Microbial activities shape the biogeochemistry of the planet and macroorganism health. Determining the metabolic processes performed by microbes is important both for understanding and for manipulating ecosystems (for example, disruption of key processes that lead to disease, conservation of environmental services, and so on). Describing microbial function is hampered by the inability to culture most microbes and by high levels of genomic plasticity. Metagenomic approaches analyse microbial communities to determine the metabolic processes that are important for growth and survival in any given environment. Here we conduct a metagenomic comparison of almost 15 million sequences from 45 distinct microbiomes and, for the first time, 42 distinct viromes and show that there are strongly discriminatory metabolic profiles across environments. Most of the functional diversity was maintained in all of the communities, but the relative occurrence of metabolisms varied, and the differences between metagenomes predicted the biogeochemical conditions of each environment. The magnitude of the microbial metabolic capabilities encoded by the viromes was extensive, suggesting that they serve as a repository for storing and sharing genes among their microbial hosts and influence global evolutionary and metabolic processes.

Aim The aim of this paper was to discuss how to understand and undertake thematic analysis based on descriptive phenomenology. Methodological principles to guide the process of analysis are offered grounded on phenomenological philosophy. This is further discussed in relation to how scientific rigour and validity can be achieved. Design This is a discursive article on thematic analysis based on descriptive phenomenology. Results This paper takes thematic analysis based on a descriptive phenomenological tradition forward and provides a useful description on how to undertake the analysis. Ontological and epistemological foundations of descriptive phenomenology are outlined. Methodological principles are explained to guide the process of analysis, as well as help to understand validity and rigour. Researchers and students in nursing and midwifery conducting qualitative research need comprehensible and valid methods to analyse the meaning of lived experiences and organize data in meaningful ways.

Salivary agglutinin is a high molecular mass component of human saliva that binds Streptococcus mutans, an oral bacterium implicated in dental caries. To study its protein sequence, we isolated the agglutinin from human parotid saliva. After trypsin digestion, a portion was analyzed by matrix-assisted laser/desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), which gave the molecular mass of 14 unique peptides. The remainder of the digest was subjected to high performance liquid chromatography, and the separated peptides were analyzed by MALDI-TOF/post-source decay; the spectra gave the sequences of five peptides. The molecular mass and peptide sequence information showed that salivary agglutinin peptides were identical to sequences in lung (lavage) gp-340, a member of the scavenger receptor cysteine-rich protein family. Immunoblotting with antibodies that specifically recognized either lung gp-340 or the agglutinin confirmed that the salivary agglutinin was gp-340. Immunoblotting with an antibody specific to the sialyl Le x carbohydrate epitope detected expression on the salivary but not the lung glycoprotein, possible evidence of different glycoforms. The salivary agglutinin also interacted with Helicobacter pylori, implicated in gastritis and peptic ulcer disease, Streptococcus agalactiae, implicated in neonatal meningitis, and several oral commensal streptococci. These results identify the salivary agglutinin as gp-340 and suggest it binds bacteria that are important determinants of either the oral ecology or systemic diseases.

Background: Fear of Childbirth (FOC) is a common problem affecting women's health and wellbeing, and a common reason for requesting caesarean section. The aims of this review were to summarise published research on prevalence of FOC in childbearing women and how it is defined and measured during pregnancy and postpartum, and to search for useful measures of FOC, for research as well as for clinical settings. Methods: Five bibliographic databases in March 2015 were searched for published research on FOC, using a protocol agreed a priori. The quality of selected studies was assessed independently by pairs of authors. Prevalence data, definitions and methods of measurement were extracted independently from each included study by pairs of authors. Finally, some of the country rates were combined and compared. Results: In total, 12,188 citations were identified and screened by title and abstract; 11,698 were excluded and full-text of 490 assessed for analysis. Of these, 466 were excluded leaving 24 papers included in the review, presenting prevalence of FOC from nine countries in Europe, Australia, Canada and the United States. Various definitions and measurements of FOC were used. The most frequently-used scale was the W-DEQ with various cut-off points describing moderate, severe/intense and extreme/phobic fear. Different 3-, 4-, and 5/6 point scales and visual analogue scales were also used. Country rates (as measured by seven studies using W-DEQ with ≥85 cut-off point) varied from 6.3 to 14.8%, a significant difference (chi-square = 104.44, d.f. = 6, p < 0.0001). Conclusions: Rates of severe FOC, measured in the same way, varied in different countries. Reasons why FOC might differ are unknown, and further research is necessary. Future studies on FOC should use the W-DEQ tool with a cut-off point of ≥85, or a more thoroughly tested version of the FOBS scale, or a three-point scale measurement of FOC using a single question as 'Are you afraid about the birth?' In this way, valid comparisons in research can be made. Moreover, validation of a clinical tool that is more focussed on FOC alone, and easier than the longer W-DEQ, for women to fill in and clinicians to administer, is required.