scholarly journals Three Novel Clostridia Isolates Produce n-Caproate and iso-Butyrate from Lactate: Comparative Genomics of Chain-Elongating Bacteria

2020 ◽  
Vol 8 (12) ◽  
pp. 1970
Author(s):  
Bin Liu ◽  
Denny Popp ◽  
Nicolai Müller ◽  
Heike Sträuber ◽  
Hauke Harms ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Energy Conservation ◽  
Core Genome ◽  
Anaerobic Fermentation ◽  
Batch Cultivation ◽  
Chain Elongation ◽  
Hydrogen Formation ◽  
Lactate Oxidation ◽  
Platform Chemicals ◽  
Genome Heterogeneity

The platform chemicals n-caproate and iso-butyrate can be produced by anaerobic fermentation from agro-industrial residues in a process known as microbial chain elongation. Few lactate-consuming chain-elongating species have been isolated and knowledge on their shared genetic features is still limited. Recently we isolated three novel clostridial strains (BL-3, BL-4, and BL-6) that convert lactate to n-caproate and iso-butyrate. Here, we analyzed the genetic background of lactate-based chain elongation in these isolates and other chain-elongating species by comparative genomics. The three strains produced n-caproate, n-butyrate, iso-butyrate, and acetate from lactate, with the highest proportions of n-caproate (18%) for BL-6 and of iso-butyrate (23%) for BL-4 in batch cultivation at pH 5.5. They show high genomic heterogeneity and a relatively small core-genome size. The genomes contain highly conserved genes involved in lactate oxidation, reverse β-oxidation, hydrogen formation and either of two types of energy conservation systems (Rnf and Ech). Including genomes of another eleven experimentally validated chain-elongating strains, we found that the chain elongation-specific core-genome encodes the pathways for reverse β-oxidation, hydrogen formation and energy conservation, while displaying substantial genome heterogeneity. Metabolic features of these isolates are important for biotechnological applications in n-caproate and iso-butyrate production.

scholarly journals Lactate-based microbial chain elongation for n-caproate and iso-butyrate production: genomic and metabolic features of three novel Clostridia isolates

2020 ◽  
Author(s):  
Bin Liu ◽  
Denny Popp ◽  
Heike Sträuber ◽  
Hauke Harms ◽  
Sabine Kleinsteuber
Keyword(s):  
Energy Conservation ◽  
Genetic Background ◽  
Core Genome ◽  
Anaerobic Fermentation ◽  
Gene Families ◽  
Chain Elongation ◽  
Hydrogen Formation ◽  
Lactate Oxidation ◽  
Coa Transferase ◽  
Butyrate Production

Abstract Background The platform chemicals n-caproate and iso-butyrate can be produced by anaerobic fermentation from agro-industrial residues in a process known as microbial chain elongation. A few chain-elongating species have been discovered to utilize lactate and used to study the physiology of lactate-based chain elongation in pure cultures. Recently we isolated three novel clostridial species (strains BL-3, BL-4 and BL-6) that convert lactate to n-caproate and iso-butyrate. Here, we analyzed the genetic background of lactate-based chain elongation in these strains and other chain-elongating species by comparative genomics. Results All three strains produced n-caproate and iso-butyrate from lactate, with the highest proportions of n-caproate (18%) for BL-6 and iso-butyrate (23%) for BL-4 in batch cultivation at pH 5.5. The strains are suggested to represent three novel species based on low similarities with their closest described relatives. The three genomes show low conservation of organization and a relatively small core-genome size (504 out of 6,654 gene families). Including data of another eleven experimentally validated chain-elongating strains, we found that the chain elongation-specific core-genome harbors genes involved in reverse β-oxidation, hydrogen formation and energy conservation, displaying substantial genome heterogeneity. The three new isolates contain the genes for lactate oxidation and a gene cluster encoding enzymes of reverse β-oxidation, including the CoA transferase for the formation of n-caproate. Our analysis gave no hints on the isomerization pathway for iso-butyrate formation. An operon encoding the Rnf complex was found in BL-3 and BL-4 but not in BL-6, which may instead use the Ech hydrogenase complex for energy conservation. BL-3 and BL-6 were predicted to have genes encoding both the BCD/EtfAB complex and the LDH/EtfAB complex for energy coupling. Conclusions The genetic background of lactate-based chain elongation was confirmed in three novel Clostridia species that convert lactate to n-caproate and iso-butyrate. They contain highly conserved genes involved in reverse β-oxidation, hydrogen formation and either of two types of energy conservation systems (Rnf and Ech). Further research is needed to elucidate the mechanism of iso-butyrate formation in these strains. Features of the three isolates may be interesting for further applications in n-caproate and iso-butyrate production.

Isobutyrate biosynthesis via methanol chain elongation: converting organic wastes to platform chemicals

2016 ◽  
Vol 92 (6) ◽  
pp. 1370-1379 ◽  
Author(s):  
Wei-Shan Chen ◽  
Shengle Huang ◽  
David PBTB Strik ◽  
Cees JN Buisman
Keyword(s):  
Organic Wastes ◽  
Chain Elongation ◽  
Platform Chemicals

Identification of a Conserved Core Genome with Group-Specific Genes from Comparative Genomics of Ten Different Candidatus Phytoplasma Strains

2014 ◽  
Vol 162 (10) ◽  
pp. 650-659 ◽  
Author(s):  
Qiang Wang ◽  
Ya Guo ◽  
Nan Wang ◽  
Yan Li ◽  
Wang Chen ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Core Genome ◽  
Conserved Core

scholarly journals Virulence and antibiotic resistance plasticity of Arcobacter butzleri: insights on the genomic diversity of an emerging human pathogen

2019 ◽  
Author(s):  
Joana Isidro ◽  
Susana Ferreira ◽  
Miguel Pinto ◽  
Fernanda Domingues ◽  
Mónica Oleastro ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Comparative Genomics ◽  
Core Genome ◽  
Human Pathogen ◽  
Genome Diversity ◽  
Pathogenic Potential ◽  
The Core ◽  
Pan Genome ◽  
Arcobacter Butzleri ◽  
Genome Scale

AbstractArcobacter butzleri is a food and waterborne bacteria and an emerging human pathogen, frequently displaying a multidrug resistant character. Still, no comprehensive genome-scale comparative analysis has been performed so far, which has limited our knowledge on A. butzleri diversification and pathogenicity. Here, we performed a deep genome analysis of A. butzleri focused on decoding its core- and pan-genome diversity and specific genetic traits underlying its pathogenic potential and diverse ecology. In total, 49 A. butzleri strains (collected from human, animal, food and environmental sources) were screened.A. butzleri (genome size 2.07-2.58 Mbp) revealed a large open pan-genome with 7474 genes (about 50% being singletons) and a small core-genome with 1165 genes. The core-genome is highly diverse (≥55% of the core genes presenting at least 40/49 alleles), being enriched with genes associated with housekeeping functions. In contrast, the accessory genome presented a high proportion of loci with an unknown function, also being particularly overrepresented by genes associated with defence mechanisms. A. butzleri revealed a plastic virulome (including newly identified determinants), marked by the differential presence of multiple adaptation-related virulence factors, such as the urease cluster ureD(AB)CEFG (phenotypically confirmed), the hypervariable hemagglutinin-encoding hecA, a putative type I secretion system (T1SS) harboring another agglutinin potentially related to adherence and a novel VirB/D4 T4SS likely linked to interbacterial competition and cytotoxicity. In addition, A. butzleri harbors a large repertoire of efflux pumps (EPs) (ten “core” and nine differentially present) and other antibiotic resistant determinants. We provide the first description of a genetic determinant of macrolides resistance in A. butzleri, by associating the inactivation of a TetR repressor (likely regulating an EP) with erythromycin resistance. Fluoroquinolones resistance correlated with the Thr-85-Ile substitution in GyrA and ampicillin resistance was linked to an OXA-15-like β-lactamase. Remarkably, by decoding the polymorphism pattern of the porin- and adhesin-encoding main antigen PorA, this study strongly supports that this pathogen is able to exchange porA as a whole and/or hypervariable epitope-encoding regions separately, leading to a multitude of chimeric PorA presentations that can impact pathogen-host interaction during infection. Ultimately, our unprecedented screening of short sequence repeats detected potential phase-variable genes related to adaptation and host/environment interaction, such as lipopolysaccharide modification and motility/chemotaxis, suggesting that phase variation likely modulate A. butzleri key adaptive functions.In summary, this study constitutes a turning point on A. butzleri comparative genomics revealing that this human gastrointestinal pathogen is equipped with vast virulence and antibiotic resistance arsenals, which, coupled with its remarkable core- and pan-genome diversity, opens a multitude of phenotypic fingerprints for environmental/host adaptation and pathogenicity.IMPACT STATEMENTDiarrhoeal diseases are the most common cause of human illness caused by foodborne hazards, but the surveillance of diarrhoeal diseases is biased towards the most commonly searched infectious agents (namely Campylobacter jejuni and C. coli). In fact, other less studied pathogens are frequently found as the etiological agent when refined non-selective culture conditions are applied. A hallmark example is the diarrhoeal-causing Arcobacter butzleri which, despite being also associated with extra-intestinal diseases, such as bacteremia in humans and mastitis in animals, and displaying high rates of antibiotic resistance, has not yet been profoundly investigated regarding its epidemiology, diversity and pathogenicity. To overcome the general lack of knowledge on A. butzleri comparative genomics, we provide the first comprehensive genome-scale analysis of A. butzleri focused on exploring the intraspecies virulome content and diversity, resistance determinants, as well as how this pathogen shapes its genome towards ecological adaptation and host invasion. The unveiled scenario of A. butzleri rampant diversity and plasticity reinforces the pathogenic potential of this food and waterborne hazard, while opening multiple research lines that will certainly contribute to the future development of more robust species-oriented diagnostics and molecular surveillance of A. butzleri.DATA SUMMARYA. butzleri raw sequence reads generated in the present study were deposited in the European Nucleotide Archive (ENA) (BioProject PRJEB34441). The assembled contigs (.fasta and .gbk files), the nucleotide sequences of the predicted transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA) (.ffn files) and the respective amino acid sequences of the translated CDS sequences (.faa files) are available at http://doi.org/10.5281/zenodo.3434222. Detailed ENA accession numbers, as well as the draft genome statistics are described in Table S1.

scholarly journals Production of a newly discovered PHA family member with an isobutyrate-fed enrichment culture

2022 ◽  
Author(s):  
Chris M. Vermeer ◽  
Larissa J. Bons ◽  
Robbert Kleerebezem
Keyword(s):  
Family Member ◽  
Metabolic Pathways ◽  
Volatile Fatty Acids ◽  
Anaerobic Fermentation ◽  
Enrichment Culture ◽  
Dry Weight ◽  
Chain Elongation ◽  
Structural Isomer ◽  
Distinct Character ◽  
Pha Production

Abstract Using microbial enrichment cultures for the production of waste-derived polyhydroxyalkanoates (PHAs) is a promising technology to recover secondary resources. Volatile fatty acids (VFAs) form the preferred substrate for PHA production. Isobutyrate is a VFA appearing in multiple waste valorization routes, such as anaerobic fermentation, chain elongation, and microbial electrosynthesis, but has never been assessed individually on its PHA production potential. This research investigates isobutyrate as sole carbon source for a microbial enrichment culture in comparison to its structural isomer butyrate. The results reveal that the enrichment of isobutyrate has a very distinct character regarding microbial community development, PHA productivity, and even PHA composition. Although butyrate is a superior substrate in almost every aspect, this research shows that isobutyrate-rich waste streams have a noteworthy PHA-producing potential. The main finding is that the dominant microorganism, a Comamonas sp., is linked to the production of a unique PHA family member, poly(3-hydroxyisobutyrate) (PHiB), up to 37% of the cell dry weight. This is the first scientific report identifying microbial PHiB production, demonstrating that mixed microbial communities can be a powerful tool for discovery of new metabolic pathways and new types of polymers. Key points • PHiB production is a successful storage strategy in an isobutyrate-fed SBR • Isomers isobutyrate and butyrate reveal a very distinct PHA production behavior • Enrichments can be a tool for discovery of new metabolic pathways and polymers Graphical abstract

Effect of ultrasonic pretreatment on chain elongation of saccharified residue from food waste by anaerobic fermentation

2021 ◽  
Vol 268 ◽  
pp. 115936 ◽  
Author(s):  
Hongzhi Ma ◽  
Yujia Lin ◽  
Yong Jin ◽  
Ming Gao ◽  
Hongai Li ◽  
...  
Keyword(s):  
Food Waste ◽  
Anaerobic Fermentation ◽  
Chain Elongation ◽  
Ultrasonic Pretreatment

scholarly journals Comparative genomics defines the core genome of the growing N4-like phage genus and identifies N4-like Roseophage specific genes

2014 ◽  
Vol 5 ◽  
Author(s):  
Jacqueline Z.-M. Chan ◽  
Andrew D. Millard ◽  
Nicholas H. Mann ◽  
Hendrik Schäfer
Keyword(s):  
Comparative Genomics ◽  
Core Genome ◽  
The Core

scholarly journals Organic waste as a sustainable feedstock for platform chemicals

2017 ◽  
Vol 202 ◽  
pp. 175-195 ◽  
Author(s):  
M. Coma ◽  
E. Martinez-Hernandez ◽  
F. Abeln ◽  
S. Raikova ◽  
J. Donnelly ◽  
...  
Keyword(s):  
Algal Blooms ◽  
Organic Waste ◽  
Anaerobic Fermentation ◽  
Biofuel Production ◽  
High Complexity ◽  
Waste Streams ◽  
Platform Chemicals ◽  
Hydrothermal Processes ◽  
By Products ◽  
Substrate Types

Biorefineries have been established since the 1980s for biofuel production, and there has been a switch lately from first to second generation feedstocks in order to avoid the food versus fuel dilemma. To a lesser extent, many opportunities have been investigated for producing chemicals from biomass using by-products of the present biorefineries, simple waste streams. Current facilities apply intensive pre-treatments to deal with single substrate types such as carbohydrates. However, most organic streams such as municipal solid waste or algal blooms present a high complexity and variable mixture of molecules, which makes specific compound production and separation difficult. Here we focus on flexible anaerobic fermentation and hydrothermal processes that can treat complex biomass as a whole to obtain a range of products within an integrated biorefinery concept.

scholarly journals Evolutionary Dynamics Based on Comparative Genomics of Pathogenic Escherichia coli Lineages Harboring Polyketide Synthase (pks) Island

mBio ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Arya Suresh ◽  
Sabiha Shaik ◽  
Ramani Baddam ◽  
Amit Ranjan ◽  
Shamsul Qumar ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Maximum Likelihood ◽  
High Throughput ◽  
Core Genome ◽  
Polyketide Synthase ◽  
Clinical Implications ◽  
Data Set ◽  
Content Type ◽  
E Coli ◽  
The Core

ABSTRACT The genotoxin colibactin is a secondary metabolite produced by the polyketide synthase (pks) island harbored by extraintestinal pathogenic E. coli (ExPEC) and other members of the Enterobacteriaceae that has been increasingly reported to have critical implications in human health. The present study entails a high-throughput whole-genome comparison and phylogenetic analysis of such pathogenic E. coli isolates to gain insights into the patterns of distribution, horizontal transmission, and evolution of the island. For the current study, 23 pks-positive ExPEC genomes were newly sequenced, and their virulome and resistome profiles indicated a preponderance of virulence encoding genes and a reduced number of genes for antimicrobial resistance. In addition, 4,090 E. coli genomes from the public domain were also analyzed for large-scale screening for pks-positive genomes, out of which a total of 530 pks-positive genomes were studied to understand the subtype-based distribution pattern(s). The pks island showed a significant association with the B2 phylogroup (82.2%) and a high prevalence in sequence type 73 (ST73; n = 179) and ST95 (n = 110) and the O6:H1 (n = 110) serotype. Maximum-likelihood (ML) phylogeny of the core genome and intergenic regions (IGRs) of the ST95 model data set, which was selected because it had both pks-positive and pks-negative genomes, displayed clustering in relation to their carriage of the pks island. Prevalence patterns of genes encoding RM systems in the pks-positive and pks-negative genomes were also analyzed to determine their potential role in pks island acquisition and the maintenance capability of the genomes. Further, the maximum-likelihood phylogeny based on the core genome and pks island sequences from 247 genomes with an intact pks island demonstrated horizontal gene transfer of the island across sequence types and serotypes, with few exceptions. This study vitally contributes to understanding of the lineages and subtypes that have a higher propensity to harbor the pks island-encoded genotoxin with possible clinical implications. IMPORTANCE Extraintestinal pathologies caused by highly virulent strains of E. coli amount to clinical implications with high morbidity and mortality rates. Pathogenic E. coli strains are evolving with the horizontal acquisition of mobile genetic elements, including pathogenicity islands such as the pks island, which produces the genotoxin colibactin, resulting in severe clinical outcomes, including colorectal cancer progression. The current study encompasses high-throughput comparative genomics and phylogenetic analyses to address the questions pertaining to the acquisition and evolution pattern of the genomic island in different E. coli subtypes. It is crucial to gain insights into the distribution, transfer, and maintenance of pathogenic islands, as they harbor multiple virulence genes involved in pathogenesis and clinical implications of the infection.

scholarly journals Effect of Oxygen Contamination on Propionate and Caproate Formation in Anaerobic Fermentation

2021 ◽  
Vol 9 ◽  
Author(s):  
Flávio C. F. Baleeiro ◽  
Magda S. Ardila ◽  
Sabine Kleinsteuber ◽  
Heike Sträuber
Keyword(s):  
Metabolic Networks ◽  
Community Dynamics ◽  
Bubble Column ◽  
Anaerobic Fermentation ◽  
Product Formation ◽  
Chain Elongation ◽  
Strictly Anaerobic ◽  
Production Rates ◽  
Air Contamination ◽  
Butyrate Production

Mixed microbial cultures have become a preferred choice of biocatalyst for chain elongation systems due to their ability to convert complex substrates into medium-chain carboxylates. However, the complexity of the effects of process parameters on the microbial metabolic networks is a drawback that makes the task of optimizing product selectivity challenging. Here, we studied the effects of small air contaminations on the microbial community dynamics and the product formation in anaerobic bioreactors fed with lactate, acetate and H2/CO2. Two stirred tank reactors and two bubble column reactors were operated with H2/CO2 gas recirculation for 139 and 116 days, respectively, at pH 6.0 and 32°C with a hydraulic retention time of 14 days. One reactor of each type had periods with air contamination (between 97 ± 28 and 474 ± 33 mL O2 L−1 d−1, lasting from 4 to 32 days), while the control reactors were kept anoxic. During air contamination, production of n-caproate and CH4 was strongly inhibited, whereas no clear effect on n-butyrate production was observed. In a period with detectable O2 concentrations that went up to 18%, facultative anaerobes of the genus Rummeliibacillus became predominant and only n-butyrate was produced. However, at low air contamination rates and with O2 below the detection level, Coriobacteriia and Actinobacteria gained a competitive advantage over Clostridia and Methanobacteria, and propionate production rates increased to 0.8–1.8 mmol L−1 d−1 depending on the reactor (control reactors 0.1–0.8 mmol L−1 d−1). Moreover, i-butyrate production was observed, but only when Methanobacteria abundances were low and, consequently, H2 availability was high. After air contamination stopped completely, production of n-caproate and CH4 recovered, with n-caproate production rates of 1.4–1.8 mmol L−1 d−1 (control 0.7–2.1 mmol L−1 d−1). The results underline the importance of keeping strictly anaerobic conditions in fermenters when consistent n-caproate production is the goal. Beyond that, micro-aeration should be further tested as a controllable process parameter to shape the reactor microbiome. When odd-chain carboxylates are desired, further studies can develop strategies for their targeted production by applying micro-aerobic conditions.

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