Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows

Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carry out a community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluate the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, laboratory-assembled human intestinal model and a human fecal sample. We observe that variability at the peptide level is predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappear at the protein group level. While differences are observed for predicted community composition, similar functional profiles are obtained across workflows. CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-laboratory studies in metaproteomics, and provides publicly available data sets for benchmarking future developments.

In vivo augmentation of a complex gut bacterial community

Efforts to model the human gut microbiome in mice have led to important insights into the mechanisms of host-microbe interactions. However, the model communities studied to date have been defined or complex but not both, limiting their utility. In accompanying work, we constructed a complex synthetic community (104 strains, hCom1) containing the most common taxa in the human gut microbiome. Here, we used an iterative experimental process to improve hCom1 by filling open metabolic and/or anatomical niches. When we colonized germ-free mice with hCom1 and then challenged it with a human fecal sample, the consortium exhibited surprising stability; 89% of the cells and 58% of the taxa derive from the original community, and the pre- and post-challenge communities share a similar overall structure. We used these data to construct a second version of the community, adding 22 strains that engrafted following fecal challenge and omitting 7 that dropped out (119 strains, hCom2). In gnotobiotic mice, hCom2 exhibited increased stability to fecal challenge and robust colonization resistance against pathogenic Escherichia coli. Mice colonized by hCom2 versus human feces are similar in terms of microbiota-derived metabolites, immune cell profile, and bacterial density in the gut, suggesting that this consortium is a prototype of a model system for the human gut microbiome.

Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab Comparison of Established Workflows

Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear.Here, we carried out the first community-driven, multi-lab comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluated the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, lab-assembled human intestinal model and a human fecal sample.We observed that variability at the peptide level was predominantly due to wet-lab workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappeared at protein group level. While differences were observed for predicted community composition, similar functional profiles were obtained across workflows.CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-lab studies in metaproteomics, and provides publicly available data sets for benchmarking future developments.

Draft Genome Sequence of Bacillus thuringiensis DPC6431, Producer of the Bacteriocin Thuricin CD

We report the draft genome sequence of Bacillus thuringiensis DPC6431, a producer of the anticlostridial bacteriocin thuricin CD and isolated from a human fecal sample. The assembly comprises 96 contigs for a total of 5,581,839 bp, with 32.5% G+C content.

Comparison of Microscopic and PCR for Detection Giardia sp. in the Human Fecal Sample at Bedog Watershed, Sleman, DIY

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Draft Genome Sequence of Megamonas funiformis Strain Marseille-P3344, Isolated from a Human Fecal Microbiota

ABSTRACT In this article, we present the draft genome sequence of Megamonas funiformis strain Marseille-P3344, isolated from a human fecal sample. The genome described here is composed of 2,464,704 nucleotides, with 2,230 protein-coding genes and 76 RNA genes.

Faktor-Faktor Yang Berhubungan Dengan Kejadian Kecacingan Soil Transmitted Helminths Pada Anak Usia 1 – 5 Tahun Di Rw 07 Geringging Kecamatan Rumbai Pesisir

Helminthiasis is a disease that occurs in the population in the tropics and subtropics area.One of the helminthiasis in humans is Soil Transmitted Helminth (STH). The prevalence of this disease is still to be a concern because the prevalence is quite high in children that is no exception in the children aged 1-5 years. The factors causing helminthiasis are included behavioral and environmental factors. This study aims to determine the factors that are related to STH helminthiasis incidence among others, the habit of washing hand of mothers, the habit of wearing footwear, the cleanliness of mother and child's nails, the availability of clean water, the availability of latrines and the availability of the trash. The sample is the total population of 55 children aged 1-5 years in RW 07 Geringging Rumbai Pesisir District. This research is an observational quantitative with cross sectional design.Data is taken from the result of questionnaire and human fecal sample. The data were analyzed using chi square test. The result of the research showing STH infected children were 7 people (12,7%). The types of the worm eggs that infect are Ascaris lumbricoides (7.2%), Trichuris trichiura (3.6%), and hookworm (1.8%). The result of statistical test showed that there was a relationship between hand washing habits (p = 0,039), children habit wearing footwear (p = 0,002), clean of mother and child nail (p = 0,041), clean water supply (p = 0,016) (p = 0,024) and there is no relation between garbage availability (p = 0,168)) to the occurrence of helminthiasis. Keywords: Helminthiasis, washing hand of mothers, wearing children's footwear, cleaning mother's and children's nails, availability of clean water, availability of latrines