov. Syst Appl Microbiol 2023; 46:126376. [PMID: 36375421 DOI: 10.1016/j.syapm.2022.126376] [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: 09/05/2022] [Revised: 10/17/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022]
Abstract
A Gram-stain positive, moderately thermophilic, acidotolerant and aerotolerant anaerobic bacterium, designated JN-28 T, was isolated from the pit mud of Chinese strong-flavor liquor. Growth was observed at 25-50 °C and pH 5.5-8.0 in the presence of 0-25 g l-1 NaCl (optimally at 45 °C, pH 6.0, without NaCl). Strain JN-28 T was heterotrophic, requiring yeast extract for growth. The major cellular fatty acids were iso-C15:0 and C14:0. The DNA G + C content of genomic DNA was 33.54 mol%. The strain was resistant to vancomycin (10 mg l-1). Genome analysis revealed the presence of genes involved in the response to mild acid stress and oxidative stress, and resistance to vancomycin. 16S rRNA gene-based phylogenetic analysis showed that strain JN-28 T shares ≤ 89.3 % sequence similarity with its closest relatives Sporanaerobacter acetigenes DSM 13106 T and other members in the order Tissierellales. Based on phenotypic and phylogenetic characteristics, Acidilutibacter cellobiosedens gen. nov., sp. nov. is proposed for the new genus and novel species with the type strain JN-28 T (=CCAM 418 T = JCM 39087 T). Further phylogenetic and phylogenomic analyses suggested strain JN-28 T represents a novel family within the order Tissierellales, for which Acidilutibacteraceae fam. nov. is proposed. In addition, the family Tissierellaceae was reclassified, Sporanaerobacteraceae fam. nov. and Tepidimicrobiaceae fam. nov. were formally proposed. Emended description of the family Tissierellaceae is also provided.
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Bandini F, Vaccari F, Soldano M, Piccinini S, Misci C, Bellotti G, Taskin E, Cocconcelli PS, Puglisi E. Rigid bioplastics shape the microbial communities involved in the treatment of the organic fraction of municipal solid waste. Front Microbiol 2022; 13:1035561. [PMID: 36439796 PMCID: PMC9691671 DOI: 10.3389/fmicb.2022.1035561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/17/2022] [Indexed: 11/03/2023] Open
Abstract
While bioplastics are gaining wide interest in replacing conventional plastics, it is necessary to understand whether the treatment of the organic fraction of municipal solid waste (OFMSW) as an end-of-life option is compatible with their biodegradation and their possible role in shaping the microbial communities involved in the processes. In the present work, we assessed the microbiological impact of rigid polylactic acid (PLA) and starch-based bioplastics (SBB) spoons on the thermophilic anaerobic digestion and the aerobic composting of OFMSW under real plant conditions. In order to thoroughly evaluate the effect of PLA and SBB on the bacterial, archaeal, and fungal communities during the process, high-throughput sequencing (HTS) technology was carried out. The results suggest that bioplastics shape the communities' structure, especially in the aerobic phase. Distinctive bacterial and fungal sequences were found for SBB compared to the positive control, which showed a more limited diversity. Mucor racemosus was especially abundant in composts from bioplastics' treatment, whereas Penicillium roqueforti was found only in compost from PLA and Thermomyces lanuginosus in that from SBB. This work shed a light on the microbial communities involved in the OFMSW treatment with and without the presence of bioplastics, using a new approach to evaluate this end-of-life option.
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Affiliation(s)
- Francesca Bandini
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, PC, Italy
| | - Filippo Vaccari
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, PC, Italy
| | - Mariangela Soldano
- Centro Ricerche Produzioni Animali S.p.A. (CRPA), Reggio Emilia, RE, Italy
| | - Sergio Piccinini
- Centro Ricerche Produzioni Animali S.p.A. (CRPA), Reggio Emilia, RE, Italy
| | - Chiara Misci
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, PC, Italy
| | - Gabriele Bellotti
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, PC, Italy
| | - Eren Taskin
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, PC, Italy
| | - Pier Sandro Cocconcelli
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, PC, Italy
| | - Edoardo Puglisi
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, PC, Italy
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Chakraborty A, Rattray JE, Drake SS, Matthews S, Li C, Jørgensen BB, Hubert CRJ. Metabolic responses of thermophilic endospores to sudden heat-induced perturbation in marine sediment samples. Front Microbiol 2022; 13:958417. [PMID: 36033870 PMCID: PMC9411986 DOI: 10.3389/fmicb.2022.958417] [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: 05/31/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Microbially mediated processes in a given habitat tend to be catalyzed by abundant populations that are ecologically adapted to exploit specific environmental characteristics. Typically, metabolic activities of rare populations are limited but may be stimulated in response to acute environmental stressors. Community responses to sudden changes in temperature and pressure can include suppression and activation of different populations, but these dynamics remain poorly understood. The permanently cold ocean floor hosts countless low-abundance microbes including endospores of thermophilic bacteria. Incubating sediments at high temperature resuscitates viable spores, causing the proliferation of bacterial populations. This presents a tractable system for investigating changes in a microbiome's community structure in response to dramatic environmental perturbations. Incubating permanently cold Arctic fjord sediments at 50°C for 216 h with and without volatile fatty acid amendment provoked major changes in community structure. Germination of thermophilic spores from the sediment rare biosphere was tracked using mass spectrometry-based metabolomics, radiotracer-based sulfate reduction rate measurements, and high-throughput 16S rRNA gene sequencing. Comparing community similarity at different intervals of the incubations showed distinct temporal shifts in microbial populations, depending on organic substrate amendment. Metabolite patterns indicated that amino acids and other sediment-derived organics were decomposed by fermentative Clostridia within the first 12–48 h. This fueled early and late phases of exponential increases in sulfate reduction, highlighting the cross-feeding of volatile fatty acids as electron donors for different sulfate-reducing Desulfotomaculia populations. The succession of germinated endospores triggered by sudden exposure to high temperature and controlled by nutrient availability offers a model for understanding the ecological response of dormant microbial communities following major environmental perturbations.
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Affiliation(s)
- Anirban Chakraborty
- Department of Biological Sciences, Idaho State University, Pocatello, ID, United States
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
- *Correspondence: Anirban Chakraborty
| | - Jayne E. Rattray
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Sienna S. Drake
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Stuart Matthews
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Carmen Li
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Bo Barker Jørgensen
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Casey R. J. Hubert
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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Prolonged acetogenic phase and biological succession during anaerobic digestion using swine manure. Folia Microbiol (Praha) 2022; 67:733-745. [PMID: 35460047 DOI: 10.1007/s12223-021-00937-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 11/28/2021] [Indexed: 11/04/2022]
Abstract
In recent years, global warming and the limitation of fossil fuels have been causing the governments of different countries to think about the search for more sustainable fuel sources. Biomethane (CH4) has gained increasing attention in recent years as an alternative option for a sustainable source of energy. Biogas is generated during the anaerobic digestion of organic materials by the metabolism of complex microbial communities in the substrates that make up this digestion. The microbial community evaluation using 16S rDNA metabarcoding in a bench covered pond bioreactor using swine effluent revealed the dominant bacteria belonging to Firmicutes, Proteobacteria, and Bacteroidetes phyla. The methanogenic group was represented by the Euryarchaeota phylum. It was possible to observe that the relative frequency of the methanogenic archaea community decreased with the anaerobic digestion, indicating a biological succession stage. On the other hand, there was a predominant acetogenic diversity in this final stage. These data showed stabilization of biomethane production, although the microbial community of methanogens has drastically reduced in the late process.
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Poirier S, Déjean S, Midoux C, Lê Cao KA, Chapleur O. Integrating independent microbial studies to build predictive models of anaerobic digestion inhibition by ammonia and phenol. BIORESOURCE TECHNOLOGY 2020; 316:123952. [PMID: 32771938 DOI: 10.1016/j.biortech.2020.123952] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/28/2020] [Accepted: 07/31/2020] [Indexed: 05/23/2023]
Abstract
Anaerobic digestion (AD) is a process that can efficiently degrade organic waste into renewable energies. AD failure is however common as the underpinning microbial mechanisms are highly vulnerable to a wide range of inhibitory compounds. Sequencing technologies enable the identification of microbial indicators of digesters inhibition, but existing studies are limited. They used different inocula, substrates, sites and types of reactors and reported different or contradictory indicators. Our aim was to identify a robust signature of microbial indicators of phenol and ammonia inhibitions across four independent AD microbial studies. To identify such signature, we applied an original multivariate integrative method on two in-house studies, then validated our approach by predicting the inhibitory status of samples from two other studies with more than 90% accuracy. Our approach shows how we can efficiently leverage on existing studies to extract reproducible microbial community patterns and predict AD inhibition to improve AD microbial management.
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Affiliation(s)
- Simon Poirier
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92761 Antony, France
| | - Sébastien Déjean
- Toulouse Mathematics Institute, UMR 5219 CNRS, Toulouse University, Toulouse, France
| | - Cédric Midoux
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92761 Antony, France
| | - Kim-Anh Lê Cao
- Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria, Australia
| | - Olivier Chapleur
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92761 Antony, France.
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Rettenmaier R, Schneider M, Munk B, Lebuhn M, Jünemann S, Sczyrba A, Maus I, Zverlov V, Liebl W. Importance of Defluviitalea raffinosedens for Hydrolytic Biomass Degradation in Co-Culture with Hungateiclostridium thermocellum. Microorganisms 2020; 8:E915. [PMID: 32560349 PMCID: PMC7355431 DOI: 10.3390/microorganisms8060915] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/06/2020] [Accepted: 06/11/2020] [Indexed: 01/02/2023] Open
Abstract
Bacterial hydrolysis of polysaccharides is an important step for the production of sustainable energy, for example during the conversion of plant biomass to methane-rich biogas. Previously, Hungateiclostridium thermocellum was identified as cellulolytic key player in thermophilic biogas microbiomes with a great frequency as an accompanying organism. The aim of this study was to physiologically characterize a recently isolated co-culture of H. thermocellum and the saccharolytic bacterium Defluviitalea raffinosedens from a laboratory-scale biogas fermenter. The characterization focused on cellulose breakdown by applying the measurement of cellulose hydrolysis, production of metabolites, and the activity of secreted enzymes. Substrate degradation and the production of volatile metabolites was considerably enhanced when both organisms acted synergistically. The metabolic properties of H. thermocellum have been studied well in the past. To predict the role of D. raffinosedens in this bacterial duet, the genome of D. raffinosedens was sequenced for the first time. Concomitantly, to deduce the prevalence of D. raffinosedens in anaerobic digestion, taxonomic composition and transcriptional activity of different biogas microbiomes were analyzed in detail. Defluviitalea was abundant and metabolically active in reactor operating at highly efficient process conditions, supporting the importance of this organism for the hydrolysis of the raw substrate.
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Affiliation(s)
- Regina Rettenmaier
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (M.S.); (W.L.)
| | - Martina Schneider
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (M.S.); (W.L.)
| | - Bernhard Munk
- Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, Lange Point 6, 85354 Freising, Germany; (B.M.); (M.L.)
| | - Michael Lebuhn
- Department for Quality Assurance and Analytics, Bavarian State Research Center for Agriculture, Lange Point 6, 85354 Freising, Germany; (B.M.); (M.L.)
| | - Sebastian Jünemann
- Center for Biotechnology (CeBiTec), Universitätsstr. 27, 33615 Bielefeld, Germany;
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany;
| | - Alexander Sczyrba
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany;
| | - Irena Maus
- Center for Biotechnology (CeBiTec), Universitätsstr. 27, 33615 Bielefeld, Germany;
| | - Vladimir Zverlov
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (M.S.); (W.L.)
- Institute of Molecular Genetics, RAS, Kurchatov Sq. 2, 123182 Moscow, Russia
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (M.S.); (W.L.)
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13
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Lv XM, Yang M, Dai LR, Tu B, Chang C, Huang Y, Deng Y, Lawson PA, Zhang H, Cheng L, Tang YQ. Zhaonella formicivorans gen. nov., sp. nov., an anaerobic formate-utilizing bacterium isolated from Shengli oilfield, and proposal of four novel families and Moorellales ord. nov. in the phylum Firmicutes. Int J Syst Evol Microbiol 2020; 70:3361-3373. [DOI: 10.1099/ijsem.0.004178] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A novel obligately anaerobic, thermophilic and formate-utilizing bacterium K32T was isolated from Shengli oilfield of China. Cells were straight rods (0.4–0.8 µm × 2.5–8.0 µm), Gram-stain-positive, non-spore-forming and slightly motile. Optimum growth occurred with pH of 7 and 0.5 g l–1 NaCl under temperature of 55–60 °C. Nitrate could be reduced into nitrite, syntrophic formate oxidation to methane and carbon dioxide occurred when co-culturing strain K32T and
Methanothermobacter thermautotrophicus
ΔH. The main cellular fatty acids were iso-C15 : 0 (24.0 %), anteiso-C15 : 0 (21.7 %), C16 : 0 (12.7 %) and C14 : 0 (10.8 %), and the main polar lipid was phosphatidylglycerol. The G+C content of the genomic DNA was 46.3 mol%. The 16S rRNA gene sequence of K32T shared ≤90.4 % of sequence similarity to closest type strains of
Desulfitibacter alkalitolerans
,
Calderihabitans maritimus
and members of the genus
Moorella
. Based on the phenotypic, biochemical and genotypic characterization, Zhaonella formicivorans gen. nov., sp. nov. is proposed with K32T (=CCAM 584T =DSM 107278T=CGMCC1.5297T) as the type strain, which is the first representative of Zhaonellaceae fam. nov. In addition, the order Thermoanaerobacterales and family
Peptococcaceae
were reclassified, and three novel families in the novel order of Moorellales ord. nov. were also proposed.
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Affiliation(s)
- Xiao-meng Lv
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
- Institute of New Energy and Low-Carbon Technology, Sichuan University, Chengdu, 610065, PR China
| | - Min Yang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
- Institute of New Energy and Low-Carbon Technology, Sichuan University, Chengdu, 610065, PR China
| | - Li-rong Dai
- China Collection of Anaerobic microorganisms, Chengdu 610041, PR China
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Bo Tu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Chen Chang
- China Collection of Anaerobic microorganisms, Chengdu 610041, PR China
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Yan Huang
- China Collection of Anaerobic microorganisms, Chengdu 610041, PR China
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Yu Deng
- China Collection of Anaerobic microorganisms, Chengdu 610041, PR China
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Paul A. Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Hui Zhang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
- China Collection of Anaerobic microorganisms, Chengdu 610041, PR China
| | - Yue-qin Tang
- Institute of New Energy and Low-Carbon Technology, Sichuan University, Chengdu, 610065, PR China
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14
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Gagliano MC, Sudmalis D, Pei R, Temmink H, Plugge CM. Microbial Community Drivers in Anaerobic Granulation at High Salinity. Front Microbiol 2020; 11:235. [PMID: 32174895 PMCID: PMC7054345 DOI: 10.3389/fmicb.2020.00235] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/31/2020] [Indexed: 01/24/2023] Open
Abstract
In the recent years anaerobic sludge granulation at elevated salinities in upflow anaerobic sludge blanket (UASB) reactors has been investigated in few engineering based studies, never addressing the microbial community structural role in driving aggregation and keeping granules stability. In this study, the combination of different techniques was applied in order to follow the microbial community members and their structural dynamics in granules formed at low (5 g/L Na+) and high (20 g/L Na+) salinity conditions. Experiments were carried out in four UASB reactors fed with synthetic wastewater, using two experimental set-ups. By applying 16S rRNA gene analysis, the comparison of granules grown at low and high salinity showed that acetotrophic Methanosaeta harundinacea was the dominant methanogen at both salinities, while the dominant bacteria changed. At 5 g/L Na+, cocci chains of Streptoccoccus were developing, while at 20 g/L Na+ members of the family Defluviitaleaceae formed long filaments. By means of Fluorescence in Situ Hybridization (FISH) and Scanning Electron Microscopy (SEM), it was shown that aggregation of Methanosaeta in compact clusters and the formation of filaments of Streptoccoccus and Defluviitaleaceae during the digestion time were the main drivers for the granulation at low and high salinity. Interestingly, when the complex protein substrate (tryptone) in the synthetic wastewater was substituted with single amino acids (proline, leucine and glutamic acid), granules at high salinity (20 g/L Na+) were not formed. This corresponded to a decrease of Methanosaeta relative abundance and a lack of compact clustering, together with disappearance of Defluviitaleaceae and consequent absence of bacterial filaments within the dispersed biomass. In these conditions, a biofilm was growing on the glass wall of the reactor instead, highlighting that a complex protein substrate such as tryptone can contribute to granules formation at elevated salinity.
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Affiliation(s)
- Maria Cristina Gagliano
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands.,Wetsus - European Centre of Excellence for Sustainable Water Technology, Leeuwarden, Netherlands
| | - Dainis Sudmalis
- Department of Environmental Technology, Wageningen University & Research, Wageningen, Netherlands
| | - Ruizhe Pei
- Wetsus - European Centre of Excellence for Sustainable Water Technology, Leeuwarden, Netherlands
| | - Hardy Temmink
- Wetsus - European Centre of Excellence for Sustainable Water Technology, Leeuwarden, Netherlands.,Department of Environmental Technology, Wageningen University & Research, Wageningen, Netherlands
| | - Caroline M Plugge
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands.,Wetsus - European Centre of Excellence for Sustainable Water Technology, Leeuwarden, Netherlands
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15
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A xylan-degrading thermophilic and obligate anaerobe Xylanivirga thermophila gen. nov., sp. nov., isolated from an anammox dominant wastewater treatment plant, and proposal of Xylanivirgaceae fam. nov. Anaerobe 2020; 61:102075. [DOI: 10.1016/j.anaerobe.2019.102075] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 07/10/2019] [Accepted: 07/17/2019] [Indexed: 01/29/2023]
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16
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Description of Biomaibacter acetigenes gen. nov., sp. nov., and proposal of Thermosediminibacterales ord. nov. containing two novel families of Tepidanaerobacteraceae fam. nov. and Thermosediminibacteraceae fam. nov. Int J Syst Evol Microbiol 2019; 69:3891-3902. [DOI: 10.1099/ijsem.0.003701] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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17
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Tan L, Nishimura H, Wang YF, Sun ZY, Tang YQ, Kida K, Morimura S. Effect of organic loading rate on thermophilic methane fermentation of stillage eluted from ethanol fermentation of waste paper and kitchen waste. J Biosci Bioeng 2019; 127:582-588. [DOI: 10.1016/j.jbiosc.2018.10.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/02/2018] [Accepted: 10/09/2018] [Indexed: 10/27/2022]
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18
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Multidisciplinary involvement and potential of thermophiles. Folia Microbiol (Praha) 2018; 64:389-406. [PMID: 30386965 DOI: 10.1007/s12223-018-0662-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/25/2018] [Indexed: 12/15/2022]
Abstract
The full biotechnological exploitation of thermostable enzymes in industrial processes is necessary for their commercial interest and industrious value. The heat-tolerant and heat-resistant enzymes are a key for efficient and cost-effective translation of substrates into useful products for commercial applications. The thermophilic, hyperthermophilic, and microorganisms adapted to extreme temperatures (i.e., low-temperature lovers or psychrophiles) are a rich source of thermostable enzymes with broad-ranging thermal properties, which have structural and functional stability to underpin a variety of technologies. These enzymes are under scrutiny for their great biotechnological potential. Temperature is one of the most critical parameters that shape microorganisms and their biomolecules for stability under harsh environmental conditions. This review describes in detail the sources of thermophiles and thermostable enzymes from prokaryotes and eukaryotes (microbial cell factories). Furthermore, the review critically examines perspectives to improve modern biocatalysts, its production and performance aiming to increase their value for biotechnology through higher standards, specificity, resistance, lowing costs, etc. These thermostable and thermally adapted extremophilic enzymes have been used in a wide range of industries that span all six enzyme classes. Thus, in particular, target of this review paper is to show the possibility of both high-value-low-volume (e.g., fine-chemical synthesis) and low-value-high-volume by-products (e.g., fuels) by minimizing changes to current industrial processes.
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19
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Zhang X, Tu B, Dai LR, Lawson PA, Zheng ZZ, Liu LY, Deng Y, Zhang H, Cheng L. Petroclostridium xylanilyticum gen. nov., sp. nov., a xylan-degrading bacterium isolated from an oilfield, and reclassification of clostridial cluster III members into four novel genera in a new Hungateiclostridiaceae fam. nov. Int J Syst Evol Microbiol 2018; 68:3197-3211. [DOI: 10.1099/ijsem.0.002966] [Citation(s) in RCA: 160] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Xue Zhang
- 1Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Bo Tu
- 1Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Li-rong Dai
- 1Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Paul A. Lawson
- 2Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Zhen-zhen Zheng
- 1Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Lai-Yan Liu
- 1Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Yu Deng
- 1Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Hui Zhang
- 1Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Lei Cheng
- 1Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
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20
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Wang C, Huang Y, Li L, Guo J, Wu Z, Deng Y, Dai L, Ma S. Lactobacillus panisapium sp. nov., from honeybee Apis cerana bee bread. Int J Syst Evol Microbiol 2018; 68:703-708. [PMID: 29458462 PMCID: PMC5882092 DOI: 10.1099/ijsem.0.002538] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A novel facultatively anaerobic, Gram-stain-positive, non-motile, non-spore-forming, catalase-negative bacterium of the genus Lactobacillus, designated strain Bb 2-3T, was isolated from bee bread of Apis cerana collected from a hive in Kunming, China. The strain was regular rod-shaped. Optimal growth occurred at 37 °C, pH 6.5 with 5.0 g l−1 NaCl. The predominant fatty acids were C18 : 1ω9c, C16 : 0 and C19 : 0 iso. Respiratory quinones were not detected. Seven glycolipids, three lipids, phosphatidylglycerol and diphosphatidylglycerol were detected. The peptidoglycan type A4α l-Lys-d-Asp was determined. Strain Bb 2-3T was closely related to Lactobacillus bombicola DSM 28793T, Lactobacillus apis LMG 26964T and Lactobacillus helsingborgensis DSM 26265T, with 97.8, 97.6 and 97.0 % 16S rRNA gene sequence similarity, respectively. A comparison of two housekeeping genes, rpoA and pheS, revealed that strain Bb 2-3T was well separated from the reference strains of species of the genus Lactobacillus. The average nucleotide identity between strain Bb 2-3T and the type strains of closely related species was lower than the 95–96 % threshold value for delineation of genomic prokaryotic species. The G+C content of the genomic DNA of strain Bb 2-3T was 37.4 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic analyses, strain Bb 2-3T is proposed to represent a novel species of the genus Lactobacillus, for which we propose the name Lactobacillus panisapium sp. nov. The type strain is Bb 2-3T (=DSM 102188T=ACCC 19955T).
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Affiliation(s)
- Cong Wang
- Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
- College of Light Industry, Textile and Food Engineering, Sichuan University, Chengdu 610065, PR China
- Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture, Chengdu 610041, PR China
| | - Yan Huang
- Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
- Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture, Chengdu 610041, PR China
| | - Li Li
- College of Light Industry, Textile and Food Engineering, Sichuan University, Chengdu 610065, PR China
| | - Jun Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, PR China
| | - Zhengyun Wu
- College of Light Industry, Textile and Food Engineering, Sichuan University, Chengdu 610065, PR China
| | - Yu Deng
- Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
- Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture, Chengdu 610041, PR China
| | - Lirong Dai
- Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
- Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture, Chengdu 610041, PR China
| | - Shichun Ma
- Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
- Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture, Chengdu 610041, PR China
- *Correspondence: Shichun Ma,
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21
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Saad S, Bhatnagar S, Tegetmeyer HE, Geelhoed JS, Strous M, Ruff SE. Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate-reducing benthic microbial populations. Environ Microbiol 2017; 19:4866-4881. [PMID: 28836729 PMCID: PMC5763382 DOI: 10.1111/1462-2920.13895] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 08/07/2017] [Accepted: 08/15/2017] [Indexed: 12/01/2022]
Abstract
For the anaerobic remineralization of organic matter in marine sediments, sulfate reduction coupled to fermentation plays a key role. Here, we enriched sulfate‐reducing/fermentative communities from intertidal sediments under defined conditions in continuous culture. We transiently exposed the cultures to oxygen or nitrate twice daily and investigated the community response. Chemical measurements, provisional genomes and transcriptomic profiles revealed trophic networks of microbial populations. Sulfate reducers coexisted with facultative nitrate reducers or aerobes enabling the community to adjust to nitrate or oxygen pulses. Exposure to oxygen and nitrate impacted the community structure, but did not suppress fermentation or sulfate reduction as community functions, highlighting their stability under dynamic conditions. The most abundant sulfate reducer in all cultures, related to Desulfotignum balticum, appeared to have coupled both acetate‐ and hydrogen oxidation to sulfate reduction. We describe a novel representative of the widespread uncultured candidate phylum Fermentibacteria (formerly candidate division Hyd24‐12). For this strictly anaerobic, obligate fermentative bacterium, we propose the name ‘USabulitectum silens’ and identify it as a partner of sulfate reducers in marine sediments. Overall, we provide insights into the function of fermentative, as well as sulfate‐reducing microbial communities and their adaptation to a dynamic environment.
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Affiliation(s)
- Sainab Saad
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Srijak Bhatnagar
- UC Davis Genome Center, University of California Davis, Davis, CA, USA
| | - Halina E Tegetmeyer
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Institute for Genome Research and Systems Biology, Center for Biotechnology, University of Bielefeld, Bielefeld, Germany
| | - Jeanine S Geelhoed
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Department of Ecosystem Studies, NIOZ Royal Netherlands Institute for Sea Research, Yerseke, The Netherlands
| | - Marc Strous
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Institute for Genome Research and Systems Biology, Center for Biotechnology, University of Bielefeld, Bielefeld, Germany.,Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - S Emil Ruff
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Department of Geoscience, University of Calgary, Calgary, AB, Canada
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