Equine stomachs harbor an abundant and diverse mucosal microbiota

Little is known about the gastric mucosal microbiota in healthy horses, and its role in gastric disease has not been critically examined. The present study used a combination of 16S rRNA bacterial tag-encoded pyrosequencing (bTEFAP) and fluorescence in situ hybridization (FISH) to characterize the composition and spatial distribution of selected gastric mucosal microbiota of healthy horses. Biopsy specimens of the squamous, glandular, antral, and any ulcerated mucosa were obtained from 6 healthy horses by gastroscopy and from 3 horses immediately postmortem. Pyrosequencing was performed on biopsy specimens from 6 of the horses and yielded 53,920 reads in total, with 631 to 4,345 reads in each region per horse. The microbiome segregated into two distinct clusters comprised of horses that were stabled, fed hay, and sampled at postmortem (cluster 1) and horses that were pastured on grass, fed hay, and biopsied gastroscopically after a 12-h fast (cluster 2). The types of bacteria obtained from different anatomic regions clustered by horse rather than region. The dominant bacteria in cluster 1 were Firmicutes (>83% reads/sample), mainly Streptococcus spp., Lactobacillus spp. and, Sarcina spp. Cluster 2 was more diverse, with predominantly Proteobacteria, Bacteroidetes, and Firmicutes, consisting of Actinobacillus spp. Moraxella spp., Prevotella spp., and Porphyromonas spp. Helicobacter sp. sequences were not identified in any of 53,920 reads. FISH (n = 9) revealed bacteria throughout the stomach in close apposition to the mucosa, with significantly more Streptococcus spp. present in the glandular region of the stomach. The equine stomach harbors an abundant and diverse mucosal microbiota that varies by individual.     

Synthetic riboswitches that induce gene expression in diverse bacterial species

We developed a series of ligand-inducible riboswitches that control gene expression in diverse species of Gram-negative and Gram-positive bacteria, including human pathogens that have few or no previously reported inducible expression systems. We anticipate that these riboswitches will be useful tools for genetic studies in a wide range of bacteria.     

Earthworm leukocyte populations specifically harbor lysosomal enzymes that may respond to bacterial challenge

Earthworm leukocytes (coelomocytes) are responsible for innate cellular immune functions such as phagocytosis and encapsulation against parasites and pathogens. Microbial killing results from the combined action of the phagocytic process with humoral immune factors such as agglutinins (e.g., lectins), lysosomal enzymes (e.g., acid phosphatase, lysozyme), and various cytotoxic and antimicrobial molecules. There is also evidence of weak adaptive immune responses against foreign transplants. This study focused on aspects of the innate immune response. First, anti-human acid phosphatase (anti-AcP) polyclonal antibody characterized different acid hydrolase patterns in coelomocytes. Second, flow cytometry identified a strongly immunoreactive coelomocyte population. Third, ultrastructural and cytochemical analyses revealed acid phosphatase in discrete granules (lysosomes) of effector hyaline and granular coelomocytes but not in mature chloragocytes. Coelomocytes were exposed to bacteria to assess how phagocytosis influences: (a) the production of acid phosphatase using Western blot, and (b) release of acid phosphatase using ELISA from cell-free coelomic fluid. Fourth, after phagocytosis, acid phosphatase levels differed between controls and experimentals. Fifth, we found a 39-kDa molecule that reacted intensely with anti-AcP. Our results suggest that effector earthworm coelomocytes may not eliminate pathogens only by phagocytosis but also by extracellular lysis.E.L. Cooper has been supported by The Alexander von Humboldt Foundation, a GAAC grant from the Federal Republic of Germany and two grants from NATO, a Cooperative Research grant (971128) and an Advanced Research Workshop grant (976680)     

Crustose coralline algae that promote coral larval settlement harbor distinct surface bacterial communities

Coral Reefs - Most benthic invertebrates, including ecosystem engineers such as corals, sponges and bivalves, have a motile planktonic larval phase and rely on specific chemical cues to identify a...     

Abundant and diverse fungal microbiota in the murine intestine

Enteric microbiota play a variety of roles in intestinal health and disease. While bacteria in the intestine have been broadly characterized, little is known about the abundance or diversity of enteric fungi. This study utilized a culture-independent method termed oligonucleotide fingerprinting of rRNA genes (OFRG) to describe the compositions of fungal and bacterial rRNA genes from small and large intestines (tissue and luminal contents) of restricted-flora and specific-pathogen-free mice. OFRG analysis identified rRNA genes from all four major fungal phyla: Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. The largest assemblages of fungal rRNA sequences were related to the genera Acremonium, Monilinia, Fusarium, Cryptococcus/Filobasidium, Scleroderma, Catenomyces, Spizellomyces, Neocallimastix, Powellomyces, Entophlyctis, Mortierella, and Smittium and the order Mucorales. The majority of bacterial rRNA gene clones were affiliated with the taxa Bacteroidetes, Firmicutes, Acinetobacter, and Lactobacillus. Sequence-selective PCR analyses also detected several of these bacterial and fungal rRNA genes in the mouse chow. Fluorescence in situ hybridization analysis with a fungal small-subunit rRNA probe revealed morphologically diverse microorganisms resident in the mucus biofilm adjacent to the cecal and proximal colonic epithelium. Hybridizing organisms comprised about 2% of the DAPI (4',6-diamidino-2-phenylindole, dihydrochloride)-positive organisms in the mucus biofilm, but their abundance in fecal material may be much lower. These data indicate that diverse fungal taxa are present in the intestinal microbial community. Their abundance suggests that they may play significant roles in enteric microbial functions.     

Toll-like receptor 2 functions as a pattern recognition receptor for diverse bacterial products

Toll-like receptors (TLRs) 2 and 4 are signal transducers for lipopolysaccharide, the major proinflammatory constituent in the outer membrane of Gram-negative bacteria. We observed that membrane lipoproteins/lipopeptides from Borrelia burgdorferi, Treponema pallidum, and Mycoplasma fermentans activated cells heterologously expressing TLR2 but not those expressing TLR1 or TLR4. These TLR2-expressing cells were also stimulated by living motile B. burgdorferi, suggesting that TLR2 recognition of lipoproteins is relevant to natural Borrelia infection. Importantly, a TLR2 antibody inhibited bacterial lipoprotein/lipopeptide-induced tumor necrosis factor release from human peripheral blood mononuclear cells, and TLR2-null Chinese hamster macrophages were insensitive to lipoprotein/lipopeptide challenge. The data suggest a role for the native protein in cellular activation by these ligands. In addition, TLR2-dependent responses were seen using whole Mycobacterium avium and Staphylococcus aureus, demonstrating that this receptor can function as a signal transducer for a wide spectrum of bacterial products. We conclude that diverse pathogens activate cells through TLR2 and propose that this molecule is a central pattern recognition receptor in host immune responses to microbial invasion.     

Changes in claw morphology of a bioindicator species across habitats that differ in human disturbance

Hydrobiologia - Variations in morphological characteristics are frequently important determinants of the physiology, ecology and inter- and intra-specific interactions of organisms. Various...     

Smokeless tobacco, oxidative stress, apoptosis, and antioxidants in human oral keratinocytes

We have investigated the effects of a smokeless tobacco extract (STE) on lipid peroxidation, cytochrome c reduction, DNA fragmentation and apoptotic cell death in normal human oral keratinocyte cells, and assessed the protective abilities of selected antioxidants. The cells, isolated and cultured from human oral tissues, were treated with STE (0-300 microl;g/ml) for 24 h. Superoxide anion production was determined by cytochrome c reductase. Oxidative tissue damage was determined by lipid peroxidation and DNA fragmentation, whereas apoptotic cell death was assessed by flow cytometry. STE-induced fragmentation of genomic DNA was also determined by gel electrophoresis. The comparative protective abilities of vitamin C (75 microM), vitamin E (75 microM), a combination of vitamins C & E (75 microM each), and a novel grape seed proanthocyanidin (IH636) extract (GSPE) (100 microg/ml) against STE induced oxidative stress and tissue damage were also determined. Following treatment of the cells with 300 microg STE/ml 1.5-7.6-fold increases in lipid peroxidation, cytochrome c reduction and DNA fragmentation were observed. The addition of the antioxidants to cells treated with STE provided 10-54% decreases in these parameters. Approximately 9, 29, and 35% increases in apoptotic cell death were observed following treatment with 100, 200, and 300 microg STE/ml, respectively, and 51-85% decreases in apoptotic cell death were observed with the antioxidants. The results demonstrate that STE produces oxidative tissue damage and apoptosis, which can be attenuated by antioxidants including vitamin C, vitamin E, a combination of vitamins C plus E and GSPE. GSPE exhibited better protection against STE than vitamins C and E, singly and in combination.     

Composition and similarity of bovine rumen microbiota across individual animals

The bovine rumen houses a complex microbiota which is responsible for cattle's remarkable ability to convert indigestible plant mass into food products. Despite this ecosystem's enormous significance for humans, the composition and similarity of bacterial communities across different animals and the possible presence of some bacterial taxa in all animals' rumens have yet to be determined. We characterized the rumen bacterial populations of 16 individual lactating cows using tag amplicon pyrosequencing. Our data showed 51% similarity in bacterial taxa across samples when abundance and occurrence were analyzed using the Bray-Curtis metric. By adding taxon phylogeny to the analysis using a weighted UniFrac metric, the similarity increased to 82%. We also counted 32 genera that are shared by all samples, exhibiting high variability in abundance across samples. Taken together, our results suggest a core microbiome in the bovine rumen. Furthermore, although the bacterial taxa may vary considerably between cow rumens, they appear to be phylogenetically related. This suggests that the functional requirement imposed by the rumen ecological niche selects taxa that potentially share similar genetic features.     

Phylogenetic analysis suggests that habitat filtering is structuring marine bacterial communities across the globe

The phylogenetic structure and community composition were analysed in an existing data set of marine bacterioplankton communities to elucidate the evolutionary and ecological processes dictating the assembly. The communities were sampled from coastal waters at nine locations distributed worldwide and were examined through the use of comprehensive clone libraries of 16S ribosomal RNA genes. The analyses show that the local communities are phylogenetically different from each other and that a majority of them are phylogenetically clustered, i.e. the species (operational taxonomic units) were more related to each other than expected by chance. Accordingly, the local communities were assembled non-randomly from the global pool of available bacterioplankton. Further, the phylogenetic structures of the communities were related to the water temperature at the locations. In agreement with similar studies, including both macroorganisms and bacteria, these results suggest that marine bacterial communities are structured by “habitat filtering”, i.e. through non-random colonization and invasion determined by environmental characteristics. Different bacterial types seem to have different ecological niches that dictate their survival in different habitats. Other eco-evolutionary processes that may contribute to the observed phylogenetic patterns are discussed. The results also imply a mapping between phenotype and phylogenetic relatedness which facilitates the use of community phylogenetic structure analysis to infer ecological and evolutionary assembly processes.     

Digging beneath the surface: incipient nest characteristics across three species of harvester ant that differ in colony founding strategy

Ants exhibit a size-associated colony founding trait that is characterized by the degree to which foundresses rely on internal reserves to raise their first brood of workers (claustrality). The reliance on stored reserves is positively correlated with degree of claustrality (claustral > facultative > semi-claustral) and is variable across species of Pogonomyrmex harvester ants. Three species of harvester ant foundresses that differ in degree of claustrality were observed initiating nests under laboratory conditions over 2 years. P. rugosus is fully claustral, P. salinus is facultative, and P. californicus is semi-claustral. Across species, degree of claustrality was positively associated with mean digging rate and nest depth over the first 3 days of nest initiation, total nest depth, and degree of nest closure. Branching and abundance of peripheral nodes were higher in semi-claustral and facultative nests than in claustral nests. The facultative species dug for the longest time and achieved the greatest tunnel length. Within each species, there were trends associating mass with digging rate, but these were not consistent in all species. There were no intraspecific trends of mass with nest depth. Also within species, a foundress’s mass did not affect her tendency to open or close her nest. These results reveal degree of claustrality is correlated across species with several nest initiation characteristics that together may represent different colony founding syndromes.     

Associations between a highly invasive species and native macrophytes differ across spatial scales

The association between invasive and native species varies across spatial scales and is affected by phylogenetic relatedness, but these issues have rarely been addressed in aquatic ecosystems. In this study, we used a non-native, highly invasive species of Poaceae (tropical signalgrass) to test the hypotheses that (i) tropical signalgrass success correlates negatively with success of most native species of macrophytes at fine spatial scales, but its success correlates positively or at random with natives at coarse spatial scales, and that (ii) tropical signalgrass is less associated with native species belonging to the family Poaceae than with species belonging to other families (Darwin’s naturalization hypothesis). We used a dataset obtained at fine (0.25 m²) and coarse (ca. 1,000 m²) scales. The presence/absence of all species was recorded at both scales, and their biomass was also measured at the fine scale. We tested the association between tropical signalgrass biomass and individual native species with logistic regressions at the fine scale, and using the T-score index between tropical signalgrass and each native species at both scales. The likelihood of the occurrence of six species (submersed and free-floating) was negatively affected by tropical signalgrass biomass at the fine scale. T-scores showed that three species were less associated with tropical signalgrass than expected by chance, but 22 species co-occurred more than expected by chance at the coarse scale. Associations between species of Poaceae and tropical signalgrass were null at the fine scale, but were positive or null at the coarse scale. In addition to showing that spatial scale affects the patterns of association among the non-native and individual native species, our results indicate that phylogeny did not explain associations between the invasive and native macrophytes, at both scales.     

Comparative study of bacterial groups within the human cecal and fecal microbiota

The composition of the human cecal microbiota is poorly known because of sampling difficulties. Samples of cecal fluid from eight subjects were collected via an intestinal tube. Feces were also collected. Total anaerobes, facultative anaerobes, bifidobacteria, and Bacteroides were enumerated by culture methods, and the predominant phylogenetic groups were quantified by molecular hybridization using a set of six rRNA-targeted probes. The numbers of strict anaerobes, bifidobacteria, Bacteroides, and members of the Clostridium coccoides group and Clostridium leptum subgroup were lower in the cecum. Facultative anaerobes represented 25% of total bacteria in the cecum versus 1% in the feces.     

Secondary products in mycorrhizal roots of tobacco and tomato

Colonization of the roots of various tobacco species and cultivars (Nicotiana glauca Grah., N. longiflora Cav., N. rustica L., N. tabacum L., N. tabacum L. cv. Samsun NN, N. sanderae hort. Sander ex Wats.) as well as tomato plants (Lycopersicon esculentum L. cv. Moneymaker) by the arbuscular mycorrhizal fungus Glomus intraradices Schenck and Smith resulted in the accumulation of several glycosylated C13 cyclohexenone derivatives. Eight derivatives were isolated from the mycorrhizal roots by preparative high performance liquid chromatography (HPLC) and spectroscopically identified (MS and NMR) as mono-, di- and triglucosides of 6-(9-hydroxybutyl)-1,1,5-trimethyl-4-cyclohexen-3-one and monoglucosides of 6-(9-hydroxybutyl)-1,5-dimethyl-4-cyclohexen-3-one-1-carboxylic acid and 6-(9-hydroxybutyl)-1,1-dimethyl-4-cyclohexen-3-one-5-carboxylic acid. In contrast to the induced cyclohexenone derivatives, accumulation of the coumarins scopoletin and its glucoside (scopolin) in roots of N. glauca Grah. and N. tabacum L. cv. Samsun NN, was markedly suppressed.     

Early season root production and zoospore infection of cultivars of flue-cured tobacco that differ in level of partial resistance to Phytophthora parasitica var. nicotianae

Root production of four cultivars of flue-cured tobacco was quantified in the field, greenhouse and phytotron. The cultivars ranged in level of partial resistance to the black shank pathogen, Phytophthora parasitica var. nicotianae, from susceptible to highly resistant. In the field, root-observation plates were installed approximately 10 cm from plants, and in greenhouse and phytotron studies, plants were grown in 4-liter containers with one sloping transparent side for root observation. Root growth was determined weekly for four weeks after transplanting in the field and daily up to 14 days after transplanting in the greenhouse and phytotron. Root tracings were made on acetate sheets placed against the sloping transparent side of the containers or against the transparent observation plates in the field following removal of soil from the outside of the observation plate. Root growth was quantified by retracing the root pattern on the acetate sheets over a digitizing tablet attached to a personal computer. Numbers of roots, root length, and mean and maximum rate of root growth were determined. Cultivars Hicks (susceptible) and K-326 (low level of resistance) had significantly larger root systems than moderately resistant G-28 or highly resistant NC 82. Differences in total root length were due to increased branching that resulted in development of significantly greater numbers of roots in Hicks and K-326. For example, between day 21 and 28, Hicks produced more than three times the number of new roots as NC 82 in the field. The mean rate of root extension observed (2.17 mm hr^–1) was similar in all four cultivars. Infection efficiency on the different cultivars was determined in the field by inoculating roots with zoospores of P. p. nicotianae. Lesions were visible as water soaked areas within 24 hr of inoculation. At 48 hr after inoculation, percentages of inoculations that resulted in lesion formation were 57, 46, 23, and 16% for Hicks, K-326, G-28 and NC 82, respectively. The possible role of rooting intensity as a mechanism of avoidance to P. p. nicotianae in tobacco cultivars is discussed.