Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases

While metagenomic sequencing has become the tool of preference to study host-associated microbial communities, downstream analyses and clinical interpretation of microbiome data remains challenging due to the sparsity and compositionality of sequence matrices. Here, we evaluate both computational and experimental approaches proposed to mitigate the impact of these outstanding issues. Generating fecal metagenomes drawn from simulated microbial communities, we benchmark the performance of thirteen commonly used analytical approaches in terms of diversity estimation, identification of taxon-taxon associations, and assessment of taxon-metadata correlations under the challenge of varying microbial ecosystem loads. We find quantitative approaches including experimental procedures to incorporate microbial load variation in downstream analyses to perform significantly better than computational strategies designed to mitigate data compositionality and sparsity, not only improving the identification of true positive associations, but also reducing false positive detection. When analyzing simulated scenarios of low microbial load dysbiosis as observed in inflammatory pathologies, quantitative methods correcting for sampling depth show higher precision compared to uncorrected scaling. Overall, our findings advocate for a wider adoption of experimental quantitative approaches in microbiome research, yet also suggest preferred transformations for specific cases where determination of microbial load of samples is not feasible

PEMBINAAN NARAPIDANA YANG MENGALAMI GANGGUAN JIWA DI DALAM LEMBAGA PEMASYARAKATAN

PEMBINAAN NARAPIDANA YANG MENGALAMI GANGGUAN JIWADI LEMBAGA PEMASYARAKATAN Agusriadi Dahlan Ali Suhaimi ABSTRAKLembaga Pemasyarakatan sebelumnya disebut Penjara adalah tempat orang-orang yang melakukan kriminalitas dan pelanggaran hukum lainnya agar mereka dapat menyadari kesalahannya dan mempertanggungjawabkan apa yang telah mereka perbuat. Hukuman yang mereka terima sebagai balasan yang setimpal terhadap perbuatan mereka, meskipun nilai-nilai kemanusiaan beserta hak asasinya kurang diperhatikan. Lembaga Pemasyarakatan merupakan tempat yang stressfull atau menekan yang dapat berpengaruh terhadap fisik dan kejiwaan (psikologi) seseorang ditambah kecemasan yang berlebihan sehingga muncul depresi yang mengakibatkan seseorang melakukan bunuh diri. Akibat stress melahirkan depresi dan depresi biasanya akan terjadi kegoncangan kejiwaan yang luar biasa yang dapat mengakibatkan seseorang menjadi tidak waras (gila). Undang-Undang No.12/1995 tentang Lembaga Pemasyarakatan maupun Peraturan Pemerintah No. 99 Tahun 2012 tentang Perubahan Kedua Atas Peraturan Pemerintah Nomor 32 Tahun 1999 tentang Syarat dan Tata Cara Pelaksanaan Hak Warga Binaan Pemasyarakatan tidak menjelaskan ketentuan terhadap narapidana yang gila di dalam lapas sebagaimana yang pernah terjadi di Lapas Kelas II-A Lambaro, Aceh Besar dan Rutan Klas I Tanjung Gusta, Medan. Selanjutnya yang bersangkutan dikirim ke Lapas Kelas Klass II-B Meulaboh tanggal 27 Januari 2014. Selama tujuh hari di Lapas Klass II-B Meulaboh Zabir bin Ilyas kemudian di titipkan di Rumah Sakit Jiwa Banda Aceh karena penyakitnya sudah mencapai stadium empat untuk mendapatkan perawatan dan penyembuhan kejiwaannya. Bagaimanakah pengaturan dan pembinaan terhadap narapidana yang mengalami gangguan kejiwaan dalam Lembaga Pemasyarakatan. Kemudian bagaimanakah kepastian hukum bagi narapidana yang sedang mengalami gangguan kejiwaan, dan bagaimana status hukum bagi narapidana yang sembuh dari gangguan kejiwaan. Penelitian dan pengkajian ini bertujuan untuk mengetahui pengaturan dan pembinaan terhadap narapidana yang mengalami gangguan kejiwaan dalam Lapas dan mengidentifikasi kepastian hukum bagi narapidana yang sedang mengalami gangguan kejiwaan serta mengetahui status hukum bagi narapidana yang sembuh dari gangguan kejiwaan.Metode yang digunakan adalah metode penelitian yuridis-normatif dengan menggunakan jenis penelitian deskriptis analisis dalam rangka untuk menemukan aturan hukum, prinsip-prinsip hukum, norma maupun doktrin-doktrin hukum dengan pendekatan undang-undang, kasus. Sumber data adalah data sekunder berupa bahan hukum primer, bahan hukum sekunder, dan bahan hukum tersier.Hasil penelitian menunjukkan bahwa Pengaturan tentang perawatan narapidana yang mengalami gangguan kejiwaan dalam Lembaga Pemasyarakatan di Indonesia belum diatur, baik dalam Undang-Undang Nomor 12 Tahun 1995 tentang Lembaga Pemasyarakatan maupun PP No. 99 Tahun 2012 tentang PP No. 99 Tahun 2012 tentang Perubahan Kedua Atas PP No.32 Tahun 1999 tentang Syarat dan Tata Cara Pelaksanaan Hak Warga Binaan Pemasyarakatan. Namun bila narapidana sakit atau gangguan kesehatan lainnya yang tidak termasuk gangguan kejiwaan ada aturan tentang perawatan medis. Adapun mengenai narapidana yang mengalami gangguan kejiwaan di Lembaga Pemasyarakatan di Indonesia hingga kini belum ada kepastian hukum karena kasus seperti ini sangat langka terjadi di Indonesia. Pihak otoritas hanya menggunakan hak diskresi yang dimilikinya untuk menyelesaikan kasus tersebut sebagaimana terjadi di Lapas Porong Surabaya. Tetapi di Aceh kasus ini baru pertama kali terjadi yang dialami Zabir bin Ilyas pada tahun 2014. Pimpinan Lapas memutuskan memasukkan Zabir bin Ilyas ke Rumah Sakit Jiwa Banda Aceh. Terkait status hukum narapidana yang sembuh dari gangguan kejiwaan masih tetap sebagai tersangka (ditahan). Tidak ada keringanan hukuman apalagi sampai dibebaskan sebelum masa hukuman habis dijalankan. Hingga kini tidak ada satupun aturan yang mengatur baik secara implisit maupun ekplisit yang mengatur tentang narapidana yang sembuh dari penyakit kejiwaan (gila).Disarankan kepada Pemerintah agar merevisi Undang-Undang Nomor 12 Tahun 1995 tentang Lembaga Pemasyarakatan dan memasukkan salah satu pasal yang mengatur mengenai narapidana yang mengalami gangguan kejiwaan di dalam Lembaga Pemasyarakatan. Agar terwujudnya kepastian hukum di Indonesia mengenai narapidana yang mengalami gangguan kejiwaan dalam lebaga pemasyarakatan untuk membuat regulasi legal baik berupa undang-undang khusus atau melalui Peraturan Pemerintah. Kemudian disarankan agar narapidana yang mengalami gangguan kejiwaan dalam Lembaga Pemasyarakatan dapat dibebaskan dan dikembalikan ke keluarganya atau dimasukkan ke rumah sakit jiwa hingga sembuh.Kata Kunci : Pembinaan, Narapidana, Gangguan Jiwa, Lembaga Pemasyarakatan.Banda Ace

Human and preclinical studies of the host-gut microbiome co-metabolite hippurate as a marker and mediator of metabolic health.

OBJECTIVE: Gut microbial products are involved in regulation of host metabolism. In human and experimental studies, we explored the potential role of hippurate, a hepatic phase 2 conjugation product of microbial benzoate, as a marker and mediator of metabolic health. DESIGN: In 271 middle-aged non-diabetic Danish individuals, who were stratified on habitual dietary intake, we applied 1H-nuclear magnetic resonance (NMR) spectroscopy of urine samples and shotgun-sequencing-based metagenomics of the gut microbiome to explore links between the urine level of hippurate, measures of the gut microbiome, dietary fat and markers of metabolic health. In mechanistic experiments with chronic subcutaneous infusion of hippurate to high-fat-diet-fed obese mice, we tested for causality between hippurate and metabolic phenotypes. RESULTS: In the human study, we showed that urine hippurate positively associates with microbial gene richness and functional modules for microbial benzoate biosynthetic pathways, one of which is less prevalent in the Bacteroides 2 enterotype compared with Ruminococcaceae or Prevotella enterotypes. Through dietary stratification, we identify a subset of study participants consuming a diet rich in saturated fat in which urine hippurate concentration, independently of gene richness, accounts for links with metabolic health. In the high-fat-fed mice experiments, we demonstrate causality through chronic infusion of hippurate (20 nmol/day) resulting in improved glucose tolerance and enhanced insulin secretion. CONCLUSION: Our human and experimental studies show that a high urine hippurate concentration is a general marker of metabolic health, and in the context of obesity induced by high-fat diets, hippurate contributes to metabolic improvements, highlighting its potential as a mediator of metabolic health

Integrated use of residues from olive mill and winery for lipase production by solid state fermentation with Aspergillus sp

Two phase olive mill waste (TPOMW) is presently the major waste produced by the olive mill industry. This waste has potential to be used as substrate for solid state fermentation (SSF) despite of its high concentration of phenolic compounds and low nitrogen content. In this work, it is demonstrated that mixtures of TPOMW with winery wastes support the production of lipase by Aspergillus spp. By agar plate screening, Aspergillus niger MUM 03.58, Aspergillus ibericus MUM 03.49 and Aspergillus uvarum MUM 08.01 were chosen for lipase production by SSF. Plackett-Burman experimental design was employed to evaluate the effect of substrate composition and time on lipase production. The highest amounts of lipase were produced by A. ibericus on a mixture of TPOMW, urea and exhausted grape mark (EGM). Urea was found to be the most influent factor for the lipase production. Further optimization of lipase production by A. ibericus using a full factorial design (32) conducted to optimal conditions of substrate composition (0.073 g urea/g and 25% of EGM) achieving 18.67 U/g of lipolytic activity.Jose Manuel Salgado is grateful for Postdoctoral fellowship (EX-2010-0402) of Education Ministry of Spanish Government. Luis Abrunhosa was supported by the grant SFRH/BPD/43922/2008 from Fundacao para a Ciencia e Tecnologia-FCT, Portugal. Authors thank Fundacao para a Ciencia e a Tecnologia (FCT) for financial support through the project FCT Pest-OE/EQB/LA0023/2011

Genomics and metagenomics of trimethylamine-utilizing Archaea in the human gut microbiome

International audienceThe biological significance of Archaea in the human gut microbiota is largely unclear. We recently reported genomic and biochemical analyses of the Methanomassiliicoccales, a novel order of methanogenic Archaea dwelling in soil and the animal digestive tract. We now show that these Methanomassiliicoccales are present in published microbiome data sets from eight countries. They are represented by five Operational Taxonomic Units present in at least four cohorts and phylogenetically distributed into two clades. Genes for utilizing trimethylamine (TMA), a bacterial precursor to an atherosclerogenic human metabolite, were present in four of the six novel Methanomassiliicoccales genomes assembled from ELDERMET metagenomes. In addition to increased microbiota TMA production capacity in long-term residential care subjects, abundance of TMA-utilizing Methanomassiliicoccales correlated positively with bacterial gene count for TMA production and negatively with fecal TMA concentrations. The two large Methanomassiliicoccales clades have opposite correlations with host health status in the ELDERMET cohort and putative distinct genomic signatures for gut adaptation

Effects of orange juice formulation on prebiotic functionality using an in vitro colonic model sytem

A three-stage continuous fermentative colonic model system was used to monitor in vitro the effect of different orange juice formulations on prebiotic activity. Three different juices with and without Bimuno, a GOS mixture containing galactooligosaccharides (B-GOS) were assessed in terms of their ability to induce a bifidogenic microbiota. The recipe development was based on incorporating 2.75g B-GOS into a 250 ml serving of juice (65°Brix of concentrate juice). Alongside the production of B-GOS juice, a control juice - orange juice without any additional Bimuno and a positive control juice, containing all the components of Bimuno (glucose, galactose and lactose) in the same relative proportions with the exception of B-GOS were developed. Ion Exchange Chromotography analysis was used to test the maintenance of bimuno components after the production process. Data showed that sterilisation had no significant effect on concentration of B-GOS and simple sugars. The three juice formulations were digested under conditions resembling the gastric and small intestinal environments. Main bacterial groups of the faecal microbiota were evaluated throughout the colonic model study using 16S rRNA-based fluorescence in situ hybridization (FISH). Potential effects of supplementation of the juices on microbial metabolism were studied measuring short chain fatty acids (SCFAs) using gas chromatography. Furthermore, B-GOS juices showed positive modulations of the microbiota composition and metabolic activity. In particular, numbers of faecal bifidobacteria and lactobacilli were significantly higher when B-GOS juice was fermented compared to controls. Furthermore, fermentation of B-GOS juice resulted in an increase in Roseburia subcluster and concomitantly increased butyrate production, which is of potential benefit to the host. In conclusion, this study has shown B-GOS within orange juice can have a beneficial effect on the fecal microbiota

Optimization of lipase production by solid-state fermentation of olive pomace: from flask to laboratory-scale packed-bed bioreactor

Lipases are versatile catalysts with many applications and can be produced by solid-state fermentation (SSF) using agro-industrial wastes. The aim of this work was to maximize the production of Aspergillus ibericus lipase under SSF of olive pomace (OP) and wheat bran (WB), evaluating the effect on lipase production of C/N ratio, lipids, phenols, content of sugars of substrates and nitrogen source addition. Moreover, the implementation of the SSF process in a packed-bed bioreactor and the improvement of lipase extraction conditions were assessed. Low C/N ratios and high content of lipids led to maximum lipase production. Optimum SSF conditions were achieved with a C/N mass ratio of 25.2 and 10.2% (w/w) lipids in substrate, by the mixture of OP:WB (1:1) and supplemented with 1.33% (w/w) (NH4)2SO4. Studies in a packed-bed bioreactor showed that the lower aeration rates tested prevented substrate dehydration, improving lipase production. In this work, the important role of Triton X-100 on lipase extraction from the fermented solid substrate has been shown. A final lipase activity of 223 ± 5 U g1 (dry basis) was obtained after 7 days of fermentation.Felisbela Oliveira acknowledges the financial support from Fundação para a Ciência e Tecnologia (FCT) of Portugal through grant SFRH/BD/87953/2012. José Manuel Salgado was supported by grant CEB/N2020–INV/01/2016 from Project ‘‘BIOTECNORTE-Underpinning Biotechnology to foster the north of Portugal bioeconomy’’ (NORTE-01-0145-FEDER-000004). Luı ´s Abrunhosa was supported by grant UMINHO/BPD/51/2015 from project UID/BIO/04469/2013 financed by FCT/MEC (OE). This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER006684) and BioTecNorte operation (NORTE-01-0145-FEDER000004) funded by the European Regional Development Fund under the scope of Norte2020–Programa Operacional Regional do Norte. Noelia Pérez-Rodríguez acknowledges the financial support of FPU fellowship from the Spanish Ministry of Education, Culture and Sports. The authors thank the Spanish Ministry of Economy and Competitiveness for the financial support of this work (Project CTQ2015-71436-C2-1-R), which has partial financial support from the FEDER funds of the European Union.info:eu-repo/semantics/publishedVersio

Large-scale association analyses identify host factors influencing human gut microbiome composition

To study the effect of host genetics on gut microbiome composition, the MiBioGen consortium curated and analyzed genome-wide genotypes and 16S fecal microbiome data from 18,340 individuals (24 cohorts). Microbial composition showed high variability across cohorts: only 9 of 410 genera were detected in more than 95% of samples. A genome-wide association study of host genetic variation regarding microbial taxa identified 31 loci affecting the microbiome at a genome-wide significant (P < 5 x 10(-8)) threshold. One locus, the lactase (LCT) gene locus, reached study-wide significance (genome-wide association study signal: P = 1.28 x 10(-20)), and it showed an age-dependent association with Bifidobacterium abundance. Other associations were suggestive (1.95 x 10(-10) < P < 5 x 10(-8)) but enriched for taxa showing high heritability and for genes expressed in the intestine and brain. A phenome-wide association study and Mendelian randomization identified enrichment of microbiome trait loci in the metabolic, nutrition and environment domains and suggested the microbiome might have causal effects in ulcerative colitis and rheumatoid arthritis

Effect of Fructooligosaccharide Metabolism on Chicken Colonization by an Extra-Intestinal Pathogenic Escherichia coli Strain

Extra-intestinal pathogenic Escherichia coli (ExPEC) strains cause many diseases in humans and animals. While remaining asymptomatic, they can colonize the intestine for subsequent extra-intestinal infection and dissemination in the environment. We have previously identified the fos locus, a gene cluster within a pathogenicity island of the avian ExPEC strain BEN2908, involved in the metabolism of short-chain fructooligosaccharides (scFOS). It is assumed that these sugars are metabolized by the probiotic bacteria of the microbiota present in the intestine, leading to a decrease in the pathogenic bacterial population. However, we have previously shown that scFOS metabolism helps BEN2908 to colonize the intestine, its reservoir. As the fos locus is located on a pathogenicity island, one aim of this study was to investigate a possible role of this locus in the virulence of the strain for chicken. We thus analysed fos gene expression in extracts of target organs of avian colibacillosis and performed a virulence assay in chickens. Moreover, in order to understand the involvement of the fos locus in intestinal colonization, we monitored the expression of fos genes and their implication in the growth ability of the strain in intestinal extracts of chicken. We also performed intestinal colonization assays in axenic and Specific Pathogen-Free (SPF) chickens. We demonstrated that the fos locus is not involved in the virulence of BEN2908 for chickens and is strongly involved in axenic chicken cecal colonization both in vitro and in vivo. However, even if the presence of a microbiota does not inhibit the growth advantage of BEN2908 in ceca in vitro, overall, growth of the strain is not favoured in the ceca of SPF chickens. These findings indicate that scFOS metabolism by an ExPEC strain can contribute to its fitness in ceca but this benefit is fully dependent on the bacteria present in the microbiota