Biochemical Mapping of Pyrodinium bahamense Unveils Molecular Underpinnings behind Organismal Processes

Proteins, lipids, and carbohydrates from the harmful algal bloom (HAB)-causing organism Pyrodinium bahamense were characterized to obtain insights into the biochemical processes in this environmentally relevant dinoflagellate. Shotgun proteomics using label-free quantitation followed by proteome mapping using the P. bahamense transcriptome and translated protein databases of Marinovum algicola, Alexandrium sp., Cylindrospermopsis raciborskii, and Symbiodinium kawagutii for annotation enabled the characterization of the proteins in P. bahamense. The highest number of annotated hits were obtained from M. algicola and highlighted the contribution of microorganisms associated with P. bahamense. Proteins involved in dimethylsulfoniopropionate (DMSP) degradation such as propionyl CoA synthethase and acryloyl-CoA reductase were identified, suggesting the DMSP cleavage pathway as the preferred route in this dinoflagellate. Most of the annotated proteins were involved in amino acid biosynthesis and carbohydrate degradation and metabolism, indicating the active roles of these molecules in the vegetative stage of P. bahamense. This characterization provides baseline information on the cellular machinery and the molecular basis of the ecophysiology of P. bahamense.

Iocasia fonsfrigidae NS-1 gen. nov., sp. nov., a Novel Deep-Sea Bacterium Possessing Diverse Carbohydrate Metabolic Pathways

Resolving metabolisms of deep-sea microorganisms is crucial for understanding ocean energy cycling. Here, a strictly anaerobic, Gram-negative strain NS-1 was isolated from the deep-sea cold seep in the South China Sea. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain NS-1 was most closely related to the type strain Halocella cellulosilytica DSM 7362T (with 92.52% similarity). A combination of phylogenetic, genomic, and physiological traits with strain NS-1, was proposed to be representative of a novel genus in the family Halanaerobiaceae, for which Iocasia fonsfrigidae NS-1 was named. It is noteworthy that I. fonsfrigidae NS-1 could metabolize multiple carbohydrates including xylan, alginate, starch, and lignin, and thereby produce diverse fermentation products such as hydrogen, lactate, butyrate, and ethanol. The expressions of the key genes responsible for carbohydrate degradation as well as the production of the above small molecular substrates when strain NS-1 cultured under different conditions, were further analyzed by transcriptomic methods. We thus predicted that part of the ecological role of Iocasia sp. is likely in the fermentation of products from the degradation of diverse carbohydrates to produce hydrogen as well as other small molecules, which are in turn utilized by other members of cold seep microbes.

Microbial Surface Biofilm Responds to the Growth-Reproduction-Senescence Cycle of the Dominant Coral Reef Macroalgae Sargassum spp.

Macroalgae play an intricate role in microbial-mediated coral reef degradation processes due to the release of dissolved nutrients. However, temporal variabilities of macroalgal surface biofilms and their implication on the wider reef system remain poorly characterized. Here, we study the microbial biofilm of the dominant reef macroalgae Sargassum over a period of one year at an inshore Great Barrier Reef site (Magnetic Island, Australia). Monthly sampling of the Sargassum biofilm links the temporal taxonomic and putative functional metabolic microbiome changes, examined using 16S rRNA gene amplicon and metagenomic sequencing, to the pronounced growth-reproduction-senescence cycle of the host. Overall, the macroalgal biofilm was dominated by the heterotrophic phyla Firmicutes (35% ± 5.9% SD) and Bacteroidetes (12% ± 0.6% SD); their relative abundance ratio shifted significantly along the annual growth-reproduction-senescence cycle of Sargassum. For example, Firmicutes were 1.7 to 3.9 times more abundant during host growth and reproduction cycles than Bacteroidetes. Both phyla varied in their carbohydrate degradation capabilities; hence, temporal fluctuations in the carbohydrate availability are potentially linked to the observed shift. Dominant heterotrophic macroalgal biofilm members, such as Firmicutes and Bacteroidetes, are implicated in exacerbating or ameliorating the release of dissolved nutrients into the ambient environment, though their contribution to microbial-mediated reef degradation processes remains to be determined.

Effect of Supplying Rosemary (Rosmarinus officinalis L.) and Garlic (Allium sativum L.) Essential Oils to Feedlot Lambs on in vitro Ruminal Fermentation

The aim of this trial was to evaluate the ruminal degradation kinetics of carbohydrates in diets with different roughage:concentrate ratios and dosages of garlic and rosemary essential oils, in order to find the most suitable dosage to supply feedlot lambs. Three roughage:concentrate ratios (50:50, 40:60, and 20:80) and six dosages of garlic and rosemary essential oils (0.0, 0.10, 0.25, 1.0, 1.50, and 2.0 g L−1) were tested. Kinetic parameters for carbohydrate breakdown were estimated using a semi-automated in vitro gas production technique. Ruminal degradation parameters were subjected to variance analysis and then regression analysis at a 5% significance level. There was no interaction between the roughage:concentrate ratios and the dosage of rosemary essential oil. The roughage:concentrate ratios in diets with rosemary oil affected the non-fiber carbohydrate degradation rate (Kdnfc), colonization time (L), gas volume and breakdown rate from the degradation of fiber carbohydrates (Vfc and Kdfc, respectively), and final gas volume of both fiber and non-fiber carbohydrates (Vfinal). Rosemary dosages affected Vnfc and Vfc, which presented a quadratic response with a peak at 0.71 g L−1 and a nip at 1.17 g L−1, respectively. Bacterial colonization time was quadratic, reaching a maximum value at 1.18 g L−1. Vfinal showed a decreasing linear trend, such that each gram of rosemary essential oil added to the diet could reduce gas production by 30.312 mL. Therefore, rosemary essential oil has an effect on carbohydrate degradation kinetics. There was no interaction between roughage:concentrate ratios and different garlic oil dosages, except for colonization time. Roughage:concentrate ratios with garlic oil had affected the Vnfc, Kdnfc, and L. Garlic oil dosages affected Vfc and Vfinal in a quadratic manner, with the lowest values of gas production at 1.35 and 1.54 g L−1, respectively. L was affected by the garlic oil dosage and roughage:concentrate ratios in a decreasing linear trend for a 50:50 ratio and quadratic response for a 40:60 ratio, peaking at 0.14 g L−1. Based on these in vitro results, a ruminal content of 1.0 g L−1 is recommended for both rosemary and garlic essential oils.

In vitro metabolic capacity of carbohydrate degradation by intestinal microbiota of adults and pre-frail elderly

Globally increased life expectancy strongly triggered interest to delay the onset of frailty, which has been associated with alterations in compositional and functional characteristics of intestinal microbiota. In the current study, we used an in vitro batch incubation model to compare the metabolic capacity of the faecal microbiota of adults (n = 6) versus pre-frail elderly (n = 6) to degrade various glycosidic carbohydrates, including galacto-oligosaccharides, 2′-fucosyllactose, chicory fructo-oligosaccharides and inulin, and isomalto/malto-polysaccharides. The in vitro metabolic capacity was also compared with an in vivo GOS intervention study based on the same subjects. Analysis of 16S rRNA gene sequences and metabolites revealed distinct portions of variation in overall microbiota and metabolite composition during incubation being explained by individuality of the subjects and carbon source. In addition, the age group of the subjects also had significant impact on microbiota variation, carbohydrate degradation and metabolite production. This was accompanied by elevated increase in the relative abundance of Bifidobacterium in the microbiota of adults compared to that of pre-frail elderly and significantly decreased effectiveness to degrade galacto-oligosaccharides by the latter group. Altogether, the carbohydrate degradation in elderly was different compared to adults, with some carbohydrates showing decreased degradation rates. Longer interventions periods may be required to enhance bifidobacterial abundance in the microbiota of pre-frail elderly and thereby to obtain associated prebiotic health benefits.

Delivery mode and perinatal antibiotics influence the predicted metabolic pathways of the gut microbiome

Delivery mode and perinatal antibiotics influence gut microbiome composition in children. Most microbiome studies have used the sequencing of the bacterial 16S marker gene but have not reported the metabolic function of the gut microbiome, which may mediate biological effects on the host. Here, we used the PICRUSt2 bioinformatics tool to predict the functional profiles of the gut microbiome based on 16S sequencing in two child cohorts. Both Caesarean section and perinatal antibiotics markedly influenced the functional profiles of the gut microbiome at the age of 1 year. In machine learning analysis, bacterial fatty acid, phospholipid, and biotin biosynthesis were the most important pathways that differed according to delivery mode. Proteinogenic amino acid biosynthesis, carbohydrate degradation, pyrimidine deoxyribonucleotide and biotin biosynthesis were the most important pathways differing according to antibiotic exposure. Our study shows that both Caesarean section and perinatal antibiotics markedly influence the predicted metabolic profiles of the gut microbiome at the age of 1 year.

Investigation of acid hydrolysis for carbohydrate analysis in kraft black liquor

Black liquor (BL) from the kraft process is considered a promising feedstock for several biorefinery scenarios. Besides lignin and carboxylic acids, this liquor also contains hemicelluloses and their degradation products. A simple and reliable detection of those is of importance for further processing of the liquor. The present paper presents a thorough investigation of quantitative analysis of carbohydrates, by performing acid hydrolysis experiments with a concentrated BL sample of 44% total dry solids. The hydrolysates were then analysed for the four monosaccharides arabinose, xylose, galactose and glucose, by high performance ion chromatography (HPIC) with pulsed amperometric detection. The amount of sulphuric acid needed for complete hydrolysis of the carbohydrates was determined in the range of 3.5–5 mol kg−1 of BL. A lower acid concentration led to insufficient liberation of galactose and glucose, while higher acid concentrations led to degradation of arabinose and xylose. The carbohydrate degradation was also investigated over time for different dilutions and hydrolysis temperatures. These experiments confirmed that the hexoses require considerably harsher conditions for complete liberation compared to xylose and arabinose. The use of internal recovery standards (RSs) was tested; the highest recoveries were obtained by direct spiking of the samples with the RS prior to hydrolysis.

Chitosan Oligosaccharide Production Potential of Mitsuaria sp. C4 and Its Whole-Genome Sequencing

Chitooligosaccharide is a kind of functional food, which is the degradation product of chitosan (COS) catalyzed by the endo-chitosanase (COSE) enzyme. A COSE with a molecular weight of 34 kDa was purified and characterized from a newly isolated Mitsuaria sp. C4 (C4), and a 38.46% recovery rate and 4.79-fold purification were achieved. The purified C4 COSE exhibited optimum activity at 40°C and pH 7.2 and was significantly inhibited in the presence of Cu2+ and Fe3+. The Km and Vmin of the COSE toward COS were 2.449 g/L and 0.042 g/min/L, respectively. The highest COSE activity reached 8.344 U/ml after optimizing, which represented a 1.34-fold of increase. Additionally, chitooligosaccharide obtained by COSE hydrolysis of COS was verified by using thin-layer chromatography and high-performance liquid chromatography analysis. Whole-genome sequencing demonstrated that the C4 strain contains 211 carbohydrate enzymes, our purified COSE belonging to GHs-46 involved in carbohydrate degradation. Phylogenetic analysis showed that the novel COSE obtained from the C4 strain was clustered into the degree of polymerization = two to three groups, which can perform catalysis in a similar manner to produce (GlcN)2 and (GlcN)3. This work indicates that the C4 strain could be a good resource for enhancing carbohydrate degradation and might represent a useful tool for chitooligosaccharide production in the functional food industry.