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Long-term vegetarian diet contributed to quantity and associated bacterial community shifts in fecal microbiota composition. Consumption of foods of animal origin (eggs, red meat, white meat, milk, yoghurt, other dairy products, fish and seafood) and vegetarian type of diet explained the largest share of variance in microbial community structure. Fecal microbiota composition was also associated with participants' age, gender and body mass.

Intracellular bacteria were observed in the hepatopancreas of the terrestrial isopod Porcellio scaber. Comparative 16S rRNA gene sequence analysis and electron microscopic observations were used to determine the taxonomic position of these intracellular bacteria. Phylogenetic analysis and a complex developmental cycle affiliate these bacteria to the order Chlamydiales, within which they form a distinctive lineage, close to the family Simkaniaceae. They share <92 % 16S rRNA gene sequence similarity with their closest relative and <88 % similarity with other members of the order Chlamydiales. A specific signature oligonucleotide sequence was identified and used as a probe, enabling the identification of intracellular bacteria in infected hepatopancreatic tissue. According to the distinctive morphology of their elementary bodies, which are rod-shaped rather than spherical and contain translucent oblong structures, their genomic properties and their crustacean host, the name ‘Candidatus Rhabdochlamydia porcellionis' is proposed for intracellular bacteria in the hepatopancreas of P. scaber.

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The effect of standard agricultural management on the genetic heterogeneity of nitrous oxide reductase (nosZ) fragments from denitrifying prokaryotes in native and cultivated soil was explored. Thirty-six soil cores were composited from each of the two soil management conditions. nosZ gene fragments were amplified from triplicate samples, and PCR products were cloned and screened by restriction fragment length polymorphism (RFLP). The total nosZ RFLP profiles increased in similarity with soil sample size until triplicate 3-g samples produced visually identical RFLP profiles for each treatment. Large differences in total nosZ profiles were observed between the native and cultivated soils. The fragments representing major groups of clones encountered at least twice and four randomly selected clones with unique RFLP patterns were sequenced to verify nosZ identity. The sequence diversity of nosZ clones from the cultivated field was higher, and only eight patterns were found in clone libraries from both soils among the 182 distinct nosZ RFLP patterns identified from the two soils. A group of clones that comprised 32% of all clones dominated the gene library of native soil, whereas many minor groups were observed in the gene library of cultivated soil. The 95% confidence intervals of the Chao1 nonparametric richness estimator for nosZ RFLP data did not overlap, indicating that the levels of species richness are significantly different in the two soils, the cultivated soil having higher diversity. Phylogenetic analysis of deduced amino acid sequences grouped the majority of nosZ clones into an interleaved Michigan soil cluster whose cultured members are ␣-Proteobacteria. Only four nosZ sequences from cultivated soil and one from the native soil were related to sequences found in ␥-Proteobacteria. Sequences from the native field formed a distinct, closely related cluster (D mean ‫؍‬ 0.16) containing 91.6% of the native clones. Clones from the cultivated field were more distantly related to each other (D mean ‫؍‬ 0.26), and 65% were found outside of the cluster from the native soil, further indicating a difference in the two communities. Overall, there appears to be a relationship between use and richness, diversity, and the phylogenetic position of nosZ sequences, indicating that agricultural use of soil caused a shift to a more diverse denitrifying community.

Pointed, rod-shaped bacteria colonizing the cuticular surface of the hindgut of the terrestrial isopod crustacean Porcellio scaber (Crustacea: Isopoda) were investigated by comparative 16S rRNA gene sequence analysis and electron microscopy. The results of phylogenetic analysis, and the absence of a cell wall, affiliated these bacteria with the class Mollicutes, within which they represent a novel and deeply branched lineage, sharing less than 82.6% sequence similarity to known Mollicutes. The lineage has been positioned as a sister group to the clade comprising the Spiroplasma group, the Mycoplasma pneumoniae group, and the Mycoplasma hominis group. The specific signature sequence was identified and used as a probe in in situ hybridization, which confirmed that the retrieved sequences originate from the attached rod-shaped bacteria from the hindgut of P. scaber and made it possible to detect these bacteria in their natural environment. Scanning and transmission electron microscopy revealed a spherically shaped structure at the tapered end of the rod-shaped bacteria, enabling their specific and exclusive attachment to the tip of the cuticular spines on the inner surface of the gut. Specific adaptation to the gut environment, as well as phylogenetic positioning, indicate the long-term association and probable coevolution of the bacteria and the host. Taking into account their pointed, rod-shaped morphology and their phylogenetic position, the name "Candidatus Bacilloplasma" has been proposed for this new lineage of bacteria specifically associated with the gut surface of P. scaber.The common woodlouse Porcellio scaber is a widely spread species of the terrestrial isopod crustaceans (Crustacea, Isopoda, Oniscidea) living in temperate climates. Like other terrestrial isopods, P. scaber is a herbivorous scavenger, feeding predominantly on decayed plant material and thus contributing to nutrient and energy cycling in terrestrial ecosystems (43). Due to its ecological importance, easy handling, breeding capability under laboratory conditions, and tolerance to polluted environments as well as the considerable body of knowledge about its biology, this crustacean is commonly used as a test organism in terrestrial ecotoxicological and ecophysiological studies (12,17).The tripartite digestive system of P. scaber consists of a short foregut comprising an esophagus and stomach, a midgut consisting of two pairs of blind-ended tubular digestive glands, and a long, tube-like hindgut. The last of these comprises two functionally different parts, an anterior chamber and a papillate region with a rectum (17). The foregut of terrestrial isopods is generally poorly inhabited by microorganisms. On the other hand, a high microbial density is found in the hindgut, particularly in the papillate region, where favorable conditions (44) allow the multiplication of those microorganisms that have survived the digestion in the anterior part of the digestive tract of P. scaber (24, 26) and those of other terrestrial isopods like Oniscus asellu...

An in vitro study in dual-flow continuous-culture fermentors was conducted with two different concentrations of monensin, cinnamaldehyde or garlic extract added to 1:1 forage-to-concentrate diet in order to determine their effects on selected rumen bacterial populations. Samples were subjected to total DNA extraction, restriction analysis of PCR amplified parts of 16S rRNA genes (ARDRA) and subsequent analysis of the restriction profiles by lab-on-chip technology with the Agilent's Bioanalyser 2100. Eub338-BacPre primer pair was used to select for the bacteria from the genera Bacteroides, Porphyromonas and Prevotella, especially the latter representing the dominant Gram-negative bacterial population in the rumen. Preliminary results of HaeIII restriction analysis show that the effects of monensin, cinnamaldehyde and garlic extract on the BacPre targeted ruminal bacteria are somewhat different in regard to targeted populations and to the nature of the effect. Garlic extract was found to trigger the most intensive changes in the structure of the BacPre targeted population. Comparison of the in silico restriction analysis of BacPre sequences deposited in different DNA databanks and of the results of performed amplified ribosomal DNA restriction analysis showed differences between the predicted and obtained HaeIII restriction profiles, and suggested the presence of novel, still unknown Prevotella populations in studied samples.

A high degree of genetic diversity among 29 strains of Prevotella (Bacteroides) ruminicola from the rumen was revealed by comparing restriction fragment length polymorphisms in 16s rRNA genes, sodium dodecyl sulfate-polyacrylamide gel profiles of total-cell proteins, and G+ C contents of chromosomal DNAs. In order to obtain information on phylogenetic relationships, the sequences of a 389-bp region of the 16s rRNA gene, including variable regions 4 and 5, were compared for 10 strains. These 10 strains formed a single group when their sequences were compared with 16s ribosomal DNA sequences from other species, including Bacteroides spp. from the human colon. On the other hand, the great genetic distances between many P. ruminicola strains, including P. ruminicola subsp. brevis B,4 and GA33 and P. ruminicoh 23T (T = type strain), support the hypothesis that these organisms should be reclassified into new species. We identified signature oligonucleotides based on 16s ribosomal DNA sequences that distinguished strains related to strains 23T, B14, GA33, and M384, as well as an oligonucleotide that specifically recognized all but one of the Bacteroides and Prevotella strains tested. On the basis of the priming activities of these signature oligonucleotides in PCR reactions and on other criteria, we concluded that 12 of the original 29 strains were related to strain 23T, 4 were related to strain B14, and 4 were related to strain GA33. While there are clear grounds for subdividing the species P.ruminicola on the basis of genotypic differences, it is appropriate to delay formal reclassification until further work on the phenotypic differentiation of the new groups is completed.Prevotellu (Bucteroides) ruminicolu has long been recognized as one of the most numerous species inhabiting the rumen (5, 20) and can also account for a high proportion of the hind gut microflora of nonruminants, including pigs and humans (18,30,31). In a recent study, Van Gylswyk (43) found that as many as 60% of bacterial isolates from rumina of silage-fed cows belonged to this species. The new genus Prevotellu was recently created (37) to distinguish certain former Bucteroides species, including Bucteroides ruminicolu, Bucteroides meluninogenicus, and Bucteroides orulis, from the "true" Bucteroides species more closely related to Bucteroides fragilis. P. ruminicolu has generally been regarded as a "widely adapted" species. One potential role of this organism is in the degradation of plant cell wall polysaccharides, such as hemicellulose (7, 47) and pectin (8). P. ruminicolu strains lack a true cellulase system, are not able to degrade crystalline cellulose, and do not cause extensive solubilization of plant cell wall material in pure cultures. On the other hand, there is evidence that these organisms contribute to plant cell wall degradation by acting synergistically with cellulolytic bacteria (28). In addition, P.ruminicolu strains can generally utilize cellodextrins (32), starch (6), and a range of soluble sugars. One of their most significant...