Studies that were identified as potentially relevant were initial

Studies that were identified as potentially relevant were initially screened (1329) after duplicates were removed. A total of 54 articles, abstracts and research papers were selected for full-text assessment from which 22 were included in this review after screening by two reviewers (a research assistant and the lead author PD) (see Figure 1, a flow diagram outlining the steps). The selected articles met at least one of the main criteria for this review by presenting data on barriers or facilitators and attitudes in relation to pharmacy professionals’ participation GDC-0068 in

CPD and/or mapping engagement with and uptake of CPD in pharmacy in GB. In relation to research papers, studies were excluded if the focus was on a different group of health professionals with no orientation towards pharmacy. Papers were excluded find more if the focus

was simply on CE or professionalism per se or if the focus was only on the pharmacy student cohort. Studies were also excluded if the country of focus was outside of GB; i.e. studies conducted in Northern Ireland were excluded. In addition, papers were excluded if the focus was purely on subsets of skills usually associated with CPD, such as reflective learning by itself, or on actual content relating to CPD, for example learning clinical pharmacy. We did not include in the review a study examining feedback on CPD provided by RPSGB because this very specific study did not investigate general attitudes to CPD but was instead a form of ‘satisfaction with feedback study’. We did nonetheless acknowledge the contribution of this study to the field in the discussion section of this paper. We did not include any studies

published or relating to the period before 2000 but viewed them as providing context ahead of the launch of CPD. A grid was created to record the summaries of the articles for further literature synchronisation and later construction of the literature review. This took the form of a data extraction form that enabled inclusion of studies based on eligibility in the first instance and then quality assessment at a later stage (see below). Astemizole This initial tabulation presented information on study characteristics as the year study was conducted; main study design and method of data collection; sector of pharmacy; geographical location of the study; the sample size; and a brief summary of the aims. It was not possible to use the PICOS (participants, interventions, comparisons, outcomes and study design) categorisation[19] because the studies were not necessarily interventional in nature. Instead quality scoring of the articles was attempted in accordance to the recommendations of the Qualitative Assessment Review Instrument (QARI) [20] (suggested by the Cochrane Collaboration).

HIV diagnosis during pregnancy may be a profoundly shocking and l

HIV diagnosis during pregnancy may be a profoundly shocking and life-changing experience for the newly diagnosed HIV-positive woman. There may be a complex mix of emotional, psychosocial, relationship, economic and even legal issues that arise directly out of the HIV diagnosis. The newly diagnosed woman also has

a relatively brief time in which she needs to be able to develop trust in her medical carers and attain sufficient medical knowledge of her situation to be able to make informed decisions that will affect the long-term health of herself, her fetus and her male partner. Prevention of MTCT can only be achieved if the pregnant woman embraces the medical interventions appropriately. To maximize the effectiveness of the interventions for pregnant women in reducing MTCT the psychosocial context of their HIV infection find more must not be overlooked. Clinical experience indicates that the management of issues including dealing with the diagnosis and uncertainty during pregnancy and robust confidentiality processes have an impact on adherence Selleck Alpelisib to ART and acceptance of recommended interventions and all clinicians must be mindful of

this. Studies from around the world have shown significant prevalence of intimate partner violence in pregnancy (14% in the UK to 63% in Zimbabwe), which seems to be greater in women who are HIV positive. NICE antenatal guidelines recommend asking all pregnant women about domestic violence and this would be even more important in women with HIV (especially those with a recent diagnosis or a positive partner) [336–338]. 9.1 Antenatal HIV care should be delivered by a multidisciplinary team (MDT), the precise composition of which will vary. Grading: 1D The minimum team would comprise an HIV specialist, obstetrician, specialist midwife and paediatrician, with the recommendation of peer- and voluntary-sector support. All efforts should be made to involve the woman’s GP and health visitor. It may be necessary to involve some of the following: patient advocates, social workers, legal advocacy, clinical EGFR inhibitor psychologists, psychiatrists, counsellors, health advisors, Citizens Advice Bureau

workers, interpreters, community midwives, clinical nurse specialists and health visitors [339]. In settings with relatively few HIV-positive pregnant women, it is still important to develop robust pathways of care with identified members of an MDT. Regular links, formal or informal, can also be established with a larger unit to provide advice and support as necessary. Good communication is vital in view of the complexity of the issues involved. An early assessment of the social circumstances of a newly diagnosed HIV-positive woman is important. Patients who initially refuse interventions or default from follow-up need to be identified and actively followed-up. Support by trained peer-support workers is a valuable component of the management of HIV-positive pregnant women.

, 2007; Zhou et al, 2009; da Miguel et al, 2010),

such

, 2007; Zhou et al., 2009; da Miguel et al., 2010),

such methods may provide an inaccurate description of the total microbial structure in that they reveal only dominant populations, which may not necessarily Proteasome inhibitors in cancer therapy play important roles in overall community dynamics. Lacticin 3147 is a potent, two-peptide broad spectrum lantibiotic (class I bacteriocin or antimicrobial peptide) produced by Lactococcus lactis DPC3147 (Fig. 1; Ryan et al., 1996; Martin et al., 2004; Lawton et al., 2007). First isolated from an Irish kefir grain in 1996, it is perhaps one of the most extensively studied bacteriocins and has been shown to inhibit such clinically relevant pathogens as Clostridium difficile, R788 methicillin-resistant Staphylococcus aureus and vancomycin-resistant enterococci (Rea et al., 2007; Piper et al., 2009). Although the microbial composition of kefir grains has been well documented (Rea et al., 1996; Ninane et al., 2007;

Zhou et al., 2009), to our knowledge, there have been no reports on the characterization of the microbiota of a kefir grain from which bacteriocin-producing strains have been isolated. In recent years, the field of microbial ecology has been revolutionized by the development and application of high-throughput DNA sequencing technologies, such as that facilitated by the 454 GS-FLX platform (Roche Diagnostics Ltd, West Sussex, UK; Keijser et al., 2008; Urich et al., 2008; McLellan et al., 2009), which allows for a more complete view of overall community composition without the bias typically associated with cloning or cultivation. Here, we use high-throughput sequencing of 16S rRNA gene amplicons to characterize the bacterial composition of the original Irish kefir from which L. lactis DPC3147 was initially isolated. The kefir grain starter used in this study was obtained from the Teagasc Food Research Centre (Fig. 1a; Teagasc, Fermoy, Ireland) kefir grain collection. The grain was cultured in sterile 10%

reconstituted skim milk at 21 °C for 24 h. The fermented Urocanase kefir milk was removed and the grain rinsed with sterile water to remove any clotted milk still adhered onto the grain surface. In order to monitor bacterial changes over the course of the kefir fermentation, kefir milk samples were enumerated for lactococci and lactobacilli; populations typically associated with the kefir community. Samples were first homogenized as 10-fold serial dilutions, further 10-fold serial dilutions were prepared and appropriate dilutions were spread plated onto M17 agar supplemented with 0.5% lactose (LM17; Difco Laboratories, Detroit, MI) for lactococci, and Lactobacillus selection agar (LBS; Difco) for lactobacilli populations. LM17 plates were incubated aerobically at 30 °C overnight and LBS plates were incubated anaerobically at 37 °C for 5 days.

1a and d) Therefore, it is possible that the extracellular prote

1a and d). Therefore, it is possible that the extracellular protease is one of major antibiofilm components in the supernatants of P. aeruginosa strains. Although it is known that both endogenous and exogenous proteases dispersed established

biofilms (Boles & Horswill, 2008; Iwase et al., 2010), it remains unclear how the proteases rapidly disperse S. aureus biofilm and what the target of the protease is. Hence, we hypothesized that the presence of protease induced the expression of endogenous protease genes in S. aureus. To investigate this hypothesis, a further protease activity assay and transcriptional assay were performed. When the proteinase K was added in the two S. aureus strains, the S. aureus cells clearly increased the protease activity compared to that

of proteinase K only (Fig. 2b and c). Specifically, the addition of proteinase K (0.01 mg mL−1) Selleck RGFP966 increased the lytic zone more than threefold with both S. aureus ATCC 25923 and S. aureus ATCC 6538. The result indicates that the exogenous protease could induce the expression of protease genes in S. aureus. Additionally, qRT-PCR was performed to study the gene expression of proteases with the supernatant of P. aeruginosa containing the protease activity. The supernatant of P. aeruginosa PAO1 clearly induced the gene expression of five major proteases (aur, clp, scpA, splA, and sspA; Fig. 3a). Particularly, splA was induced 61-fold by the CDK inhibitor Adenylyl cyclase treatment of P. aeruginosa PAO1 supernatant than without treatment. Also, further qRT-PCR showed that the P. aeruginosa PAO1 supernatant induced quorum-sensing agrA, hemolysin hla, and histidine protein kinase saeS, but not icaA (Fig. 3b). This result supports the previous report that protease activity is mediated in the agr quorum-sensing system but in an ica-independent manner (Boles & Horswill, 2008). To identify the main antibiofilm protease in P. aeruginosa, the supernatants of various protease-deficient mutants

of P. aeruginosa were tested for the biofilm reduction in S. aureus. Interestingly, two mutants (lasB and rhlR) showed much lower activity of protease in the milk agar plate (Fig. 2d) and also had much lower antibiofilm activity against S. aureus (Fig. 4), while other eleven protease mutants including lasA mutant showed high protease activity as well as antibiofilm activity. The lasB gene encodes LasB elastase, and the rhlR gene encodes a transcriptional activator protein of the rhl quorum-sensing system that is necessary for the production of LasA protease, LasB protease, Apr alkaline protease, pyocyanin, cyanide, and rhamnolipid (Van Delden & Iglewski, 1998). Because both lasB mutant and rhlR mutant are deficient in the production of LasB elastase, it appears that LasB elastase is one of major antibiofilm protease in the supernatant of P. aeruginosa against S. aureus.

Table 4 also demonstrates the effect of the use of HAART on semin

Table 4 also demonstrates the effect of the use of HAART on seminal parameters, with a significant drop being found in total sperm count (172.2 vs. 147.5 million; P=0.05), progressive motility (48.8 vs. 44.4%; P=0.01), post-preparation concentration (15.1 vs. 12.7 million; P=0.006) and post-preparation TMCI (7.1 vs. 6.1 million; P=0.002)

and a significant increase in the percentage of abnormal sperm (76.7 vs. 74.5%; P=0.01) in samples from men on HAART. This effect of HAART on semen parameters was supported by the negative correlation demonstrated in Table 3 between duration p38 MAPK activation of use and concentration (r=−0.16, P=0.02), total count (r=−0.12, P=0.09) and post-preparation progressive motility (r=−0.19, P=0.01). Paradoxically, there was a positive correlation (r=0.17, P=0.02) between duration of use and pre-preparation progressive motility. Similarly, there was a negative correlation between duration of HIV disease and concentration (r=−0.14, P=0.01) and post-preparation progressive motility (r=−0.15, P=0.02) and a paradoxical positive correlation with

selleck chemicals pre-preparation progressive motility (r=0.12, P=0.05). A decade as the UK tertiary referral centre for the infertility care of HIV-positive men allows us to present data demonstrating a negative effect of falling CD4 cell count and the use of HAART on semen parameters; this is the only study to demonstrate such effects on post-wash sperm available for treatment. The first study to present data on sperm characteristics in HIV-positive men found no difference in any parameter between their small (n=24) cohort and a control group of HIV-negative men providing semen for general fertility investigation [11]. However, more recently, four larger studies have demonstrated Osimertinib cell line a consistent significant impairment in semen parameters compared with control groups. In one study of 250 men [15], significantly lower ejaculate volume, sperm concentration and sperm motility were

demonstrated compared with a small control group of ‘fertile’ HIV-negative men. In a clinically homogeneous group of 189 HIV-positive men free of AIDS symptoms and who were therefore well enough to be considered for fertility treatment, a significant decrease in ejaculate volume and total sperm count and a detrimental shift in motility from type ‘a’ to type ‘b’ was demonstrated compared with healthy partners of women undergoing IVF for tubal subfertility [14]. Compared with a similar control group, and thus avoiding any bias from the use of sperm from men of proven fertility, we previously reported significant declines in ejaculate volume, sperm concentration, total sperm count, progressive sperm motility and sperm morphology in 104 HIV-positive men [18]. Most recently, semen volume, total sperm count, sperm motility and sperm morphology were found to be impaired in 190 HIV-positive men compared with fertile controls [26].

Nonetheless, GPD activity was

Nonetheless, GPD activity was selleck chemical detected almost exclusively in the membrane fraction. Extensive washing of the membrane preparations with increasing concentrations of NaCl (up to 1 M) in 10 mM Tris buffer (pH 7.5) with or without 10 mM EDTA did not affect the levels of GPD activity in the membranes (data not shown), suggesting that the GPD is not a loosely bound membrane protein adsorbed onto the membrane surface. The identification

of the M. hyorhinis GPD was further strengthened by showing its homology to the active GPD of M. pneumoniae and to the GPD of Thermoanaerobacter tengcongensis (GenBank accession no. 2PZ0_A) where strictly conserved residues involved in the activity were identified (Fig. 2, Shi et al., 2008). We suggest that GPD is an essential enzyme in the turnover of glycerophospholipids, the major building blocks of the lipid bilayer of M. hyorhinis membranes. First, the fatty acids are cleaved resulting in the formation of glycerophosphodiesters, which are then further cleaved by GPD to yield glycerol-3-phosphate (Schmidl et al., 2011). Upon incubation

of M. hyorhinis extracts with radiolabeled PG, a decrease in the radioactivity of the PG band with a concomitant increase in the radioactivity of the lysophospholipid and FFA fractions were noticed (data not shown), suggesting a phospholipase activity. The activity was almost exclusively associated with isolated membrane preparations (data not shown). When reaction mixtures containing M. hyorhinis membranes and the fluorescent substrate C12-NBD-PC were incubated for up to 4 h at 37 °C, two fluorescently labeled breakdown products were detected on the TLC plates, the learn more major being C12-NBD-LPC with nonfluorescent fatty acid in position 1 hydrolyzed and the minor C12-NBD-FFA (Fig. 3), suggesting the activity of a PLA in M. hyorhinis membranes. In control experiments, using snake venom PLA2, the breakdown product of C12-NBD-PC was exclusively C12-NBD-FFA. The PLA activity of M. hyorhinis was neither stimulated by Ca2+ (0.1–10 mM) nor inhibited

by EGTA (5 mM) and had a broad pH spectrum (pH 7.0–8.5). Quantitative analysis of the fluorescence Metalloexopeptidase products obtained by the hydrolysis of C12-NBD-PC by M. hyorhinis membranes is shown in Table 1. The ratio of C12-NBD-LPC to C12-NBD-FFA after treatment of C12-NBD-PC with M. hyorhinis membranes was 2.5 after a short incubation period (up to 1 h) and 0.8 after a prolonged incubation period (4 h), suggesting that M. hyorhinis possess a nonspecific PLA activity capable of hydrolyzing both position 1 and position 2 of the C12-NBD-PC, but with a somewhat higher affinity to position 1. The possibility that M. hyorhinis possess a PLA1 (Istivan & Coloe, 2006) or PLA2 (Rigaud & Leblanc, 1980) as well as a lysophospholipase (Gatt et al., 1982) was excluded as we were unable to demonstrate lysophospholipase activity using C12-NBD-LPC (data not shown). The in silico analysis of M.

The cultures were then removed and the plates were washed twice w

The cultures were then removed and the plates were washed twice with distilled water. The number of the adherent cells in an area of 1 mm2 was counted under an optic microscope (Olympus CKX41) to estimate the primary attachment ability of the bacteria in different mediums. The culture of S. aureus NCTC8325 was started

by diluting the overnight culture to an OD600 nm=0.05 and was then allowed to grow at 37 °C (200 r.p.m.) to exponential phase (OD600 nm=0.6). The cultures were then treated with 5 mM dithiothreitol, 10 mM cysteine or 20 mM BME, respectively, for 30 min. Staphylococcus aureus cells were predigested with digestion buffer containing 40 U mL−1 lysostaphin, 10 mg mL−1 lysozyme and 10% (v/v) glycerol. RNA extraction was performed using the SV Total RNA Isolation System (Promega). Residue DNA in extracted RNA was removed by treatment with 10 U of DNaseI (Takara) at 37 °C for an hour. Purified total RNA were qualified and quantified GPCR Compound Library molecular weight by a DU730 Nucleic click here Acid/Protein Analyzer (Beckman Coulter). Reverse transcription of ica was carried out following the technical manual of ImProm-II Reverse Transcription System (Promega) with primer PicaD-R (TCACGATTCTCTTCCTCTC). Q-PCR was performed using StepOne Real-time System (Applied Biosystems) with primers PicaD-F (ATGGTCAAGCCCAGACAG) and PicaD-R. The crude extracellular matrix was prepared as described previously (Sadovskaya et al., 2005). Briefly, S. aureus

cells were grown in the respective medium at 37 °C with moderate shaking (50 r.p.m.) to reach an OD600 nm of 2.0. Bacterial cells were collected by centrifugation (3000 g), resuspended in phosphate-buffered saline (pH 7.4) and sonicated immediately on ice to extract the cell-associated extracellular material. Bacterial cells and insoluble material were removed by centrifugation (10 000 g). Then, the Elson–Morgan assay was performed to measure the amount of PIA in the supernatant after acidolysis as described previously

(Morgan & Elson, 1934). The cultures of S. aureus NCTC8325 were started by diluting the overnight culture to an OD600 nm=0.05 in TSB or TSB supplemented with 5 mM dithiothreitol and incubating at 37 °C (200 r.p.m.) for an additional 6 h. Total protein was purified Ureohydrolase by trichloroacetic acid/ice-cold acetone precipitation as described previously (Resch et al., 2006). Protein sample (500 μg) was loaded in each 17-cm gradient gel strip in the pH range of 4–7 and separated by isoelectrofocusing (IEF) using a Protean IEF cell (Bio-Rad). Second-dimension electrophoresis was carried out on a sodium dodecyl sulfate polyacrylamide gel. The gels were stained with Coomassie G-250 and then scanned on a flatbed scanner. Images were analyzed with imagemaster 2d-platium 5.0 (Amersham), setting the threshold at 3.0-fold. Differential protein dots of interest were marked and 21 of them were excised manually and digested with trypsin (Worthington). The digests were analyzed by HPLC-ES-MS (MDLC-LTQ, Amersham).

We recommend annual influenza vaccination (level of evidence 1B)

We recommend annual influenza vaccination (level of evidence 1B). We recommend vaccination selleck compound against pneumococcus and hepatitis B virus (level of evidence 1D). We recommend

that patients with antibodies against hepatitis B core antigen (HBcAb) should be treated with prophylactic antivirals in line with BHIVA hepatitis guidelines (level of evidence 1B). Kaposi sarcoma is still the most common tumour in people with HIV infection, is an AIDS-defining illness and is caused by the Kaposi sarcoma herpesvirus (KSHV). The diagnosis is usually based on the characteristic appearance of cutaneous or mucosal lesions and should be confirmed histologically since even experienced clinicians misdiagnose KS [1] (level of evidence 1C). Lesions are graded histopathologically into patch, plaque or nodular grade disease. Visceral disease is uncommon, affecting about 14% at diagnosis [2] and CT scans, bronchoscopy and endoscopy are not warranted in the absence of symptoms (level of evidence 2D). The AIDS Clinical Trial Group (ACTG) staging system for AIDS-related KS was developed in the pre-HAART BGJ398 nmr era to predict survival and includes tumour-related criteria

(T), host immunological status (I) and the presence of systemic illness (S) (see Table 3.1) [3,4]. The ACTG also established uniform criteria for response evaluation Arachidonate 15-lipoxygenase in AIDS KS (see Table 3.2) [3]. In the era of HAART, the prognostic value of this staging system has been questioned and one study suggested that only the T and S stages identify patients with poor survival [5], whilst another study from Nigeria found that I and S stages but not T stage were of prognostic significance [6]. However, a comprehensive evaluation of prognostic factors in 326 patients diagnosed with AIDS KS in the era of HAART, externally validated on 446 patients from the US HIV/AIDS Cancer Match Study, has established

a prognostic scoring scheme [7] and more detailed immune subset analysis does not provide additional prognostic information [8]. Having KS as the first AIDS-defining illness (-3 points) and increasing CD4 cell count (-1 for each complete 100 cells/μL in counts at KS diagnosis) improved prognosis, whereas age at KS ≥50 years old (+2) and S1 stage (+3) conveyed a poorer prognosis. On the basis of this index it was suggested that patients with a poor risk prognostic index (score >12) should be initially treated with HAART and systemic chemotherapy together, whilst those with a good risk (score <5) should be treated initially with HAART alone, even if they have T1 disease. Over time, there has been a rise in the CD4 cell count at diagnosis of KS, and the impact of initiation of treatment may also change [9–12].

The number of VCT sites increased from 4293 in 2007 to 7335 in 20

The number of VCT sites increased from 4293 in 2007 to 7335 in 2009 [8, 18]. In addition, China also commenced the provider-initiated testing and counselling (PITC) programme in 2005 to expand HIV testing coverage [19]. Currently, four out of 31 Chinese provinces (Sichuan, Guangdong, Shandong and Liaoning) provide PITC services [8]. However, despite the scaling-up of HIV testing programmes, very few specifically target MSM [20]. The national HIV sentinel surveillance system is the sole government-initiated mechanism that provides targeted HIV testing for MSM. As only 25 out of 1029 of these sites were targeting MSM in 2009 [21], HIV diagnosis for MSM remains insufficient

and limited in many parts of China. A recent modelling study estimated find more that only 12–15% SCH727965 solubility dmso of HIV-positive MSM know that they are positive [22]. As the majority of targeted HIV testing activities among MSM were implemented by independent research bodies and nongovernment organizations [23], it is important to integrate these scattered sources of information in order to infer current trends of HIV testing among MSM in China. In this study, we performed a comprehensive literature review to investigate the percentage of MSM who (1) had ever been tested for HIV, (2) had been tested for HIV in the past 12 months, and (3) had been tested for HIV and notified of the results.

We then examined the temporal trends in these indicators over the past decade, and the association of testing rates with the age profile of MSM

in available studies. This study provides timely and useful evidence for understanding HIV testing rates among Chinese MSM. Two investigators (EPFC and LZ) conducted a comprehensive literature review of www.selleck.co.jp/products/Rapamycin.html published articles and local reports, for the period 2001–2011, in the following English and Chinese electronic databases: PubMed, Medline, Embase, Web of Science, Global Health, Chinese Scientific Journals Fulltext Database (CQVIP), China National Knowledge Infrastructure (CNKI) and Wanfang Data (Figure S1). Keywords and Medical Subject Headings (MeSH) used in the search were (‘HIV [MeSH]’ OR ‘AIDS [MeSH]’ OR ‘HIV testing’ OR ‘behaviour’) AND (‘homosexual’ OR ‘gay’ OR ‘bisexual’ OR ‘men who have sex with men’ OR ‘MSM’) AND ‘China’. Studies were included if they reported the percentage of MSM who had been tested for HIV in the past 12 months or the percentage of MSM who had ever been tested for HIV, and the design of the study (i.e. study year, location and sample size). Review papers, theses and conference abstracts were excluded from this review. For each included study, we extracted information on study design (study period, recruitment and sampling method), the demographics of MSM participants (age), the study location, and estimates of HIV testing rates (Table 1). All studies were assessed using a validated quality assessment checklist (Table S1) [24].

, 2006; Wagner et al, 2007) However, the molecular mechanism by

, 2006; Wagner et al., 2007). However, the molecular mechanism by which

L. pneumophila Mip acts on these substrates remains unclear. The data obtained from Western blotting analysis show that MipXcc is localized in the periplasmic space. In contrast, the Mips and Mip-like proteins of L. pneumophila, N. gonorrhoeae, and C. trachomatis are located on the cell surface (Cianciotto et al., 1989; Leuzzi et al., 2005; Neff et al., 2007). The Mip-like proteins of T. cruzi and C. pneumoniae are secreted into the extracellular environment (Moro et al., 1995; Herrmann et al., 2006). It may be that Mips and Mip-like proteins that have different locations may influence virulence via different mechanisms. The role of the periplasmic MipXcc in pathogenesis may be quite different from those of the cell surface and extracellular Mips and Mip-like proteins. The Ibrutinib latter may interact directly with host substrates in ways that a periplasmic protein could not. The results presented herein demonstrate that at least one of the major roles of the periplasmic Mip protein of Xcc in pathogenesis is assisting the maturation of proteins required for virulence. They also show that this process takes place in the periplasm. The Mip-like

protein FkpA is also located in the periplasm, and it has been suggested that it may be involved in the stress response or serve as a heat-shock protein that functions as a chaperone for envelope proteins (Missiakas et al., 1996; Arie et al., 2001). We are grateful

AZD8055 cell line to J. Maxwell Dow and Robert P. Ryan for helpful discussions and critical reading of the manuscript. This work was supported by the National Natural Science Foundation of China (30730004). Q.-L.M. and D.-J.T. contributed equally to this work. “
“The 16S rRNA gene has been widely used as a marker of gut bacterial diversity and phylogeny, yet we do not know the model of evolution that best explains the differences in its nucleotide composition within and among taxa. Over 46 000 good-quality near-full-length 16S rRNA gene sequences from five bacterial phyla were obtained from the ribosomal database project (RDP) by study and, when possible, by Ureohydrolase within-study characteristics (e.g. anatomical region). Using alignments (RDPX and MUSCLE) of unique sequences, the FINDMODEL tool available at http://www.hiv.lanl.gov/ was utilized to find the model of character evolution (28 models were available) that best describes the input sequence data, based on the Akaike information criterion. The results showed variable levels of agreement (from 33% to 100%) in the chosen models between the RDP-based and the MUSCLE-based alignments among the taxa. Moreover, subgroups of sequences (using either alignment method) from the same study were often explained by different models. Nonetheless, the different representatives of the gut microbiota were explained by different proportions of the available models.