Our knowledge about the gut microbiota of pigs is still scarce, despite the importance of these animals for biomedical research and agriculture. Here, we present a collection of cultured bacteria ...from the pig gut, including 110 species across 40 families and nine phyla. We provide taxonomic descriptions for 22 novel species and 16 genera. Meta-analysis of 16S rRNA amplicon sequence data and metagenome-assembled genomes reveal prevalent and pig-specific species within Lactobacillus, Streptococcus, Clostridium, Desulfovibrio, Enterococcus, Fusobacterium, and several new genera described in this study. Potentially interesting functions discovered in these organisms include a fucosyltransferase encoded in the genome of the novel species Clostridium porci, and prevalent gene clusters for biosynthesis of sactipeptide-like peptides. Many strains deconjugate primary bile acids in in vitro assays, and a Clostridium scindens strain produces secondary bile acids via dehydroxylation. In addition, cells of the novel species Bullifex porci are coccoidal or spherical under the culture conditions tested, in contrast with the usual helical shape of other members of the family Spirochaetaceae. The strain collection, called 'Pig intestinal bacterial collection' (PiBAC), is publicly available at www.dsmz.de/pibac and opens new avenues for functional studies of the pig gut microbiota.
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Microalgae are a group of microorganisms considered to be a potential source of next-generation biofuel owing to high photosynthetic rate. However, biofuel compounds including lipid, ...carbohydrate, and hydrogen are not sufficiently produced by microalgae under normal conditions; therefore economical viability of microalgal biofuel production has not reached the ultimate stage of commercial viability. In order to overcome the above limitation, various stress conditions have been applied on microalgae to boost lipid, carbohydrate and hydrogen production. Even though stress conditions increases the production of biofuel compounds, microalgae growth is severely affected. In this regard, a two-stage cultivation mode wherein first stage involving high biomass production under media optimized heterotrophic condition and second stage involving lipid, carbohydrate and hydrogen accumulation under stress integrated phototrophic mode is considered as a potential route for biofuel production in microalgae. The present review critically evaluates various two-stage strategies adopted in microalgal biofuel production by comparing lipid, carbohydrate and hydrogen productivities with that of single stage cultivation. In addition, advantages of two-stage cultivation including co-product generation, less bacterial contamination, improved biodiesel quality, auto-flocculation, and bioremediation potential are also discussed. Finally, the paper summarizes the two-stage cultivation modes by identifying the bottlenecks and suggesting the future potentialities of the process.
Clostridium scindens is a gut microbe capable of removing the side-chain of cortisol, forming 11β-hydroxyandrostenedione. A cortisol-inducible operon (desABCD) was previously identified in C. ...scindens ATCC 35704 by RNA-Seq. The desC gene was shown to encode a cortisol 20α-hydroxysteroid dehydrogenase (20α-HSDH). The desD encodes a protein annotated as a member of the major facilitator family, predicted to function as a cortisol transporter. The desA and desB genes are annotated as N-terminal and C-terminal transketolases, respectively. We hypothesized that the DesAB forms a complex and has steroid-17,20-desmolase activity. We cloned the desA and desB genes from C. scindens ATCC 35704 in pETDuet for overexpression in Escherichia coli. The purified recombinant DesAB was determined to be a 142 ± 5.4 kDa heterotetramer. We developed an enzyme-linked continuous spectrophotometric assay to quantify steroid-17,20-desmolase. This was achieved by coupling DesAB-dependent formation of 11β-hydroxyandrostenedione with the NADPH-dependent reduction of the steroid 17-keto group by a recombinant 17β-HSDH from the filamentous fungus, Cochliobolus lunatus. The pH optimum for the coupled assay was 7.0 and kinetic constants using cortisol as substrate were Km of 4.96 ± 0.57 µM and kcat of 0.87 ± 0.076 min−1. Substrate-specificity studies revealed that rDesAB recognized substrates regardless of 11β-hydroxylation, but had an absolute requirement for 17,21-dihydroxy 20-ketosteroids.
Bacteria in the gut can modulate the availability and efficacy of therapeutic drugs. However, the systematic mapping of the interactions between drugs and bacteria has only started recently
and the ...main underlying mechanism proposed is the chemical transformation of drugs by microorganisms (biotransformation). Here we investigated the depletion of 15 structurally diverse drugs by 25 representative strains of gut bacteria. This revealed 70 bacteria-drug interactions, 29 of which had not to our knowledge been reported before. Over half of the new interactions can be ascribed to bioaccumulation; that is, bacteria storing the drug intracellularly without chemically modifying it, and in most cases without the growth of the bacteria being affected. As a case in point, we studied the molecular basis of bioaccumulation of the widely used antidepressant duloxetine by using click chemistry, thermal proteome profiling and metabolomics. We find that duloxetine binds to several metabolic enzymes and changes the metabolite secretion of the respective bacteria. When tested in a defined microbial community of accumulators and non-accumulators, duloxetine markedly altered the composition of the community through metabolic cross-feeding. We further validated our findings in an animal model, showing that bioaccumulating bacteria attenuate the behavioural response of Caenorhabditis elegans to duloxetine. Together, our results show that bioaccumulation by gut bacteria may be a common mechanism that alters drug availability and bacterial metabolism, with implications for microbiota composition, pharmacokinetics, side effects and drug responses, probably in an individual manner.
► Lipase catalyzed cinnamyl acetate synthesis from cinnamyl alcohol and vinyl acetate. ► Candida Antarctica B supported polyacrylic resin (Novozym 435) is the best. ► With 1:2mol ratio of alcohol to ...acetate at 40°C, conversion of 96% in 1h is obtained. ► Cinnamyl alcohol deactivates the enzyme at high concentration. ► Reaction follows the ternary complex mechanism.
Cinnamyl acetate is used as flavor and fragrance ingredient in food and cosmetic industries. This work focuses on the synthesis of cinnamyl acetate via lipase catalyzed transesterification of cinnamyl alcohol with vinyl acetate in non-aqueous medium. Among the different immobilized lipases employed, Novozym 435 was found to be the best catalyst in toluene as solvent. The effects of various parameters were studied systematically. With a mole ratio of 1:2 of cinnamyl alcohol to vinyl acetate and 10mg catalyst, 96% conversion was obtained in 1h at 40°C. The ternary complex mechanism with inhibition by cinnamyl alcohol was found to fit the data well. The kinetics of the reaction was studied by using non-linear regression analysis. Enzymatic synthesis of cinnamyl acetate is an efficient process vis-à-vis chemical catalysis.
Members of the gastrointestinal microbiota are known to convert glucocorticoids to androstanes, which are subsequently converted to potent androgens by other members of the gut microbiota or host ...tissues. Butyricicoccus desmolans and Clostridium cadaveris have previously been reported for steroid-17,20-desmolase and 20β-hydroxysteroid dehydrogenase (HSDH) activities that are responsible for androstane formation from cortisol; however, the genes encoding these enzymes have yet to be reported. In this work, we identified and located a gene encoding 20β-HSDH in both B. desmolans and C. cadaveris. The 20β-HSDH of B. desmolans was heterologously overexpressed and purified from Escherichia coli. The enzyme was determined to be a homotetramer with subunit molecular mass of 33.8 ± 3.7 kDa. The r20β-HSDH displayed pH optimum in the reductive direction at pH 9.0 and in the oxidative direction at pH 7.0–7.5 with (20β-dihydro)cortisol and NAD(H) as substrates. Cortisol is the preferred substrate with Km, 0.80 ± 0.06 μM; Vmax, 30.36 ± 1.97 μmol·min−1; Kcat, 607 ± 39 μmol·μM−1·min−1; Kcat/Km, 760 ± 7.67. Phylogenetic analysis of the 20β-HSDH from B. desmolans suggested that the 20β-HSDH is found in several Bifidobacterium spp., one of which was shown to express 20β-HSDH activity. Notably, we also identified a novel steroid-17,20-desmolase-elaborating bacterium, Propionimicrobium lymphophilum, a normal inhabitant of the urinary tract.
The cement industry generates a substantial amount of gaseous pollutants that cannot be treated efficiently and economically using standard techniques. Microalgae, a promising bioremediation and ...biodegradation agent used as feedstock for biofuel production, can be used for the biotreatment of cement flue gas. In specific, components of cement flue gas such as carbon dioxide, nitrogen, and sulfur oxides are shown to serve as nutrients for microalgae. Microalgae also have the capacity to sequestrate heavy metals present in cement kiln dust, adding further benefits. This work provides an extensive overview of multiple approaches taken in the inclusion of microalgae biofuel production in the cement sector. In addition, factors influencing the production of microalgal biomass are also described in such an integrated plant. In addition, process limitations such as the adverse impact of flue gas on medium pH, exhaust gas toxicity, and efficient delivery of carbon dioxide to media are also discussed. Finally, the article concludes by proposing the future potential for incorporating the microalgae biofuel plant into the cement sector.
Adaptive laboratory evolution has proven highly effective for obtaining microorganisms with enhanced capabilities. Yet, this method is inherently restricted to the traits that are positively linked ...to cell fitness, such as nutrient utilization. Here, we introduce coevolution of obligatory mutualistic communities for improving secretion of fitness‐costly metabolites through natural selection. In this strategy, metabolic cross‐feeding connects secretion of the target metabolite, despite its cost to the secretor, to the survival and proliferation of the entire community. We thus co‐evolved wild‐type lactic acid bacteria and engineered auxotrophic Saccharomyces cerevisiae in a synthetic growth medium leading to bacterial isolates with enhanced secretion of two B‐group vitamins, viz., riboflavin and folate. The increased production was specific to the targeted vitamin, and evident also in milk, a more complex nutrient environment that naturally contains vitamins. Genomic, proteomic and metabolomic analyses of the evolved lactic acid bacteria, in combination with flux balance analysis, showed altered metabolic regulation towards increased supply of the vitamin precursors. Together, our findings demonstrate how microbial metabolism adapts to mutualistic lifestyle through enhanced metabolite exchange.
SYNOPSIS
Adaptive laboratory evolution of obligatory mutualistic communities shows how coevolution can be used for targeted improvement in fitness‐costly metabolite secretion.
Mutualistic cross‐feeding exerts selection pressure for increased production of a target compound.
Lactic acid bacteria were co‐evolved with yeast for improved vitamin secretion; the enhanced secretion was retained in monocultures in milk.
Multi‐omics analysis of evolved strains uncovered how cellular networks adapt to a mutualistic lifestyle.
Adaptive laboratory evolution of obligatory mutualistic communities shows how coevolution can be used for targeted improvement in fitness‐costly metabolite secretion.
In the human gut,
ATCC 35704 is a predominant bacterium and one of the major bile acid 7α-dehydroxylating anaerobes. While this organism is well-studied relative to bile acid metabolism, little is ...known about the basic nutrition and physiology of
ATCC 35704. To determine the amino acid and vitamin requirements of
, the leave-one-out (one amino acid group or vitamin) technique was used to eliminate the nonessential amino acids and vitamins. With this approach, the amino acid tryptophan and three vitamins (riboflavin, pantothenate, and pyridoxal) were found to be required for the growth of
In the newly developed defined medium,
fermented glucose mainly to ethanol, acetate, formate, and H
The genome of
ATCC 35704 was completed through PacBio sequencing. Pathway analysis of the genome sequence coupled with transcriptome sequencing (RNA-Seq) under defined culture conditions revealed consistency with the growth requirements and end products of glucose metabolism. Induction with bile acids revealed complex and differential responses to cholic acid and deoxycholic acid, including the expression of potentially novel bile acid-inducible genes involved in cholic acid metabolism. Responses to toxic deoxycholic acid included expression of genes predicted to be involved in DNA repair, oxidative stress, cell wall maintenance/metabolism, chaperone synthesis, and downregulation of one-third of the genome. These analyses provide valuable insight into the overall biology of
which may be important in treatment of disease associated with increased colonic secondary bile acids.
is one of a few identified gut bacterial species capable of converting host cholic acid into disease-associated secondary bile acids such as deoxycholic acid. The current work represents an important advance in understanding the nutritional requirements and response to bile acids of the medically important human gut bacterium,
ATCC 35704. A defined medium has been developed which will further the understanding of bile acid metabolism in the context of growth substrates, cofactors, and other metabolites in the vertebrate gut. Analysis of the complete genome supports the nutritional requirements reported here. Genome-wide transcriptomic analysis of gene expression in the presence of cholic acid and deoxycholic acid provides a unique insight into the complex response of
ATCC 35704 to primary and secondary bile acids. Also revealed are genes with the potential to function in bile acid transport and metabolism.
The formation of secondary bile acids by gut microbes is a current topic of considerable biomedical interest. However, a detailed understanding of the biology of anaerobic bacteria in the genus ...Clostridium that are capable of generating secondary bile acids is lacking. We therefore sought to determine the transcriptional responses of two prominent secondary bile acid producing bacteria, Clostridium hylemonae and Clostridium hiranonis to bile salts (in vitro) and the cecal environment of gnotobiotic mice. The genomes of C. hylemonae DSM 15053 and C. hiranonis DSM 13275 were closed, and found to encode 3,647 genes (3,584 protein-coding) and 2,363 predicted genes (of which 2,239 are protein-coding), respectively, and 1,035 orthologs were shared between C. hylemonae and C. hiranonis. RNA-Seq analysis was performed in growth medium alone, and in the presence of cholic acid (CA) and deoxycholic acid (DCA). Growth with CA resulted in differential expression (>0.58 log
2
FC; FDR < 0.05) of 197 genes in C. hiranonis and 118 genes in C. hylemonae. The bile acid-inducible operons (bai) from each organism were highly upregulated in the presence of CA but not DCA. We then colonized germ-free mice with human gut bacterial isolates capable of metabolizing taurine-conjugated bile acids. This consortium included bile salt hydrolase-expressing Bacteroides uniformis ATCC 8492, Bacteroides vulgatus ATCC 8482, Parabacteroides distasonis DSM 20701, as well as taurine-respiring Bilophila wadsworthia DSM 11045, and deoxycholic/lithocholic acid generating Clostridium hylemonae DSM 15053 and Clostridium hiranonis DSM 13275. Butyrate and iso-bile acid-forming Blautia producta ATCC 27340 was also included. The Bacteroidetes made up 84.71% of 16S rDNA cecal reads, B. wadsworthia, constituted 14.7%, and the clostridia made up <.75% of 16S rDNA cecal reads. Bile acid metabolomics of the cecum, serum, and liver indicate that the synthetic community were capable of functional bile salt deconjugation, oxidation/isomerization, and 7α-dehydroxylation of bile acids. Cecal metatranscriptome analysis revealed expression of genes involved in metabolism of taurine-conjugated bile acids. The in vivo transcriptomes of C. hylemonae and C. hiranonis suggest fermentation of simple sugars and utilization of amino acids glycine and proline as electron acceptors. Genes predicted to be involved in trimethylamine (TMA) formation were also expressed.
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