Following birth, the breast-fed infant gastrointestinal tract is rapidly colonized by a microbial consortium often dominated by bifidobacteria. Accordingly, the complete genome sequence of Bifidobacterium longum subsp. infantis ATCC15697 reflects a competitive nutrientutilization strategy targeting milk-borne molecules which lack a nutritive value to the neonate. Several chromosomal loci reflect potential adaptation to the infant host including a 43 kbp cluster encoding catabolic genes, extracellular solute binding proteins and permeases predicted to be active on milk oligosaccharides. An examination of in vivo metabolism has detected the hallmarks of milk oligosaccharide utilization via the central fermentative pathway using metabolomic and proteomic approaches. Finally, conservation of gene clusters in multiple isolates corroborates the genomic mechanism underlying milk utilization for this infant-associated phylotype.carbohydrate metabolism ͉ co-evolution ͉ genomics ͉ human milk oligosaccharides

Storage of swine manure is associated with the microbiological production of a variety of odorous chemicals including ammonia, organic acids and alcohols, and sulphides. Although largely the product of microbiological activity, little is known about the microorganisms present in swine manure. In order to gain a better understanding of the types and activities of the microorganisms present, representative strains of microorganisms were isolated from faeces and stored manure slurry, identified, and physiologically characterized. For swine manure slurry samples, total anaerobe colony counts were greatest when a non-selective, habitat simulating medium containing clarified swine manure slurry was used whereas the highest counts for faecal anaerobes were obtained on rumen fluid containing medium. Faecal and slurry samples were also plated onto the appropriate medium containing the antibiotics tetracycline, erythromycin and tylosin (10 micro g ml-1, individually) and the proportional counts of organisms capable of growing in the presence of these antibiotics determined. Randomly selected isolates from the highest dilutions were identified by 16 s rDNA sequence analysis, and selected physiological characteristics were determined. The results of these examinations indicate that the predominant culturable microorganisms from these environments are obligately anaerobic, low mol percentage G + C Gram positive bacteria (Firmicutes) who are members of Clostridial, Eubacterial, and Lactobacillus/Streptococcus phylogenetic groups. Isolates similar to Sporomusa and Flexibacter/Cytophaga/Bacteroides (CFB or Bacteroidetes) groups were also obtained. Although similar overall, faecal and slurry samples differed in bacterial composition. Manure slurry samples were dominated by organisms similar to Clostridium coccoides and Enterococcus species whereas the distribution of species present in faeces appeared much broader. Whereas most of the pure cultures could be assigned to known phylogenetic groupings, few could be identified as known species. Examination of some growth and physiological characteristics of faecal and slurry isolates showed these to be primarily carbohydrate fermenters, although some were able to ferment lactate and amino acids. When the ability of manure and faecal isolates to ferment protein, peptides and amino acids was examined, a relatively small percentage of these were able to do so and most of these fermented carbohydrates in addition to the amino acid sources provided. The predominant amino acid fermenters were most closely related to C. coccoides and C. botulinum, but representatives of the Bacteroides, Staphylococcus, Enterococcus and other phylogenetic groups were also found. The results reported here are compared with those obtained from clone libraries prepared from the same environmental samples.

Skatole (3-methylindole) is a malodorous chemical in stored swine manure and is implicated as a component of foul-tasting pork. Definitive evidence for the skatole pathway is lacking. Deuterium-labeled substrates were employed to resolve this pathway in the acetogenic bacterium Clostridium drakei and Clostridium scatologenes and to determine if a similar pathway is used by microorganisms present in stored swine manure. Indoleacetic acid (IAA) was synthesized from tryptophan by both bacteria, and skatole was synthesized from both IAA and tryptophan. Microorganisms in swine manure produced skatole and other oxidation products from tryptophan, but IAA yielded only skatole. A catabolic mechanism for the synthesis of skatole is proposed.Storage of swine manure is associated with the generation of a number of malodorous compounds (18,22,30), and the production of odor associated with concentrated livestock facilities creates a nuisance and has resulted in considerable conflicts between producers and rural neighbors. These odors are produced as a result of anaerobic degradation of materials present in manure and include sulfides, organic acids, ammonia, phenols, amines, and other volatile compounds (30). One of the more malodorous compounds identified in swine manure odor is skatole (3-methylindole). Skatole has also been implicated as an off-flavor component of pig meat (referred to as "boar taint") (4,6,17,19) and as a contributing factor in acute bovine pulmonary edema and emphysema (15,23,27).Although the production of skatole has been attributed to the bacterial degradation of the amino acid tryptophan, the pathway by which skatole is produced from tryptophan has not been elucidated. The primary metabolite of tryptophan fermentation is indole (26,27), and skatole is produced from tryptophan and indoleacetic acid (IAA) by pig fecal slurries (13). However, very few bacterial isolates have been shown to produce skatole. A Lactobacillus species from the rumen has been reported to produce skatole from IAA but not directly from tryptophan (28,29). Clostridium scatologenes and the acetogen Clostridium drakei (originally isolated as C. scatologenes SL1) (14, 16) have also been reported to produce skatole (13, 14) and were selected for resolving the skatole catabolic pathway by using deuterium-labeled substrates and a combination of gas chromatography-mass spectrometry (GC-MS) and matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS).Bacterial strains, cultivation conditions, and swine manure. C. drakei SL1 DSM 12750 and C. scatologenes ATCC 25775 were utilized in this study. Preparation of media and inoculations were performed under anaerobic conditions using the method of Hungate as modified by Bryant (2). The basic medium for culturing C. drakei and C. scatologenes contained macrominerals, microminerals, buffers, reducing agents, and other components in routine growth medium (RGM) (9) and was supplemented with 1% (wt/vol) tryptone and either 1% (wt/vol) tryptophan or 1% (wt/vol) IAA...