Significant Intra-species Variation Research Articles

Uncharacterized and lineage-specific accessory genes within the Proteus mirabilis pan-genome landscape.

Proteus mirabilis is a Gram-negative bacterium recognized for its unique swarming motility and urease activity. A previous proteomic report on four strains hypothesized that, unlike other Gram-negative bacteria, P. mirabilis may not exhibit significant intraspecies variation in gene content. However, there has not been a comprehensive analysis of large numbers of P. mirabilis genomes from various sources to support or refute this hypothesis. We performed comparative genomic analysis on 2,060 Proteus genomes. We sequenced the genomes of 893 isolates recovered from clinical specimens from three large US academic medical centers, combined with 1,006 genomes from NCBI Assembly and 161 genomes assembled from Illumina reads in the public domain. We used average nucleotide identity (ANI) to delineate species and subspecies, core genome phylogenetic analysis to identify clusters of highly related P. mirabilis genomes, and pan-genome annotation to identify genes of interest not present in the model P. mirabilis strain HI4320. Within our cohort, Proteus is composed of 10 named species and 5 uncharacterized genomospecies. P. mirabilis can be subdivided into three subspecies; subspecies 1 represented 96.7% (1,822/1,883) of all genomes. The P. mirabilis pan-genome includes 15,399 genes outside of HI4320, and 34.3% (5,282/15,399) of these genes have no putative assigned function. Subspecies 1 is composed of several highly related clonal groups. Prophages and gene clusters encoding putatively extracellular-facing proteins are associated with clonal groups. Uncharacterized genes not present in the model strain P. mirabilis HI4320 but with homology to known virulence-associated operons can be identified within the pan-genome. IMPORTANCE Gram-negative bacteria use a variety of extracellular facing factors to interact with eukaryotic hosts. Due to intraspecies genetic variability, these factors may not be present in the model strain for a given organism, potentially providing incomplete understanding of host-microbial interactions. In contrast to previous reports on P. mirabilis, but similar to other Gram-negative bacteria, P. mirabilis has a mosaic genome with a linkage between phylogenetic position and accessory genome content. P. mirabilis encodes a variety of genes that may impact host-microbe dynamics beyond what is represented in the model strain HI4320. The diverse, whole-genome characterized strain bank from this work can be used in conjunction with reverse genetic and infection models to better understand the impact of accessory genome content on bacterial physiology and pathogenesis of infection.

Survey of the Intestinal Bacterial Compositions of Three Sympatric Passeriformes Species

Aims: The gut microbiota of avian species, especially wild birds, is studied less than that of mammals. Moreover, due to ethical concerns, a vast majority of microbiota studies have been limited to their feces. In this study, we investigated the microbial composition in the upper intestinal tract of sympatric, heterospecific bird species.
 Study Design: We obtained samples from three wild bird species belonging in the same Order Passeriformes: Cedar Waxwing (Bombycilla cedrorum), American Robin (Turdus migratorius) and Dark-eyed Junco (Junco hyemalis). The samples were obtained from wild birds soon after they died due to physical injury. Microbial diversity was analyzed via high-throughput sequencing of 16S rRNA gene fragments.
 Place and Duration of Study: Indiana University Kokomo campus, Indiana. United States, between October 2019 and December 2020.
 Methodology: Illumina Miseq sequencing of V3-V4 region of the 16S rRNA gene was employed to determine microbial composition. The α and β diversity were determined by Shannon’s diversity index and principal coordinate analysis, respectively. Pair-wise comparison of Bray-Curtis dissimilarity between birds of same species, different species, collection dates and years were analyzed.
 Results: The proteobacterial sequences were predominant in all samples. However, the comparison at the level of bacterial class revealed a significant intraspecies variation in both α and β diversity. Additionally, some microbiota exhibited higher interspecies similarity than intraspecies similarity, despite these birds not sharing the same foraging guilds.
 Conclusion: Our study revealed high variability in the microbial compositions within the upper part of the digestive tract of closely related Passeriform birds in their natural environment.

Volatile profiles of commercial vetch prepared via different processing methods

Vicia sativa (Common Vetch) is currently an underutilised leguminous crop species with high protein content and superior drought tolerance. This study aimed to understand the mechanisms behind vetch flavor development following processing to facilitate its uptake as a future source of dietary protein. A total of 95 volatile compounds were identified by solid-phase microextraction gas chromatography-mass spectrometry (SPME GC–MS) for a range of vetches processed by dehulling, soaking, germination, microwaving, and fermentation.2-pentyl furan, benzyl alcohol, benzaldehyde, 1-octen-3-ol and 1-hexanol were found to be characteristic aroma compounds of V. sativa. Analysis of a V. sativa landrace demonstrated significant intraspecies variation in volatile abundance, three-fold that of commercial varieties. Both natto and tempeh fermentation produced significant quantities of alcohols, esters, and carboxylic acids with specifically natto generating significant pyrazines. Concentrations of 1-octen-3-ol significantly decreased after tempeh fermentation indicating its potential to reduce documented off flavor generating volatiles within V. sativa.

Comparative Grain Chemical Composition, Ruminal Degradation In Vivo, and Intestinal Digestibility In Vitro of Vicia Sativa L. Varieties Grown on the Tibetan Plateau.

Simple SummaryCommon vetch (Vicia sativa L.) grain is an important source of protein in rations for ruminants, but little information is available on the protein value of common vetch grains, both in terms of chemical composition and protein degradability, and regarding variation between intra-species and year. The objective of this study was to evaluate grain chemical composition, ruminal protein degradability in vivo, and intestinal protein digestibility in vitro of four common vetch varieties over two cropping years on the Tibetan Plateau. This study was also conducted to establish correlations of grain chemical composition with ruminal degradability parameters of grain protein and with intestinal digestibility of grain protein. Results of this study demonstrated that grain quality characteristics varied significantly among varieties and years. The relationship between grain chemical composition and intestinally absorbable digestible protein (IADP) was best described by a linear regression equation, and coefficients of determination remained very high (R2 = 0.891). Overall, the results indicated that in terms of effective crude protein degradability and IADP of grain, common vetch varieties Lanjian No. 2 and Lanjian No. 3 have the greatest potential among varieties examined for supplementing ruminant diets when grown on the Tibetan Plateau.Four varieties of common vetch, three improved varieties and one local variety, were evaluated for grain chemical composition, rumen protein degradability, and intestinal protein digestibility over two cropping years on the Tibetan Plateau. This study also examined correlations of grain chemical composition with rumen degradability parameters of grain protein and with intestinal digestibility of grain protein. Results of this study showed that grain quality attributes varied (p < 0.05) among varieties and cropping years. Significant intra-species variation was observed for concentrations (g/kg dry matter) of crude protein (CP; range = 347–374), ether extract (range = 15.8–19.6), neutral detergent fiber (aNDF; range = 201–237), acid detergent fiber (range = 58.2–71.6), ash (range = 27.6–31.0), effective CP degradability (EDCP; range = 732–801 g/kg CP), and intestinally absorbable digestible protein (IADP; range = 136–208 g/kg CP). The relationship between grain chemical composition and IADP was best described by the linear regression equation IADP = –0.828CP + 8.80ash + 0.635aNDF + 70.2 (R2 = 0.891), indicating that chemical analysis offers a quick and reliable method for IADP of common vetch grain. In terms of EDCP and IADP of grain, common vetch varieties, Lanjian No.2 and Lanjian No. 3, have the greatest potential among varieties tested for supplementing ruminant diets when grown on the Tibetan Plateau.

Application of the consolidated species concept to identify the causal agent of strawberry anthracnose in Iran and initial molecular dating of the Colletotrichum acutatum species complex

Anthracnose caused by Colletotrichum spp. is one of main strawberry diseases worldwide. The disease recently arrived in Iran and become epidemic in the Kurdistan province. A combination of morphological, molecular and pathogen-host interaction approaches (referred to the consolidated species concept) were applied to isolates from symptomatic strawberry tissues collected in Iran. Multi-gene phylogenetic analysis based on ITS-rDNA, beta-tubulin (TUB2) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) identified the species as the S5 clade of Colletotrichum nymphaeae. No significant intraspecies variation was observed in terms of morphology and pathogenicity. No significant genetic variation was observed among the isolates using inter simple sequence repeat analysis (ISSR) and primer pair combination of ERIC1/BOX and ERIC2/BOX fingerprinting markers. Based on the results of this study, it can be postulated that the C. nymphaeae population in Iran established itself from a single origin due to a founder effect. More generally, molecular dating based on relaxed clocks indicates co-radiation of C. nymphaeae S5 and strawberry plants and suggests high reciprocal specificity between the host and pathogen.

Molecular characterization and population structure of blackberry vein banding associated virus, new ampelovirus associated with yellow vein disease

Blackberry yellow vein disease is the most important viral disease of blackberry in the United States. Experiments were conducted to characterize a new virus identified in symptomatic plants. Molecular analysis revealed a genome organization resembling Grapevine leafroll-associated virus 3, the type species of the genus Ampelovirus in the family Closteroviridae. The genome of the virus, provisionally named blackberry vein banding associated virus (BVBaV), consists of 18,643 nucleotides and contains 10 open reading frames (ORFs). These ORFs encode closterovirid signature replication-associated and quintuple gene block proteins, as well as four additional proteins of unknown function. Phylogenetic analyses of taxonomically relevant products consistently placed BVBaV in the same cluster with GLRaV-3 and other members of the subgroup I of the genus Ampelovirus. The virus population structure in the U.S. was studied using the replication associated polyprotein 1a, heat shock 70 homolog and minor coat proteins of 25 isolates. This study revealed significant intra-species variation without any clustering among isolates based on their geographic origin. Further analyses indicated that these proteins are under stringent purifying selections. High genetic variability and incongruent clustering of isolates suggested the possible involvement of recombination in the evolution of BVBaV.

A chemotaxonomic assessment of four indigenous South African Lippia species using GC–MS and vibrational spectroscopy of the essential oils

Lippia species are widely used as traditional remedies by many South African communities. The identification of Lippia spp. indigenous to South Africa is currently based on the morphology and geographical origin of the specimen. However, morphological similarities are evident and due to sympatric distributions, different species may co-occur in the same natural environment, thereby presenting difficulties in the taxonomic delimitation of these taxa. In this paper, gas chromatography–mass spectrometry (GC–MS) and vibrational spectroscopic analyses were used to investigate the chemotaxonomic differentiation of four Lippia species (L. javanica, L. scaberrima, L. rehmannii and L. wilmsii), based on the essential oil composition. The results demonstrate that multivariate classification of chromatographic data enabled separation of Lippia oils into three distinct clusters representing L. scaberrima, L. rehmannii and L. javanica. With the aid of chemometric algorithms, it was also possible to use both mid infrared (MIR) and near infrared (NIR) spectroscopy for a clear distinction of the Lippia spp., with results comparable to those obtained by GC–MS. Orthogonal projections to latent structures (OPLS) presented a better classification algorithm than principal component analysis (PCA), in both GC–MS and spectroscopy analyses. Chemical variations within the Lippia spp. complex were evident, particularly for L. javanica and L. scaberrima, which exhibited significant intra-species variation.

Anatomical, biochemical, and photosynthetic responses to recent allopolyploidy in Glycine dolichocarpa (Fabaceae)

Previous studies have shown that polyploidy has pronounced effects on photosynthesis. Most of these studies have focused on synthetic or recently formed autopolyploids, and comparatively little is known about the integrated effects of natural allopolyploidy, which involves hybridity and genome doubling and often incorporates multiple genotypes through recurrent origins and lineage recombination. Glycine dolichocarpa (designated T2) is a natural allotetraploid with multiple origins. We quantified 21 anatomical, biochemical, and physiological phenotypes relating to photosynthesis in T2 and its diploid progenitors, G. tomentella (D3) and G. syndetika (D4). To assess how direction of cross affects these phenotypes, we included three T2 accessions having D3-like plastids (T2(D3)) and two accessions having D4-like plastids (T2(D4)). T2 accessions were transgressive (more extreme than any diploid accession) for 17 of 21 phenotypes, and species means differed significantly in T2 vs. both progenitors for four of 21 phenotypes (higher for guard cell length, electron transport capacity [J(max)] per palisade cell, and J(max) per mesophyll cell; lower for palisade cells per unit leaf area). Within T2, four of 21 parameters differed significantly between T2(D3) and T2(D4) (palisade cell volume; chloroplast number and volume per unit leaf area; and J(max) per unit leaf area). T2 is characterized by transgressive photosynthesis-related phenotypes (including an ca. 2-fold increase in J(max) per cell), as well as by significant intraspecies variation correlating with plastid type. These data indicate prominent roles for both nucleotypic effects and cytoplasmic factors in photosynthetic responses to allopolyploidy.

Altitudinal size clines, species richness and population density: case studies in Orthoptera

We examined size clines for various external body structures in two grasshopper species (Chorthippus vagans and Oedipoda miniata) and one katydid species (Poecilimon birandi), along an altitudinal gradient ranging from sea level to 1,980 m in southwest Anatolia (Turkey). In O. miniata and P. birandi all measured structures (body, tegmina, pronotum, and hind femur) were smallest at the highest altitude for both sexes. Hence, in these species, different structures covaried in the same direction, with increasing altitude. In contrast, there was no clear relationship between altitude and size in C. vagans, and different structures covaried in different directions in males and females (i.e., some structures became larger at higher elevations, whereas others became smaller, and this differed with sex). For some other C. vagans traits, there was no significant intraspecies variation. Hence, O. miniata and P. birandi followed the converse Bergmann's Rule, whereas there was no consistent pattern for C. vagans. For C. vagans, small body size was not associated with either local population density (measured as relative abundance) or local species richness, suggesting that neither intra- nor interspecific competition determined body size for this species. For O. miniata, the smallest individuals were found at the site with the highest grasshopper diversity, suggesting that interspecific competition could have influenced O. miniata body sizes at this altitude. However, the largest O. miniata individuals generally occurred at the sites with the highest relative abundance of O miniata. Hence, in this species, body sizes were generally larger at sites with high population densities — consistent with sites that were most favorable and so able to support high densities of O miniata also producing the largest individuals of this species. Observational data on P. birandi similarly suggested that, for this katydid, there is little relationship between local diversity/abundance and altitudinal size-clines.

Waterlogging tolerance and recovery of 10 Lotus species

Medicago sativa L. is the most widely sown perennial forage legume in farming systems of southern Australia. However, M. sativa lacks adaptation to winter waterlogged conditions. This constraint has highlighted the need for new perennial forage legumes adapted to winter waterlogged conditions and to locations where the summer is too dry for the survival of Trifolium repens L. and T. fragiferum L. To explore new perennial legume options suitable for these circumstances, 10 species of Lotus were evaluated for waterlogging tolerance including: two accessions of L. corniculatus L., four accessions of L. tenuis Waldst. &amp; Kit., two accessions of L. pedunculatus Cav., two accessions of L. australis Andrew, three accessions of L. creticus L., three accessions of L. glaucus Sol., one accession of L. cruentus Court., one accession of L. argyrodes R.P. Murray, one accession of L. campylocladus Webb &amp; Berthel and one accession of L. latifolius Brand. These were compared with the M. sativa cultivar Sceptre. The ability to grow in waterlogged conditions, and to recover, was assessed in a pot experiment conducted over 19 weeks. The Lotus species most tolerant of waterlogging were L. corniculatus, L. tenuis and L. pedunculatus. Each of these species developed aerenchyma, adventitious roots, surface roots and split stems at the base to improve oxygen transport into the roots. Significant intra-species variation was also found within each of the three tolerant species, highlighting the opportunity for genetic improvement. By comparison, the remaining Lotus species were susceptible to waterlogging and showed poor recovery, whereas M. sativa Sceptre partially recovered after waterlogging.

&lt;b&gt;Intra-species variation of the properties of gum exudates from &lt;i&gt;Acacia Senegal&lt;/i&gt; var. &lt;i&gt;Senegal&lt;/i&gt; and &lt;i&gt;Acacia seyal&lt;/i&gt; var.&lt;i&gt; fistula&lt;/i&gt; from Tanzania&lt;/b&gt;

Gum exudates from Acacia senegal var. senegal and Acacia seyal var. fistula from Tanzania have been analyzed and their inter- and intra-species variation of their properties evaluated. The results show that significant inter-species variation of the properties of the gum exudates from the two species exist, whereas only some parameters show significant intra-species variation. The specific optical rotations of the gum exudates have been found to vary from –43.2 o to –52 o for Acacia senegal var. senegal and +36.0 o to +60.0 o for A. seyal var. fistula. Likewise, the acid equivalent weights (AEWs) have been found to vary from 1093 to 1920 for A. senegal var. senegal and 1063 to 1749 for A. seyal var. fistula . Significant intra-species variation for the tannin content has also been observed for the species studied, whereas the nitrogen content has been observed to vary significantly only in A. seyal var. fistula. The results in this study show that the variation of the properties among batches of commercial Acacia gum may be due to admixture of gums from different Acacia species as well as intra-species variation. KEY WORDS: Acacia senegal var. senegal , Acacia seyal var. fistula , Gum exudates, Intra-species variation, Inter-species variation Bull. Chem. Soc. Ethiop. 2003 , 17(1), 67-74.

Adhesion of Candida parapsilosis to epithelial and acrylic surfaces correlates with cell surface hydrophobicity.

We investigated in vitro adherence of 24 isolates of Candida parapsilosis and 12 isolates of Candida albicans with regard to their relative cell-surface hydrophobicity (CSH), adherence to human buccal epithelial cells (BEC) and acrylic surfaces. There was no significant interspecies difference in the relative adherence of C. parapsilosis and C. albicans isolates to BEC, although the former demonstrated a tendency for increased adherence. However, a significant intra-species variation in adherence among isolates of C. parapsilosis (P < 0.0001) to BEC, but not of C. albicans was noted. The superficial isolates of C. parapsilosis demonstrated a higher avidity (33%) to BEC than the systemic isolates. On regression analysis a significant positive correlation between C. parapsilosis adherence to BEC and denture acrylic surfaces was noted (r = 0.45, P = 0.02). Similarly, buccal cell adherence correlated strongly with CSH of C. parapsilosis (r = 0.63, P = 0.0008). These results shed further light on the intimate relationship between adherence and CSH in candidal colonization and imply that both C. parapsilosis and C. albicans are equally potent in colonizing mucosal surfaces with respect to the attributes investigated.

In vitro susceptibility of Candida species to lactoferrin.

Lactoferrin is an antimicrobial protein present in human mucosal secretions as well as saliva. As there is no information on the relative fungicidal activity of human and bovine lactoferrin, an oral isolate of Candida albicans was studied for its susceptibility to these two proteins. Exposure to a concentration of 20 micrograms ml-1 of either HLF or BLF at 37 degrees C inactivated the yeast to the same degree irrespective of the incubation time of 45, 90 or 150 min. A similar study, using 20 micrograms ml-1 BLF and an incubation time of 150 min, elicited varying anticandidal activity against 35 isolates belonging to six different Candida species. Thus, BLF was fungicidal for the six Candida species in the following decreasing order, C. tropicalis > C. krusei > C. albicans > C. guilliermondii > C. parapsilosis > C. glabrata; the latter being the most resistant. These Candida species also demonstrated significant intra-species variation in susceptibility to the protein (P < 0.05). When the yeast cells exposed to BLF were examined by cryo-scanning electron microscopy, profound cell wall changes such as cell surface blebs, swelling and cell collapse were noted. These findings suggest that lactoferrin, a constituent of saliva, may differentially modulate the carriage of Candida species in the oral cavity.

Adhesion to denture acrylic surfaces and relative cell‐surface hydrophobicity of Candida parapsilosis and Candida albicans

C. parapsilosis is an opportunistic emerging pathogen which together with C. albicans causes diseases in immunocompromised patients. Adhesion of Candida species to various surfaces is an important event in colonization and pathogenesis, and the relative cell-surface hydrophobicity (CSH) of the organism is a contributory physical force involved. Therefore, in vitro adhesion to acrylic surfaces and relative CSH of 24 isolates of C. parapsilosis and 10 isolates of C. albicans were studied. There was no significant difference in relative adhesion of C. parapsilosis isolates and C. albicans, although the former demonstrated a tendency for increased adhesion. There was significant intra-species variation in adhesion among isolates of C. parapsilosis (p=0.0001), but not C. albicans. In general, C. parapsilosis isolates demonstrated a two-fold greater relative CSH than C. albicans (p=0.0003). When the relative CSH of superficial and systemic isolates of C. parapsilosis were compared, the former showed a significantly higher (49.15%) relative CSH than their systemic counterparts (p<0.01). A highly significant positive correlation between adhesion and relative CSH of C. parapsilosis (p=0.74, p<0.0001) was also noted. Taken together, these data suggest that the attributes of adhesion and relative CSH of Candida species may contribute differentially in varying disease states of the human host, such as superficial and systemic Candida infections.

Antifungal activityin vitroof Ro 14-4767/002, a phenylpropyl-morpholine

Minimal inhibitory concentrations (MICs) of Ro 14-4767/002 for pathogenic yeasts, Aspergillus spp., dermatophytes and other filamentous fungi were determined in dilution tests under a variety of experimental conditions and, for the most of the species and a number of different isolates. Ro 14-4767/002 showed the highest effect against dermatophytes and Cryptococcus neoformans, followed by Candida spp., whereas its activity against Aspergillus spp. was weak. Its activity against most pathogens compared favourably with antifungals of the imidazole class. The activity of Ro 14-4767/002 not only differed between the species but there was also a significant intra-species variation. The MICs were influenced by the inoculum size, the incubation time, and by the composition of the medium. The activity of the compound was significantly higher on Casitone agar than on a chemically defined medium (Yeast Nitrogen Base + glucose). Ro 14-4767/002 was also found to exert fungicidal activity which was time- and concentration-dependent.

Intraspecies and interspecies variations in the substrate specificity of d-amino acid oxidase

1. 1. Substrate specificity of d-amino acid oxidase was examined in the kidney homogenates of the mouse and the six species of fishes. 2. 2. The enzyme of the mouse did not show a significant intraspecies variation in the substrate specificity. The sex and age of the mouse did not affect the substrate specificity of the enzyme. 3. 3. The degree of similarity in the substrate specificity of the enzymes was quantified as the variation index. The values of the variation index among the enzymes of the fishes paralleled their taxonomic relatedness.