Comprehensive total evidence phylogeny of chinchillids (Rodentia,Caviomorpha): Cheek teeth anatomy and evolution

Rodents are the most diverse order of extant mammals, and caviomorph rodents, or New World hystricognaths, have a remarkable morphological disparity and a long fossil record that begins in the Eocene. Chinchilloidea is a poorly understood clade within Caviomorpha, from an evolutionary and phylogenetic perspective. It includes the extant families Chinchillidae and Dinomyidae, the extinct Neoepiblemidae and Cephalomyidae, and several extinct chinchilloids without a clear phylogenetic position, like Eoincamys, Borikenomys, Chambiramys, Ucayalimys, Incamys, Saremmys, Garridomys and Scotamys. The family Chinchillidae includes the extant Chinchilla and Lagidium, grouped in Chinchillinae, and the only living Lagostominae, Lagostomus maximus. Among extinct chinchillids, Eoviscaccia (early Oligocene-early Miocene of Argentina, Bolivia and Chile), Prolagostomus (early-middle Miocene of Argentina, Bolivia and Chile) and Pliolagostomus (early-middle Miocene of Argentina) are the only genera originally described as members of the family. Based on the study of specimens with unworn or little-worn cheek teeth, belonging to extinct and extant taxa, we propose homologies of the cheek teeth structures and perform a combined molecular and morphological phylogenetic analysis including extinct and extant taxa of all families of Chinchilloidea and all genera of Chinchillidae. Our phylogenetic analysis recovered three major lineages in the evolutionary history of Chinchilloidea. The first major lineage is composed of the extant taxa Chinchilla, Lagidium and Lagostomus, and the extinct genera Eoviscaccia, Prolagostomus, Pliolagostomus, Garridomys, Incamys, Loncolicu and Saremmys. Cephalomyid (Banderomys, Cephalomys, Litodontomys, Soriamys) and neoepiblemid (Neoepiblema, Perimys, Phoberomys, Scotamys) genera are part of the second major lineage, while dinomyids such as Dinomys, Drytomomys, Scleromys, ‘Scleromys’ and Tetrastylus constitute the third major lineage within Chinchilloidea. The phylogenetic position of some taxa previously considered as incertae sedis chinchilloids or without a clear suprageneric group (i.e. Incamys, Saremmys, Garridomys and Loncolicu) show that they belong to pan-Chinchillidae and conform the stem Chinchillidae along with Eoviscaccia. The euhypsodont crown Chinchillidae includes the living subfamilies Chinchillinae and Lagostominae. Dinomyidae and Eoincamys pascuali are recovered as the sisters of a major clade composed by ‘Cephalomyidae’+Neopiblemidae and pan-Chinchillidae, and Chambiramys sylvaticus occupies a basal position to the same clade. Four major radiation events are identified in the evolutionary history of Chinchilloidea. The analysis of new morphological characters linked with molecular evidence as well as the addition of taxa of uncertain or unstable phylogenetic position or not considered in previous studies allowed us resolve part of the relationships within Chinchilloidea, particularly that of Chinchillidae, supporting preceding morphological hypotheses.     

Can hominin ‘handedness’ be accurately assessed?

The expression of a strong, population-level right hand preference has, to date only been unequivocally identified in Homo sapiens and is often considered to be unique to this species. For this reason, and because of purported co-evolutionary links between this trait and language capabilities in modern humans, the identification of hand preference in the hominin fossil record has long been of interest to researchers studying the evolution of ‘handedness’ within the genus Homo.

Identifying hand preference in skeletal samples, however, is not straightforward. Problems arise from difficulties in determining the precise nature of the relationship between hand use and bone morphology, the methods by which hand preference is assessed, the paucity of material available for study, and even what is meant by the term ‘handedness’.

Various attempts have been made to address these issues, encompassing a range of methodological approaches, such as comparisons of osteological techniques, studies of prehistoric material culture and ethnographic analysis of hand use behaviours in modern hunter–gatherer societies and non-human primate groups. What such research suggests is that hand preference is a complex phenomenon, in both extant and extinct groups, and in order to assess its expression in extinct populations care must be paid to the questions asked of the available material and the methodologies used to answer them.     

Some studies on insect parasitic nematodes (Oxyurida,Thelastomatoidea, Thelastomatidae) from Manipur,North-East India

Four known species of insect parasitic nematodes were recovered from Periplaneta americana and Gryllotalpa africana. They are all redescribed in the present study. Key to species along with comparative measurement chart of all known species of Leidynema, Gryllophila and Hammerschmidtiella have been provided. Based on additional features that were not provided by previous workers the emended generic diagnosis of Thelastoma, Leidynema, and Hammerschmidtiella have been provided in the present study.     

The middle ear of the pink fairy armadillo Chlamyphorus truncatus (Xenarthra,Cingulata, Chlamyphoridae): comparison with armadillo relatives using computed tomography

The pink fairy armadillo Chlamyphorus truncatus is the smallest extant armadillo and one of the least-known fossorial mammals. The aim of this study was to establish if its middle ear is specially adapted to the subterranean environment, through comparison with more epigeic relatives of the groups Euphractinae (Chaetophractus villosus, Chaetophractus vellerosus, Zaedyus pichiy) and Dasypodinae (Dasypus hybridus). We examined the middle ears using micro-computed tomography and subsequent three-dimensional reconstructions. D. hybridus has a relatively small middle ear cavity, an incomplete bulla and ‘ancestral’ ossicular morphology. The other species, including Chlamyphorus, have fully ossified bullae and middle ear ossicles, with a morphology between ‘transitional’ and ‘freely mobile’, but in all armadillos the malleus retains a long anterior process. Unusual features of armadillo ears include the lack of a pedicellate lenticular apophysis and the presence, in some species, of an element of Paaw within the stapedius muscle. In common with many subterranean mammals, Chlamyphorus has a relatively flattened malleo-incudal articulation and appears to lack a functional tensor tympani muscle. Its middle ear cavity is not unusually enlarged, and its middle ear ossicles seem less robust than those of the other armadillos studied. In comparison with the euphractines, there is no reason to believe that the middle ear of this species is specially adapted to the subterranean environment; some aspects may even be indicative of degeneration. The screaming hairy armadillo, Chaetophractus vellerosus, has the most voluminous middle ear in both relative and absolute terms. Its hypertrophied middle ear cavity likely represents an adaptation to low-frequency hearing in arid rather than subterranean conditions.     

Virtual endocranial and inner ear endocasts of the Paleocene ‘condylarth’ Chriacus: new insight into the neurosensory system and evolution of early placental mammals

The end-Cretaceous mass extinction allowed placental mammals to diversify ecologically and taxonomically as they filled ecological niches once occupied by non-avian dinosaurs and more basal mammals. Little is known, however, about how the neurosensory systems of mammals changed after the extinction, and what role these systems played in mammalian diversification. We here use high-resolution computed tomography (CT) scanning to describe the endocranial and inner ear endocasts of two species, Chriacus pelvidens and Chriacus baldwini, which belong to a cluster of ‘archaic’ placental mammals called ‘arctocyonid condylarths’ that thrived during the ca. 10 million years after the extinction (the Paleocene Epoch), but whose relationships to extant placentals are poorly understood. The endocasts provide new insight into the paleobiology of the long-mysterious ‘arctocyonids’, and suggest that Chriacus was an animal with an encephalization quotient (EQ) range of 0.12–0.41, which probably relied more on its sense of smell than vision, because the olfactory bulbs are proportionally large but the neocortex and petrosal lobules are less developed. Agility scores, estimated from the dimensions of the semicircular canals of the inner ear, indicate that Chriacus was slow to moderately agile, and its hearing capabilities, estimated from cochlear dimensions, suggest similarities with the extant aardvark. Chriacus shares many brain features with other Paleocene mammals, such as a small lissencephalic brain, large olfactory bulbs and small petrosal lobules, which are likely plesiomorphic for Placentalia. The inner ear of Chriacus also shares derived characteristics of the elliptical and spherical recesses with extinct species that belong to Euungulata, the extant placental group that includes artiodactyls and perissodactyls. This lends key evidence to the hypothesized close relationship between Chriacus and the extant ungulate groups, and demonstrates that neurosensory features can provide important insight into both the paleobiology and relationships of early placental mammals.     

Hominid mandibular corpus shape variation and its utility for recognizing species diversity within fossil Homo

Mandibular corpora are well represented in the hominin fossil record, yet few studies have rigorously assessed the utility of mandibular corpus morphology for species recognition, particularly with respect to the linear dimensions that are most commonly available. In this study, we explored the extent to which commonly preserved mandibular corpus morphology can be used to: (i) discriminate among extant hominid taxa and (ii) support species designations among fossil specimens assigned to the genus Homo. In the first part of the study, discriminant analysis was used to test for significant differences in mandibular corpus shape at different taxonomic levels (genus, species and subspecies) among extant hominid taxa (i.e. Homo, Pan, Gorilla, Pongo). In the second part of the study, we examined shape variation among fossil mandibles assigned to Homo (including H. habilis sensu stricto, H. rudolfensis, early African H. erectus/H. ergaster, late African H. erectus, Asian H. erectus, H. heidelbergensis, H. neanderthalensis and H. sapiens). A novel randomization procedure designed for small samples (and using group ‘distinctness values’) was used to determine whether shape variation among the fossils is consistent with conventional taxonomy (or alternatively, whether a priori taxonomic groupings are completely random with respect to mandibular morphology). The randomization of ‘distinctness values’ was also used on the extant samples to assess the ability of the test to recognize known taxa. The discriminant analysis results demonstrated that, even for a relatively modest set of traditional mandibular corpus measurements, we can detect significant differences among extant hominids at the genus and species levels, and, in some cases, also at the subspecies level. Although the randomization of ‘distinctness values’ test is more conservative than discriminant analysis (based on comparisons with extant specimens), we were able to detect at least four distinct groups among the fossil specimens (i.e. H. sapiens, H. heidelbergensis, Asian H. erectus and a combined ‘African Homo’ group consisting of H. habilis sensu stricto, H. rudolfensis, early African H. erectus/H. ergaster and late African H. erectus). These four groups appear to be distinct at a level similar to, or greater than, that of modern hominid species. In addition, the mandibular corpora of H. neanderthalensis could be distinguished from those of ‘African Homo’, although not from those of H. sapiens, H. heidelbergensis, or the Asian H. erectus group. The results suggest that the features most commonly preserved on the hominin mandibular corpus have some taxonomic utility, although they are unlikely to be useful in generating a reliable alpha taxonomy for early African members of the genus Homo.     

Phylogenetic diversity and antagonistic traits of root and rhizosphere pseudomonads of bean from Iran for controlling Rhizoctonia solani

Fluorescent pseudomonads from bean root and rhizosphere in Iran were investigated for biocontrol of the fungal pathogen Rhizoctonia solani. Phylogenetic analysis of concatenated 16S rRNA, gyrB and rpoD sequences for 33 Pseudomonas isolates showed that 15 belonged to four clusters within the ‘P. fluorescens’ group, i.e. one corresponding to P. thivervalensis, two others including P. moraviensis or P. baetica, and the last one without closely-related established species. The 18 other isolates belonged to five clusters within the ‘P. putida’ group, one including P. mosselii and P. entomophila, another including strains currently described as P. putida, and three without closely-related species described. Ten isolates were selected based on in vitro inhibition of R. solani. Cellulase activity was identified in three pseudomonads, chitinase activity in two pseudomonads, extracellular protease activity in nine pseudomonads and hydrogen cyanide production in two pseudomonads. Genes coding for production of phenazine, pyoluteorin, pyrrolnitrin and 2,4-diacetylphloroglucinol were not found, whereas the 1-aminocyclopropane-1-carboxylate deamination gene acdS was present in three pseudomonads. The antagonistic acdS⁺ strain VKh13 from the ‘P. putida’ group effectively protected soil-grown bean from R. solani AG 4-HGI. Results show that pseudomonads from uncharacterized taxa were readily obtained from Iranian soils and displayed biocontrol potential against R. solani.     

The skull of the Miocene Spheniscus urbinai (Aves,Sphenisciformes): osteology,brain morphology,and the cranial pneumatic systems

Spheniscus urbinai represents one of four extinct Spheniscus species from the Cenozoic of southern South America, known from several poorly described diversely complete skulls and postcranial elements. Here, we present a review of the cranial osteology of all known specimens (collected in Argentina, Chile, and Peru), including a paleoneurological analysis using CT scans, and an exploration of its cranial pneumaticity compared to other extinct and living seabirds. Our results show that among Spheniscus species, S. urbinai exhibits slightly greater cranial pneumaticity than the living species. Additionally, we confirm previous findings which indicate that the marked reduction of cranial pneumaticity—which is characteristic of living penguins—occurred early during the Eocene (as observed in the Antarctic penguin MLP 12-I-20-1, but not in the coeval Anthropornis).     

Two novel forms of ERG oscillation in Drosophila: age and activity dependence

Over an animal’s lifespan, neuronal circuits and systems often decline in an inherently heterogeneous fashion. To compare the age-dependent progression of changes in visual behavior with alterations in retinal physiology, we examined phototaxis and electroretinograms (ERGs) in a wild-type D. melanogaster strain (Canton-S) across their lifespan. In aged flies (beyond 50% median lifespan), we found a marked decline in phototaxis, while motor coordination was less disrupted, as indicated by relatively stronger negative geotaxis. These aged flies displayed substantially reduced ERG transient amplitudes while the receptor potentials (RP) remained largely intact. Using a repetitive light flash protocol, we serendipitously discovered two forms of activity-dependent oscillation in the ERG waveforms of young flies: ‘light-off’ and ‘light-on’ oscillations. After repeated 500?ms light flashes, light-off oscillations appeared during the ERG off-transients (frequency: 50–120?Hz, amplitude: ～1?mV). Light-on oscillations (100–200?Hz, ～0.3?mV) were induced by a series of 50?ms flashes, and were evident during the ERG on-transients. Both forms of oscillation were observed in other strains of D. melanogaster (Oregon-R, Berlin), additional Drosophila species (D. funerbris, D. euronotus, D. hydei, D. americana), and were evoked by a variety of light sources. Both light-off and light-on oscillations were distinct from previously described ERG oscillations in the visual mutant rosA in terms of location within the waveform and frequency. However, within rosA mutants, light-off oscillations, but not light-on oscillations could be recruited by the repetitive light flash protocol. Importantly though, we found that both forms of oscillation were rarely observed in aged flies. Although the physiological bases of these oscillations remain to be elucidated, they may provide important clues to age-related changes in neuronal excitability and synaptic transmission.     

Stillbirth, neonatal death and birth interval

1. The time interval between a confinement and the initiation of a subsequent pregnancy is called a ‘conception delay’. Under some circumstances, the interval between the two confinements (‘birth interval’) is a useful criterion of conception delay. 2. When data from a large sample of women are pooled, both stillbirths and neonatal deaths are associated with both long and short birth intervals. 3. However, there is evidence that brief birth intervals are not associated with stillbirths within sibships. It follows that short conception delays are not a cause of the stillbirths associated with them. 4. In contrast, stillbirths are associated, within sibships, with long birth intervals. 5. The cause of this association cannot be uncovered by analyses of this sort, but it seems very possible that very long conception delays may be one cause: others have been suggested. 6. The evidence in regard to neonatal death is less clear: but on balance, there seems to be an association, within sibships, between neonatal death and short birth intervals. There are grounds for believing this association to be, partly at least, the result of statistical artifacts.     

Evaluation of the Staph-Zym system in the identification of staphylococci isolated from ovine milk and the ewe environment

The Staph-Zym and the Rosco Set methods were used to assign species to 142 strains of staphylococci isolated from the milk of sheep with subclinical intramammary infection or teat skin, mouth of lambs or milking machine teat cups. One hundred eleven of the same strains were also tested by Standard Laboratory Culture Media. The Rosco Set assigned species to all strains tested, but the other two methods were unable to assign species to a similar proportion of isolates. Seventy six (68.5%) of the strains tested with all three methods were not assigned the same species, each method shown a preference for particular species. The Staph-Zym and the Rosco Set identified most of the strains as members of the ‘epidermidis’ group with the ‘aureus’ second, while the reverse was observed with the Standard Laboratory Culture Media. Only in the case of Staphylococcus epidermidis all methods were in close agreement. When the results of the Staph-Zym and the Rosco Set are compared, although they agree on the predominant group, they disagree on the predominant species within the same group.     

Linkage studies on Peptidases A, B, C and D in man

Linkage data obtained from studies on families segregating for electrophoretic variants of red cell peptidases A, b, C, D, are presented in the form of lod scores and of recombinants and non-recombinants. No significant linkages were found, but ‘hints’ of linkage between pep B and Gm, between Pep C and Rh, and between Pep D, Lu and Secretor are discusse. There appears to be no close linkage between the four peptidase loci A, B, C, and D.     

Determination of minimum inhibitory concentrations of itraconazole,terbinafine and ketoconazole against dermatophyte species by broth microdilution method

Purpose: Various antifungal agents both topical and systemic have been introduced into clinical practice for effectively treating dermatophytic conditions. Dermatophytosis is the infection of keratinised tissues caused by fungal species of genera Trichophyton, Epidermophyton and Microsporum, commonly known as dermatophytes affecting 20–25% of the world’s population. The present study aims at determining the susceptibility patterns of dermatophyte species recovered from superficial mycoses of human patients in Himachal Pradesh to antifungal agents; itraconazole, terbinafine and ketoconazole. The study also aims at determining the minimum inhibitory concentrations (MICs) of these agents following the recommended protocol of Clinical and Laboratory Standards Institute (CLSI) (M38-A2). Methodology: A total of 53 isolates of dermatophytes (T. mentagrophyte-34 in no., T. rubrum-18 and M. gypseum-1) recovered from the superficial mycoses were examined. Broth microdilution method M38-A2 approved protocol of CLSI (2008) for filamentous fungi was followed for determining the susceptibility of dermatophyte species. Results: T. mentagrophyte isolates were found more susceptible to both itraconazole and ketoconazole as compared to terbinafine (MIC₅₀: 0.125 μg/ml for itraconazole, 0.0625 μg/ml for ketoconazole and 0.5 μg/ml for terbinafine). Three isolates of T. mentagrophytes (VBS-5, VBSo-3 and VBSo-73) and one isolate of T. rubrum (VBPo-9) had higher MIC values of itraconazole (1 μg/ml). Similarly, the higher MIC values of ketoconazole were observed in case of only three isolates of T. mentagrophyte (VBSo-30 = 2 μg/ml; VBSo-44, VBM-2 = 1 μg/ml). The comparative analysis of the three antifungal drugs based on t-test revealed that ‘itraconazole and terbinafine’ and ‘terbinafine and ketoconazole’ were found independent based on the P < 0.005 in case of T. mentagrophyte isolates. In case of T. rubrum, the similarity existed between MIC values of ‘itraconazole and ketoconazole’ and ‘terbinafine and ketoconazole’. Conclusion: The MIC values observed in the present study based on standard protocol M38-A2 of CLSI 2008 might serve as reference for further studies covering large number of isolates from different geographic regions of the state. Such studies might reflect on the acquisition of drug resistance among isolates of dermatophyte species based on MIC values.     

Effect of the bacterial growth phase and coculture conditions on the interaction of Acanthamoeba castellanii with Shigella dysenteriae,Shigella flexneri,and Shigella sonnei

Shigella species and Acanthamoeba castellanii share the same ecological niches, and their interaction has been addressed in a limited number of research. However, there are still uncertain aspects and discrepant findings of this interaction. In the present study, the effects of the bacterial growth phase, cocultivation temperature and the type of culture media on the interaction of A. castellanii with Shigella dysenteriae, Shigella sonnei and Shigella flexneri were evaluated. In nutrient‐poor page's amoeba saline (PAS) medium, the number of recovered bacteria and the uptake rates were significantly higher in stationary phase cells than logarithmic phase cells. However, no significant differences were observed in the number of recovered bacteria and the uptake rates between logarithmic and stationary phase cells in nutrient‐rich peptone–yeast extract–glucose (PYG) medium. While the number of recovered bacteria was significantly higher in nutrient‐rich than nutrient‐poor media, in all the three Shigella species, the bacterial uptake rates were significantly higher in nutrient‐poor than nutrient‐rich media at both cocultivation temperatures. In both nutrient‐poor and nutrient‐rich media and at both cocultivation temperatures, the number of viable Shigella species after 24 h incubation were not influenced by the presence of A. castellanii. Although Shigella species did not proliferate in A. castellanii trophozoites, a considerable number of bacteria were survived in the trophozoites up to 15 days. From the public health perspective, the results of this study are important for further understanding of the nature of the interaction of these organisms and to deal with Shigella species in the environment.     

Chromosomal evolution in bovids: a comparison of cattle,sheep and goat G- and R-banded chromosomes and cytogenetic divergences among cattle,goat and river buffalo sex chromosomes

A G- and R-banding comparison of cattle (Bos taurus, 2n=60), goat (Capra hircus, 2n=60) and sheep (Ovis aries, 2n=54) chromosomes at the 450 band level was made. The study revealed a large number of banding homologies among the autosomes of the three species and resolved some ambiguities in arranging some of their small disputed acrocentrics by direct and indirect comparisons with some bovid marker chromosomes. A loss of the subcentromeric G-positive band in sheep chromosome 2q was observed when the G-banding patterns of sheep 2q and homologous cattle and goat chromosome 2 were compared. The chromosomal divergences among cattle, goat and river buffalo (Bubalus bubalis, 2n=50) sex chromosomes are shown to have occurred by pericentric and paracentric inversions with a loss (or acquisition) of constitutive heterochromatin.     

Newly identified human rhinoviruses: molecular methods heat up the cold viruses

Human rhinovirus (HRV) infections cause at least 70% of virus‐related wheezing exacerbations and cold and flu‐like illnesses. They are associated with otitis media, sinusitis and pneumonia. Annually, the economic impact of HRV infections costs billions in healthcare and lost productivity. Since 1987, 100 officially recognised HRV serotypes reside in two genetically distinct species; HRV A and HRV B, within the genus Enterovirus, family Picornaviridae. Sequencing of their ～7kb genomes was finalised in 2009. Since 1999, many globally circulating, molecularly‐defined ‘strains’, perhaps equivalent to novel serotypes, have been discovered but remain uncharacterised. Many of these currently unculturable strains have been assigned to a proposed new species, HRV C although confusion exists over the membership of the species. There has not been sufficient sampling to ensure the identification of all strains and no consensus criteria exist to define whether clinical HRV detections are best described as a distinct strain or a closely related variant of a previously identified strain (or serotype). We cannot yet robustly identify patterns in the circulation of newly identified HRVs (niHRVs) or the full range of associated illnesses and more data are required. Many questions arise from this new found diversity: what drives the development of so many distinct viruses compared to other species of RNA viruses? What role does recombination play in generating this diversity? Are there species‐ or strain‐specific circulation patterns and clinical outcomes? Are divergent strains sensitive to existing capsid‐binding antivirals? This update reviews the findings that trigger these and other questions arising during the current cycle of intense rhinovirus discovery. Copyright © 2010 John Wiley & Sons, Ltd.     

The ade4 gene of Schizosaccharomyces pombe: cloning,sequence and regulation

We report the isolation and sequence of the Schizosaccharomyces pombe ade4 gene which encodes the glutamine phosphoribosylpyrophosphate amidotransferase, the first enzyme of the purine nucleotide de-novo biosynthetic pathway. The enzyme contains 533 amino acids and its sequence exhibits homologies to the corresponding enzymes of Saccharomyces cerevisiae, Escherichia coli, Bacillus subtilis, chicken, rat, and human. In contrast to the situation in S. cerevisiae, adenine does not repress ade4 expression at the mRNA level and also other nutritional signals seem not to affect its expression.     

Phylogenomic study of the subfamily Caprinae by cross-species chromosome painting with Chinese muntjac paints

Chromosomal homologies have been established between the Chinese muntjac (Muntiacus reevesi, MRE, 2n = 46) and five ovine species: wild goat (Capra aegagrus, CAE, 2n = 60), argali (Ovis ammon, OAM, 2n = 56), snow sheep (Ovis nivicola, ONI, 2n = 52), red goral (Naemorhedus cranbrooki, NCR, 2n = 56) and Sumatra serow (Capricornis sumatraensis, CSU, 2n = 48) by chromosome painting with a set of chromosome-specific probes of the Chinese muntjac. In total, twenty-two Chinese muntjac autosomal painting probes detected thirty-five homologous segments in the genome of each species. The chromosome X probe hybridized to the whole X chromosomes of all ovine species while the chromosome Y probe gave no signal. Our results demonstrate that almost all homologous segments defined by comparative painting show a high degree of conservation in G-banding patterns and that each speciation event is accompanied by specific chromosomal rearrangements. The combined analysis of our results and previous cytogenetic and molecular systematic results enables us to map the chromosomal rearrangements onto a phylogenetic tree, thus providing new insights into the karyotypic evolution of these species.     

Relationship between early intestinal colonization, mucosal immunoglobulin A production and systemic immune development

Background Variations in early intestinal colonization patterns have been implicated in the predispostion to allergic disease through effects on mucosal and systemic immune function. Methods Colonization patterns and mucosal IgA production at 6 months of age were examined in relation to early exposures, systemic immune development and early allergic outcomes. This was performed in a cohort (n=189) who had received either Lactobacillus acidophilus or a placebo since birth. Results Children who developed sensitization to one or more allergens by 12 months of age had significantly higher total (but not secretory) IgA levels at 6 months (P=0.024), but this was independent of probiotic treatment. There were no relationships between colonization patterns and IgA (total or secretory IgA) levels or allergic outcomes (sensitization, atopic dermatitis or food allergies). Breastfeeding, and the use of yoghurt or probiotic supplements were independently associated with significantly higher proportions of ‘favourable’ lactobacilli and bifidobacteria species. Caesarean delivery and the use of antibiotics during the first 6 months were not associated with significant variations in colonization. Higher proportions of ‘favourable’ bacteria (notably bifidobacteria) were associated with reduced production of most cytokine response to allergens, but increased expression of regulatory cell markers (P=0.009) and transforming growth factor‐β (P=0.016). Conclusion ‘Favourable’ colonization, particularly with bifidobacteria, was associated with effects on cellular immune function, but this was not associated with mucosal immunity (secretory IgA) or reduced risk of allergic disease.