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Additional file 11: Supplemental Figure 11. Taxonomic contributions to gene expression profiles for proteins involved in cell wall biogenesis for jejunum samples collected at day 40. Each node in the network indicates groups of orthologs corresponding to a specific E. coli gene (as indicated) involved in cell wall biogenesis. Links between nodes indicate a functional interaction as previously defined [53]. Size of the node indicates the relative expression of genes associated with each set of orthologs, with sector colours indicating the taxonomic contribution to gene expression (see key for color code). Red arrows indicate sets of orthologs that are significantly up-regulated in comparisons involving the presence/absence of AGPs.

Additional file 8: Supplemental Figure 8. Taxonomic contributions to expressed enzymes in Purine metabolic pathway across different AGP treatments and diets with Day40 ceca samples. Shown here are the De novo biosynthesis and salvage pathways for purine, integrated with data generated from ceca collected at day 40. Each pie chart represents the taxonomic distributions of an enzyme (see key for color code). The size of pie charts indicates the average expression value (with log2 transform) of genes encoding that enzyme. Pie charts with red arrows refer to enzymes that are significantly up-regulated relative to the paired (+/- AGPs) sample. The abbreviations used here can be found in Supplemental Table 11.

Additional file 13. Figure S3. Bar plots representing the relative abundance of C. jejuni in all samples, grouped by treatment and age. Figure S4. Alpha and beta diversity of cecal microbial communities. (A) Boxplots representing alpha diversity metrics of richness (observed number of OTUs and Chao1) and evenness (Shannon and Simpson) for 30-day samples grouped according to treatment (no. of OTUs at 97% similarity). Each point represents the diversity score for a sample, colour-coded according to treatment. (B) Non-metric multidimensional scaling (nMDS) plot based on Bray���Curtis dissimilarity matrix on relative abundance data in 30-day samples. Colours indicate treatment group

Additional file 4: Supplemental Figure 4. Principal component analysis based on annotated metabolic enzymes expression in ceca samples. Each node represents an individual ceca sample, with colours and shapes indicating specific treatment types (see inset key).

Additional file 7: Supplemental Figure 7. Taxonomic contributions to expressed enzymes in Purine metabolic pathway across different AGP treatments and diets with Day24 ceca samples. Shown here are the De novo biosynthesis and salvage pathways for purine, integrated with data generated from ceca collected at day 24. Each pie chart represents the taxonomic distributions of an enzyme (see key for color code). The size of pie charts indicates the average expression value (with log2 transform) of genes encoding that enzyme. Pie charts with red arrows refer to enzymes that are significantly up-regulated relative to the paired (+/- AGPs) sample. The abbreviations used here can be found in Supplemental Table 11.

Additional file 13: Supplemental Figure 13. Taxon-specific expression profiles for genes encoding proteins involved in cell wall biogenesis for ceca samples collected at day 24. Each network represents proteins and their interactions associated with the three select taxa. Nodes represent an ortholog of an E. coli protein previously predicted to be involved in cell wall biogenesis [53]. Size of the node indicates the relative expression of genes associated with the ortholog for that taxon. Links between nodes indicate a functional interaction as defined by the STRING protein interaction database [75], with those in green also found in the previously described E. coli network, and those in orange, not found in the previously described E. coli network.

Additional file 12. Figure S1. Samples collection yielded 158 cecal content samples, which were sent for 16S rRNA sequencing. (A) After quality filtering, 2,195,510 paired-end reads were retained with a median of 13,562 reads (5753���29,542 reads) per sample. (B) Sequences were clustered into 1305 Operational Taxonomic Units (OTUs) based on a de novo assignment with similarity set at 97%. Figure S2. Scatter plots showing the Spearman correlation between enumerated CFUs of C. jejuni and sequence counts assigned to C. jejuni in samples at (A) 30 and (B) 39 days post-hatch

Additional file 5: Supplemental Figure 5. Expression heatmap of metabolic pathways enriched in significantly differentially expressed enzymes. There are 35 KEGG metabolic pathways enriched in significantly differentially expressed enzymes associated with samples from either ceca or jejunum. Changes of the average expression value (log2) of each gene associated with an enzyme in that pathway are indicated by red-green or blue-yellow gradients for ceca and jejunum samples, respectively.

Additional file 1: Supplemental Figure 1. PCoA plots of weighted UniFrac distances for samples associated with each gastrointestinal site. Samples are coloured according to time of sampling. Sample shape represents diet.

Additional file 9: Supplemental Figure 9. AGPs disrupt age related changes in metabolite profiles from chicken serum. PCA of metabolomic profiles generated from either AGP+ or AGP- samples. Samples are coloured and grouped based on age of bird from which the sample was taken.

Additional file 16: Supplemental Table 3. Shannon diversity indices of samples classified according to age, site, and treatment. Averages of each grouping are shown with standard deviation in brackets.

Additional file 2: Supplemental Figure 2. Heatmap showing normalized abundance of taxa for taxa exhibiting significant differential abundance in at least one of the comparisons shown on the right. Each column in the heatmap represents a single sample, grouped by treatment. Each row indicates an individual taxon. Columns on the right indicate significant differences in abundance across each of eight pair-wise comparisons. Taxa are ordered on the basis of magnitude of fold change across the various pairwise comparisons.

Additional file 10: Supplemental Figure 10. Taxonomic contributions to gene expression profiles for proteins involved in cell wall biogenesis for ceca samples collected at day 40. Each node in the network indicates groups of orthologs corresponding to a specific E. coli gene (as indicated) involved in cell wall biogenesis. Links between nodes indicate a functional interaction as previously defined [53]. Size of the node indicates the relative expression of genes associated with each set of orthologs, with sector colours indicating the taxonomic contribution to gene expression (see key for color code). Red arrows indicate sets of orthologs that are significantly up-regulated in comparisons involving the presence/absence of AGPs.

Additional file 3: Supplemental Figure 3. Pie-chart heatmap of metabolic pathways enriched with significantly differentially expressed enzymes through comparisons between diets. There are 35 KEGG metabolic pathways enriched with significantly differentially expressed enzymes which were annotated from either ceca or jejunum samples based on comparisons between diets. Each node in the heatmap is a pie chart showing proportion of enzymes that were significantly up-regulated (orange), significantly down-regulated (blue), and not significantly different (white) with the wheat diet. In addition, the size of each node indicates the number of expressed enzymes in each KEGG pathway.

The rapid loss of reef-building corals due to ocean warming is driving the development of interventions such as coral propagation and restoration, selective breeding and assisted gene flow. Many of these interventions target naturally heat-tolerant individuals to boost climate resilience, but the challenges of quickly and reliably quantifying heat tolerance and identifying thermotolerant individuals have hampered implementation. Here, we used coral bleaching automated stress systems to perform rapid, standardized heat tolerance assays on 229 colonies of Acropora cervicornis across six coral nurseries spanning Florida's Coral Reef Tract, USA. Analysis of heat stress dose–response curves for each colony revealed a broad range in thermal tolerance among individuals (approx. 2.5°C range in Fv/Fm ED50), with highly reproducible rankings across independent tests (r = 0.76). Most phenotypic variation occurred within nurseries rather than between them, pointing to a potentially dominant role of fixed genetic effects in setting thermal tolerance and widespread distribution of tolerant individuals throughout the population. The identification of tolerant individuals provides immediately actionable information to optimize nursery and restoration programmes for Florida's threatened staghorn corals. This work further provides a blueprint for future efforts to identify and source thermally tolerant corals for conservation interventions worldwide.

Additional file 1: Table S1. Breeds and Naming Convention for the 15 Samples Analyzed in this Study. The main text uses the abbreviation to refer to each breed. Genomes sequenced from pooled blood samples are specified in brackets in the “Name” column.

Figure S1. Comparative analysis of the mapped and unmapped transcripts of Toronto and PlanMine transcriptomes onto dd_Smes_g4 genome assembly. Figure S2. Phylogenetic profiling of S. mediterranea based on GO Slim terms. Piecharts showing phylogenetic breakdown of various GO Slim groupings. Figure S3. Phylogenetic distribution of cadherins from human, C. elegans, Platyhelminthes, and S. mediterranea. Phylogenetic tree of cadherins. Figure S4. Gene expression profiles of Cluster 7 subclusters. Figure S5. Smed-egr5 gene expression and phenotypes. (PDF 1428 kb)

Comparison of glycolysis pathway enzyme expression between sample types. Three comparisons are shown: (A) Plin2-LF vs. WT-LF; (B) Plin2-HF vs. Plin2-LF; (C) WT-HF vs. WT-LF. Circular nodes indicate enzymes, with size indicating relative difference in expression between sample types and color indicating direction of change (see inset key). Associated heatmaps indicate global changes in expression for each enzyme, in addition to taxon-specific changes in expression for each of the 17 defined taxa colored according to phylum. (PDF 1138Â kb)

Genotype-based comparisons of pantothenate pathway enzyme expression. Two comparisons are shown: (A) Plin2-HF vs. WT-HF and (B) Plin2-LF vs. WT-LF. Circular nodes indicate enzymes, with size indicating relative difference in expression between sample types and color indicating direction of change (see inset key). Associated heatmaps indicate global changes in expression for each enzyme, in addition to taxon-specific changes in expression for each of the 17 defined taxa colored according to phylum. The following abbreviations are used: 5,6-dh-uracil (5,6-dihydro-uracil), N-cm-β-alanine (N-carbamoyl-β-alanine), N-pt-Cys (N-pantothenoyl-cysteine), and (R)-4′-P-pt-L-Cys ((R)-4′-phospho-pantothenoyl-l-cysteine. (PDF 1370 kb)

Rarefaction analysis of annotated mRNA reads. Recovery of species (A) and enzymes (B) with increasing numbers of annotated mRNA reads (reads mapped to known transcripts) indicate that sequencing depth for each sample was sufficient to recover the vast majority of species and enzymes present within each of the 16 samples. Rarefaction analysis was performed using R. (PDF 16825Â kb)

Diet-based comparisons of enzyme expression in pantothenate pathway. Two comparisons are shown: (A) Plin2-HF vs. Plin2-LF and (B) WT-HF vs. WT-LF. Circular nodes indicate enzymes, with size indicating relative difference in expression between sample types and color indicating direction of change (see inset key). Associated heatmaps indicate global changes in expression for each enzyme, in addition to taxon-specific changes in expression for each of the 17 defined taxa colored according to phylum. The following abbreviations are used: 5,6-dh-uracil (5,6-dihydro-uracil), N-cm-β-alanine (N-carbamoyl-β-alanine), N-pt-Cys (N-pantothenoyl-cysteine), and (R)-4′-P-pt-L-Cys ((R)-4′-phospho-pantothenoyl-l-cysteine. (PDF 1119 kb)

Comparison of TCA cycle enzyme expression in between sample types. Three comparisons are shown: (A) Plin2-LF vs. WT-LF; (B) Plin2-HF vs. Plin2-LF; (C) WT-HF vs. WT-LF. Circular nodes indicate enzymes, with size indicating relative difference in expression between sample types and color indicating direction of change (see inset key). Associated heatmaps indicate global changes in expression for each enzyme, in addition to taxon-specific changes in expression for each of the 17 defined taxa colored according to phylum. (PDF 1246Â kb)

Comparison of TCA cycle enzyme expression in between sample types. Three comparisons are shown: (A) Plin2-LF vs. WT-LF; (B) Plin2-HF vs. Plin2-LF; (C) WT-HF vs. WT-LF. Circular nodes indicate enzymes, with size indicating relative difference in expression between sample types and color indicating direction of change (see inset key). Associated heatmaps indicate global changes in expression for each enzyme, in addition to taxon-specific changes in expression for each of the 17 defined taxa colored according to phylum. (PDF 1246Â kb)

Genotype-based comparisons of pantothenate pathway enzyme expression. Two comparisons are shown: (A) Plin2-HF vs. WT-HF and (B) Plin2-LF vs. WT-LF. Circular nodes indicate enzymes, with size indicating relative difference in expression between sample types and color indicating direction of change (see inset key). Associated heatmaps indicate global changes in expression for each enzyme, in addition to taxon-specific changes in expression for each of the 17 defined taxa colored according to phylum. The following abbreviations are used: 5,6-dh-uracil (5,6-dihydro-uracil), N-cm-β-alanine (N-carbamoyl-β-alanine), N-pt-Cys (N-pantothenoyl-cysteine), and (R)-4′-P-pt-L-Cys ((R)-4′-phospho-pantothenoyl-l-cysteine. (PDF 1370 kb)

Global metabolic network indicating taxonomic representation of metabolic activities within the deepsea dataset. Global metabolic network indicating taxonomic representation of metabolic activities within the deepsea dataset. Pie charts indicate the relative proportion of each taxon, size of pie chart indicates relative expression (see key). Indicated are specific metabolic pathways. (PDF 2066 kb)

Taxonomic contributions to select hydrogenase modules as defined through protein-interaction networks for the four well sampled datasets. Each network indicates the taxonomic representation of components of hydrogenases as defined through protein-interaction networks for four metatranscriptome datasets: mouse, kimchi, cow and deep sea. Pie charts indicate genes, with coloured sectors indicating the relative contribution to gene expression for each taxon, size of pie chart indicates relative expression (see key). (PDF 190 kb)

Detailed views of taxonomic contributions to specific components of the alanine, aspartate and glutamate pathways for four metatranscriptomic datasets. Each schematic indicates the taxonomic representation of enzymatic activities involved in the alanine, aspartate and glutamate pathways for four metatranscriptome datasets: mouse, kimchi, cow and deep sea. Pie charts indicate enzymes, with coloured sectors indicating the relative proportion of each taxon, size of pie chart indicates relative expression (see key). Small triangles indicate substrates with links indicating enzyme-substrate relationships. (PDF 658 kb)

Venn diagram illustrating overlap of genera defined by putative 16S rRNA and mRNA reads for five metatranscriptomic datasets. Numbers indicate the number of genera defined by each type of sequence data. (PDF 112 kb)

Global metabolic network indicating taxonomic representation of metabolic activities within the cow rumen dataset. Global metabolic network indicating taxonomic representation of metabolic activities within the cow rumen dataset. Pie charts indicate the relative proportion of each taxon, size of pie chart indicates relative expression (see key). Indicated are specific metabolic pathways. (PDF 1162 kb)

Taxonomic contributions to flagella biosynthesis and chemotaxis modules as defined through protein-interaction networks for the four well sampled datasets. Each network indicates the taxonomic representation of components of flagella biosynthesis and chemotaxis modules as defined through protein-interaction networks for four metatranscriptome datasets: mouse, kimchi, cow and deepsea. Pie charts indicate genes, with coloured sectors indicating the relative contribution to gene expression for each taxon, size of pie chart indicates relative expression (see key). (PDF 202 kb)

iPath representation of common and unique enzymes in a global metabolism map from KEGG. The global metabolic map was generated using the online iPath tool [83] with reactions coloured according to their presence in different metatranscriptomic datasets (see inset key). (PDF 1815 kb)

HAMP domains mediate input-output communication in many bacterial signalling proteins. To explore the dynamic bundle model of HAMP signalling (Zhou et al., Mol. Microbiol. 73: 801, 2009), we characterized the signal outputs of 118 HAMP missense mutants of the serine chemoreceptor, Tsr, by flagellar rotation patterns. Receptors with proline or charged amino acid replacements at critical hydrophobic packing residues in the AS1 and AS2 HAMP helices had locked kinase-off outputs, indicating that drastic destabilization of the Tsr-HAMP bundle prevents kinase activation, both in the absence and presence of the sensory adaptation enzymes, CheB and CheR. Attractant-mimic lesions that enhance the structural stability of the HAMP bundle also suppressed kinase activity, demonstrating that Tsr-HAMP has two kinase-off output states at opposite extremes of its stability range. HAMP mutants with locked-on kinase outputs appeared to have intermediate bundle stabilities, implying a biphasic relationship between HAMP stability and kinase activity. Some Tsr-HAMP mutant receptors exhibited reversed output responses to CheB and CheR action that are readily explained by a biphasic control logic. The findings of this study provide strong support for a three-state dynamic bundle model of HAMP signalling in Tsr, and possibly in other bacterial transducers as well.

Background: Codon usage has direct utility in molecular characterization of species and is also a marker for molecular evolution. To understand codon usage within the diverse phylum Nematoda, we analyzed a total of 265,494 expressed sequence tags (ESTs) from 30 nematode species. The full genomes of Caenorhabditis elegans and C. briggsae were also examined. A total of 25,871,325 codons were analyzed and a comprehensive codon usage table for all species was generated. This is the first codon usage table available for 24 of these organisms. Results: Codon usage similarity in Nematoda usually persists over the breadth of a genus but then rapidly diminishes even within each clade. Globodera, Meloidogyne, Pristionchus, and Strongyloides have the most highly derived patterns of codon usage. The major factor affecting differences in codon usage between species is the coding sequence GC content, which varies in nematodes from 32% to 51%. Coding GC content (measured as GC3) also explains much of the observed variation in the effective number of codons (R = 0.70), which is a measure of codon bias, and it even accounts for differences in amino acid frequency. Codon usage is also affected by neighboring nucleotides (N1 context). Coding GC content correlates strongly with estimated noncoding genomic GC content (R = 0.92). On examining abundant clusters in five species, candidate optimal codons were identified that may be preferred in highly expressed transcripts. Conclusion: Evolutionary models indicate that total genomic GC content, probably the product of directional mutation pressure, drives codon usage rather than the converse, a conclusion that is supported by examination of nematode genomes.

Resumen tomado parcialmente de la publicación Está dirigido para ayudar a los profesores -tanto nuevos como experimentados- a mejorar sus prácticas y la efectividad de sus clases. Se examinan cada uno de los métodos comunes de enseñanza en ciencias en relación con el aprendizaje de los estudiantes y proporciona guías en la gestión de usos y procedimientos. Se hace especial hincapié en las materias que interesan a los alumnos en ciencias y su motivación para aprender, cómo aprenden las ciencias, el tipo de ciencias que actualmente les enseñan en las escuelas y el valor de la investigación en la educación. Londres Biblioteca de Educación del Ministerio de Educación, Cultura y Deporte; Calle San Agustín 5 -3 Planta; 28014 Madrid; Tel. +34917748000; biblioteca@mecd.es GBR

[15] leaves : ; Includes bibliographical references. ; This study looked at the impact on ROA of aligning budgeting and HRM decisions with strategy. A Lisrel model was tested on 79 large Canadian and U.S. firms. While HR policy alignment was positively associated with ROA, budgetary alignment was only positively associated with ROA inconjunction with process participation.

My thesis traces the historical and theoretical formation of a "Canadian" writing. Traditionally, Canadian literature and the "Canadian identity" have been studied thematically. For instance, our relationships to wilderness, animals and geography (the inhospitable land), and the sense of community that develops in reaction to these circumstances are themes which have been examined exhaustively. In contrast, I am theorizing how writing was practiced in seventeenth-eighteenth- and nineteenth-century Canadian exploration narratives. The main chapters of this thesis are separated by shoner, more detailed. analyses of visual works, including maps, engravings from exploration books, and Frances Anne Hopkins's voyageur paintings. My explication of these pictures works dialectically with the longer chapters on prose narratives to reveal different aspects of exploration's expansive colonial discourse. In chapter two I identify four distinct forms of writing, including "writing as inscription," the physical act of inscribing on surfaces. These surfaces include the North American landscape where territory is claimed in the name of a sovereign and as an act of imperial expansion. I also discuss writing's role as an agent of capitalism: it structures systems of exchange and records the European's interventions into indigenous cultures. Writing is a portable technology which the explorers use to transmit and store information on the peoples and geographies of the newly found lands. Chapter four discusses the early sea voyages of Thomas James (The Strange and Dangerous Voyage of Captain Thomas James and Luke Foxe (North-West Fox, or. Fox from the North-west Passage). Both men found an inhospitable land barren of resources which would not yield a North West Passage. In chapter six Samuel Hearne's A Journey from Prince of Wales's Fort in Hudson's Bay...to the Northern Ocean provides an exemplary model for the role of commerce in the eighteenth century. Hearne's narrative is the most important and influential of the many first-person narratives written by traders in the eighteenth and nineteenth centuries and his geography is much more detailed and economically productive than those of James and Foxe because he explores for trade and mining purposes. The thesis ends with a reading of the three Franklin expeditions. Although the published texts only detail the first two (Narrative of a Journey to the Shores of the Polar Sea and Narrative of a Second Expedition to the Shores of the Polar Sea), the loss of Franklin and his men with the third expedition, and the enormous media interest in the subsequent searches for their various "traces," demonstrates the entry of explorers into the "modern" world of communications technologies. The contemporary image of Franklin which has been recuperated through forensic technology mirrors the technology of writing discussed throughout the thesis. My analysis of exploration narratives and the extensive role of writing throughout the colonizing of Canada offers a valuable insight into our literary and cultural history. Doctor of Philosophy (PhD)

Emily Carr is a critically neglected figure in Canadian literature. Our current perception of her is defined almost totally by biographies and myth. This thesis attempts to demonstrate the sorts of strategies of truth which permeate the discourses of biography and autobiography. I confront the question of identity by examining how Emily Carr's writing about herself differs from that of her biographers. Where does the self that is allegedly carried by and through language find itself to be? Writing is treated as a representational medium; the page is the canvas painted by the grapheme. While I believe that we cannot avoid defining Carr in traditional terms of family, society, geography etc., I hope that this thesis provides an alternate reading of familiar concepts. I wish to represent Emily Carr as a Western writer but one with a "difference." Master of Arts (MA)

[missing page 51] In this Master's thesis I have attempted to provide a reliable and readable text of Lydgate's Hertford Mumming and London Mumming. This text is generally faithful to that of Trinity College Cambridge MS. R.3.20, although the copy contained in British Library Additional MS. 29729 has been consulted at all points. The method of editing applied here could and should be applied to the other poems by Lydgate which are contained only in these two manuscripts, especially his other Mummings. Following the text itself, a full commentary is provided in the form of notes. This commentary is intended to shed light on Lydgate's craftmanship and his use of specific traditions and techniques in writing for performed presentations. In addition, it is designed to clarify difficult points within the text itself. A further aim of this thesis has been to establish a starting point for the understanding of secular "dramatic" activity in and around London during the first quarter of the Fifteenth Century. The intention of my Introduction has been less to envision a pattern of development of dramatic forms and practices than to give a description of the various uses to which staged performances were put at this time. Lydgate's own role as foremost public poet of his time; his probable involvement in major events and celebrations; his awareness of contemporary literary and dramatic conventions in England and France; and his possible emulation of what he saw to be a Classical tradi tion of recitation and performance: all these factors are to be considered in determining his particular contribution t o secular dramatic activity at Court and in the City of London. Master of Arts (MA)

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Detailed views of taxonomic contributions to specific components of the glycolysis/gluconeogenesis pathway for four metatranscriptomic datasets. Each schematic indicates the taxonomic representation of enzymatic activities involved in the glycolysis/gluconeogenesis pathways for four metatranscriptome datasets: mouse, kimchi, cow and deepsea. Pie charts indicate enzymes, with coloured sectors indicating the relative proportion of each taxon, size of pie chart indicates relative expression (see key). Small triangles indicate substrates with links indicating enzyme-substrate relationships. (PDF 635 kb)

Figure S1. Eukaryotic microbiota of Malawian cohort suffering from SAM. a Relative sequence abundances of all eukaryotic phyla identified in the V4 V5 amplicon of the 18S rRNA gene (n = 44). Columns represent individual patients, and samples are numbered for comparison with DNA gels. b PCR validation of presence of Pentatrichomonas and Cryptosporidium using published primers Th4, Th5, Cr254F and CR323R (Crucitti et al. 2004; Bruijnesteijn et al. 2009), and an Entamoeba coli specific forward primer 5′-GGTTTCTAATATCAACAGGCTAC-3′ to 18S rRNA gene FR686446 with 18S-V9-15_R. NT, no template control; samples marked with an asterisk are not expected to be positive. Related to Fig. 3 a. Figure S2. Differential composition analysis of bacterial OTUs in Malawian samples. Plots were generated with the ALDEx2 R-package, and show OTU fold-change versus median abundance (left) and OTU fold-change between versus within conditions (right). No significant compositional changes in OTUs were found by Wilcoxon rank test. Tests compare subjects positive and negative for a, Cryptosporidium (18S rRNA V4 V5 amplicon), b, Enterocytozoon (transITS amplicon), c, Giardia or d, HIV. Cryptosporidium and Enterocytozoon presence are defined as a minimum of 5 amplicon reads, and Giardia and HIV infection status were determined by clinical diagnostic tests. Related to Fig. 5b. Supplementary Methods. Supplementary information is included on clinical sample collection. (PDF 1241 kb)

Figure S1. Eukaryotic microbiota of Malawian cohort suffering from SAM. a Relative sequence abundances of all eukaryotic phyla identified in the V4 V5 amplicon of the 18S rRNA gene (n = 44). Columns represent individual patients, and samples are numbered for comparison with DNA gels. b PCR validation of presence of Pentatrichomonas and Cryptosporidium using published primers Th4, Th5, Cr254F and CR323R (Crucitti et al. 2004; Bruijnesteijn et al. 2009), and an Entamoeba coli specific forward primer 5′-GGTTTCTAATATCAACAGGCTAC-3′ to 18S rRNA gene FR686446 with 18S-V9-15_R. NT, no template control; samples marked with an asterisk are not expected to be positive. Related to Fig. 3 a. Figure S2. Differential composition analysis of bacterial OTUs in Malawian samples. Plots were generated with the ALDEx2 R-package, and show OTU fold-change versus median abundance (left) and OTU fold-change between versus within conditions (right). No significant compositional changes in OTUs were found by Wilcoxon rank test. Tests compare subjects positive and negative for a, Cryptosporidium (18S rRNA V4 V5 amplicon), b, Enterocytozoon (transITS amplicon), c, Giardia or d, HIV. Cryptosporidium and Enterocytozoon presence are defined as a minimum of 5 amplicon reads, and Giardia and HIV infection status were determined by clinical diagnostic tests. Related to Fig. 5b. Supplementary Methods. Supplementary information is included on clinical sample collection. (PDF 1241 kb)

Principal component analysis for four data types (Taxa, Enzymes, Significant Differentially Expressed Transcripts and Metabolic Pathways). With each plot, p values (

Diet-based comparisons of enzyme expression in butanoate pathway. Two comparisons are shown: (A) Plin2-HF vs. Plin2-LF and (B) WT-HF vs. WT-LF. Circular nodes indicate enzymes, with size indicating relative difference in expression between sample types and color indicating direction of change (see inset key). Associated heatmaps indicate global changes in expression for each enzyme, in addition to taxon-specific changes in expression for each of the 17 defined taxa colored according to phylum. The following abbreviations are used: 3Bâ CoA (3-butenoyl-CoA), 4HB-CoA (4-hydroxy-butanoyl-CoA), C-CoA (crotonoyl-CoA), G-CoA (glutaconyl-CoA), 3HB-CoA (3-hydroxybutanoyl-CoA), HMG-CoA (hydroxy-3-methylglutaryl-CoA). (PDF 1262Â kb)