Preferential sugar utilization by bifidobacterial species.

Aim: Bifidobacteria benefit host health and homeostasis by breaking down diet- and host-derived carbohydrates to produce organic acids in the intestine. However, the sugar utilization preference of bifidobacterial species is poorly understood. Thus, this study aimed to investigate the sugar utilization preference (i.e., glucose or lactose) of various bifidobacterial species. Methods: Strains belonging to 40 bifidobacterial species/subspecies were cultured on a modified MRS medium supplemented with glucose and/or lactose, and their preferential sugar utilization was assessed using high-performance thin-layer chromatography. Comparative genomic analysis was conducted with a focus on genes involved in lactose and glucose uptake and genes encoding for carbohydrate-active enzymes. Results: Strains that preferentially utilized glucose or lactose were identified. Almost all the lactose-preferring strains harbored the lactose symporter lacS gene. However, the comparative genomic analysis could not explain all their differences in sugar utilization preference. Analysis based on isolate source revealed that all 10 strains isolated from humans preferentially utilized lactose, whereas all four strains isolated from insects preferentially utilized glucose. In addition, bifidobacterial species isolated from hosts whose milk contained higher lactose amounts preferentially utilized lactose. Lactose was also detected in the feces of human infants, suggesting that lactose serves as a carbon source not only for infants but also for gut microbes in vivo. Conclusion: The different sugar preference phenotypes of Bifidobacterium species may be ascribed to the residential environment affected by the dietary habits of their host. This study is the first to systematically evaluate the sugar uptake preference of various bifidobacterial species.

A unique global metabolic trait of Pseudomonas bharatica CSV86T: metabolism of aromatics over simple carbon sources and co-metabolism with organic acids.

Hierarchical utilization of substrate by microbes (utilization of simple carbon sources prior to complex ones) poses a major limitation to the efficient remediation of aromatic pollutants. Aromatic compounds, being complex and reduced in nature, appear to be a deferred choice as the carbon source in the presence of a plethora of simple organic compounds in the environment. The soil bacterium Pseudomonas bharatica CSV86T displays a unique carbon source utilization hierarchy. It preferentially utilizes aromatics over glucose and co-metabolizes them with succinate or pyruvate (Basu et al., 2006, Applied and Environmental Microbiology, 72 : 22226-2230). In the present study, the substrate utilization hierarchy for strain CSV86T was tested for additional simple carbon sources such as glycerol, acetate, and tri-carboxylic acid (TCA) cycle intermediates like α-ketoglutarate and fumarate. When grown on a mixture of aromatics (benzoate or naphthalene) plus glycerol, the strain displayed a diauxic growth profile with significantly high activity of aromatic utilization enzymes (catechol 1,2- or 2,3-dioxygenase, respectively) in the first-log phase. This suggests utilization of aromatics in the first-log phase followed by glycerol in the second-log phase. On a mixture of an aromatic plus organic acid (acetate, α-ketoglutarate or fumarate), the strain displayed a monoauxic growth profile, indicating co-metabolism. Interestingly, the presence of glycerol, acetate, α-ketoglutarate or fumarate does not repress metabolism/utilization of the aromatic. Thus, the substrate utilization hierarchy of strain CSV86T is aromatics=organic acids>glucose/glycerol, which is unique as compared to other Pseudomonas species, where degradation of aromatics is repressed by glycerol, glucose, acetate or organic acids, including TCA cycle intermediates. This novel substrate utilization hierarchy appears to be a global metabolic phenomenon in strain CSV86T, thus implying it to be an ideal host for metabolic engineering as well as for its potential application in bioremediation.

Sequential uptake of aldoses over fructose and enhanced phosphate solubilization in Rhizobium sp. RM.

Rhizobium sp. RM solubilized tri-calcium phosphate (TCP: 324-463 µg ml-1) and rock phosphate (RP: 36-46.58 µg ml-1) in the presence of common rhizospheric sugars-glucose, arabinose, xylose and their combinations. Fructose, though did not support RP solubilization individually, surprisingly solubilized significantly higher phosphate when combined with aldoses. The highest TCP (644 µg ml-1) and RP (75 µg ml-1) solubilization was achieved in fructose + glucose combination. Presence of gluconate, malate and oxalate in culture supernatant indicated functioning of periplasmic glucose oxidation, the non-phosphorylative arabinose dehydrogenase pathway and the tricarboxylate (TCA) cycle, respectively. Aldoses, when present together, were co-utilized (monoauxic growth) however, when added with fructose, prevented the uptake of fructose yielding a typical diauxic growth. This presented an unusual sequential utilization of aldoses over a ketose (fructose) in strain RM. The prevention of fructose uptake by aldoses was investigated through real-time expression of key genes coding fructose transport proteins and initial enzymes of sugar metabolism. Fructose was actively transported via fructose-specific ABC transporters as suggested by upregulation of frcB and frcC only in fructose and fructose growth phases of fructose + aldose combinations. The probable route of initial fructose metabolism involved either fructokinase and/or xylose isomerase, as confirmed by enzyme activities. The upregulation of hfq and hprK genes only in aldose phase of fructose + aldose combinations suggested their possible involvement in governing the preferential utilization. The novel aspects of this study are enhanced organic acid mediated P solubilization in fructose + aldose combinations and a rare hierarchy of aldoses over fructose which is possibly regulated at the level of fructose transport and fructokinase. KEY POINTS: • Sugars when provided in different dual combinations, supported enhanced P solubilization from complex phosphate sources like TCP and RP in Rhizobium sp. RM. • Transcriptional status of genes in cells of RM when grown in different individual sugars and their combinations suggested that fructose might be a less preferred carbon source and hence was utilized after aldoses with the possible regulation by Hfq and HPrK. • First study to present a unique phenomenon of sequential utilization of aldoses (glucose, arabinose and xylose) over fructose in a concentration-independent manner in Rhizobium sp. RM. and to present the effect of dual combinations of sugars on organic acid mediated P solubilization trait of rhizobia.

Preferential utilization and colonization of keratin baits by different myco-keratinophiles.

Myco-keratinophilic species have a predilection for different keratinous substrates but show variability in their affinity towards them. Keeping this in view, a survey was conducted in the Khardung and Khardung La soils of Ladakh (India) and 28 myco-keratinophilic species belonging to 15 fungal genera (Sarocladium, Aspergillus, Beauveria, Chrysosporium, Cladosporium, Alternaria, Epicoccum, Fusarium, Gibberella, Clonostachys, Paecilomyces, Purpureocillium, Metarhizium, Penicillium and Sagenomella) were isolated by using keratin bait technique. These isolated species were tested for their preferential utilization ability and colonization on different baits by morphological assessment. Different types of keratin baits used were feathers, human hair, human nails and wool. Overall assessment revealed that feathers were colonized and utilized by all the species (100 %), followed in decreasing order by nails (89.29 %), hair (85.71 %) and sheep wool (67.86 %). So, it is concluded that feather baiting technique, could be more useful in trapping keratinophilic fungi than the hair baiting technique which is till date regarded as the best method for the isolation of myco-keratinophiles. On the basis of succession on keratinous baits, the recovered keratinophilic species were also categorized into four categories: early successional species (pioneer colonizers), late successional species (final colonizers), persistent species and no-pattern species.

Analysis of preference for carbon source utilization among three strains of aromatic compounds degrading Pseudomonas.

Soil isolates Pseudomonas putida CSV86, Pseudomonas aeruginosa PP4 and Pseudomonas sp. C5pp degrade naphthalene, phthalate isomers and carbaryl, respectively. Strain CSV86 displayed a diauxic growth pattern on phenylpropanoid compounds (veratraldehyde, ferulic acid, vanillin or vanillic acid) plus glucose with a distinct second lag-phase. The glucose concentration in the medium remained constant with higher cell respiration rates on aromatics and maximum protocatechuate 3,4-dioxygenase activity in the first log-phase, which gradually decreased in the second log-phase with concomitant depletion of the glucose. In strains PP4 and C5pp, growth profile and metabolic studies suggest that glucose is utilized in the first log-phase with the repression of utilization of aromatics (phthalate or carbaryl). All three strains utilize benzoate via the catechol 'ortho' ring-cleavage pathway. On benzoate plus glucose, strain CSV86 showed preference for benzoate over glucose in contrast to strains PP4 and C5pp. Additionally, organic acids like succinate were preferred over aromatics in strains PP4 and C5pp, whereas strain CSV86 co-metabolizes them. Preferential utilization of aromatics over glucose and co-metabolism of organic acids and aromatics are found to be unique properties of P. putida CSV86 as compared with strains PP4 and C5pp and this property of strain CSV86 can be exploited for effective bioremediation.