The human gut contains a dense, complex and diverse microbial community, comprising the gut microbiome. Metagenomics has recently revealed the composition of genes in the gut microbiome, but provides no direct information about which genes are expressed or functioning. Therefore, our goal was to develop a novel approach to directly identify microbial proteins in fecal samples to gain information about the genes expressed and about key microbial functions in the human gut. We used a non-targeted, shotgun mass spectrometry-based whole community proteomics, or metaproteomics, approach for the first deep proteome measurements of thousands of proteins in human fecal samples, thus demonstrating this approach on the most complex sample type to date. The resulting metaproteomes had a skewed distribution relative to the metagenome, with more proteins for translation, energy production and carbohydrate metabolism when compared to what was earlier predicted from metagenomics. Human proteins, including antimicrobial peptides, were also identified, providing a non-targeted glimpse of the host response to the microbiota. Several unknown proteins represented previously undescribed microbial pathways or host immune responses, revealing a novel complex interplay between the human host and its associated microbes.

Enhanced biological phosphorus removal (EBPR) selects for polyphosphate accumulating microorganisms to achieve phosphate removal from wastewater. We used high-resolution community proteomics to identify key metabolic pathways in 'Candidatus Accumulibacter phosphatis' (A. phosphatis)-mediated EBPR and to evaluate the contributions of co-existing strains within the dominant population. Overall, 702 proteins from the A. phosphatis population were identified. Results highlight the importance of denitrification, fatty acid cycling and the glyoxylate bypass in EBPR. Strong similarity in protein profiles under anaerobic and aerobic conditions was uncovered (only 3% of A. phosphatis-associated proteins exhibited statistically significant abundance differences). By comprehensive genome-wide alignment of 13 930 orthologous proteins, we uncovered substantial differences in protein abundance for enzyme variants involved in both core-metabolism and EBPR-specific pathways among the A. phosphatis population. These findings suggest an essential role for genetic diversity in maintaining the stable performance of EBPR systems and, hence, demonstrate the power of integrated cultivation-independent genomics and proteomics for the analysis of complex biotechnological systems.

The aim of this study was to investigate the different combinations of red (R) and blue (B) light emitting diode (LEDs’) lighting effects on growth, pigment content, and antioxidant capacity in lettuce, spinach, kale, basil, and pepper in a growth chamber. The growth chamber was equipped with R and B light percentages based on total light intensity: 83% R + 17% B; 91% R + 9% B; 95% R + 5% B; and control was 100% R. The photosynthetic photon flux density (PPFD), photoperiod, temperature, and relative humidity of the growth chamber were maintained at 200 ± 5 μmol m−2 s−1, 16 h, 25/21 ± 2.5 °C, and 65 ± 5%, respectively. It is observed that the plant height of lettuce, kale, and pepper was significantly increased under 100% R light, whereas the plant height of spinach and basil did not show any significant difference. The total leaf number of basil and pepper was significantly increased under the treatment of 95% R + 5% B light, while no significant difference was observed for other plant species in the same treatment. Overall, the fresh and dry mass of the studied plants was increased under 91% R + 9% B and 95% R + 5% B light treatment. The significantly higher flower and fruit numbers of pepper were observed under the 95% R + 5% B treatment. The chlorophyll a, chlorophyll b, and total chlorophyll content of lettuce, spinach, basil, and pepper was significantly increased under the 91% R + 9% B treatment while the chlorophyll content of kale was increased under the 95% R + 5% B light treatment. The total carotenoid content of lettuce and spinach was higher in the 91% R + 9% B treatment whereas the carotenoid content of kale, basil, and pepper was increased under the 83% R + 17% B treatment. The antioxidant capacity of the lettuce, spinach, and kale was increased under the 83% R + 17% B treatment while basil and pepper were increased under the 91% R + 9% B treatment. This result indicates that the addition of B light is essential with R light to enhance growth, pigment content, and antioxidant capacity of the vegetable plant in a controlled environment. Moreover, the percentage of B with R light is plant species dependent.

We analyzed near-complete population (composite) genomic sequences for coexisting acidophilic ironoxidizing Leptospirillum group II and III bacteria (phylum Nitrospirae) and an extrachromosomal plasmid from a Richmond Mine, Iron Mountain, CA, acid mine drainage biofilm. Community proteomic analysis of the genomically characterized sample and two other biofilms identified 64.6% and 44.9% of the predicted proteins of Leptospirillum groups II and III, respectively, and 20% of the predicted plasmid proteins. The bacteria share 92% 16S rRNA gene sequence identity and >60% of their genes, including integrated plasmid-like regions. The extrachromosomal plasmid carries conjugation genes with detectable sequence similarity to genes in the integrated conjugative plasmid, but only those on the extrachromosomal element were identified by proteomics. Both bacterial groups have genes for community-essential functions, including carbon fixation and biosynthesis of vitamins, fatty acids, and biopolymers (including cellulose); proteomic analyses reveal these activities. Both Leptospirillum types have multiple pathways for osmotic protection. Although both are motile, signal transduction and methyl-accepting chemotaxis proteins are more abundant in Leptospirillum group III, consistent with its distribution in gradients within biofilms. Interestingly, Leptospirillum group II uses a methyldependent and Leptospirillum group III a methyl-independent response pathway. Although only Leptospirillum group III can fix nitrogen, these proteins were not identified by proteomics. The abundances of core proteins are similar in all communities, but the abundance levels of unique and shared proteins of unknown function vary. Some proteins unique to one organism were highly expressed and may be key to the functional and ecological differentiation of Leptospirillum groups II and III.To understand how microorganisms contribute to biogeochemical cycling, it is necessary to determine the roles of uncultivated as well as cultivated groups and to establish how these roles vary during ecological succession and when environmental conditions change. Shotgun genomic sequencing (metagenomics) has opened new opportunities for cultureindependent studies of microbial communities. Examples include investigations of acid mine drainage (AMD) biofilm communities (4, 43, 75), symbiosis in a marine worm involving sulfur-oxidizing and sulfate-reducing bacteria (85), and enhanced biological phosphorous removal by sludge communities (32). From these genomic data sets, it has been possible to reconstruct aspects of the metabolism of individual organisms (32) and coexisting community members (29, 75) and to identify which organisms contribute community-essential functions (75). An interesting question relates to how differences in metabolic potential between organisms from the same lineage allow them to occupy distinct niches. Identification of potentially adaptive traits in closely related organisms is also important from an evolutionary perspective.Genomic data do not...