scholarly journals 16S ribosomal RNA-based gut microbiome composition analysis in infants with breast milk jaundice

2018 ◽  
Vol 13 (1) ◽  
pp. 208-216 ◽  
Author(s):  
Miao Duan ◽  
Jialin Yu ◽  
Jinxing Feng ◽  
Yu He ◽  
Sa Xiao ◽  
...  
Keyword(s):  
Breast Milk ◽  
Gut Microbiome ◽  
High Throughput Sequencing ◽  
Pcr Amplification ◽  
Control Group ◽  
Composition Analysis ◽  
Sequencing Data ◽  
Sequencing Platform ◽  
Breastfed Infants ◽  
Breast Milk Jaundice

AbstractBackgroundThis case-control study investigated an association between breast milk jaundice (BMJ) and infants’ gut microbiome. The study included determination of the diversity of the gut microbiome and identification of bacterial genera associated with BMJ.MethodsThe study population consisted of 12 infants with BMJ and 22 breastfed infants without jaundice (control). DNA collected from feces was analyzed by PCR amplification and 1% agarose gel electrophoresis, and then sequenced with a MiSeq system. Relative quantification bioinformatics was employed to analyze the DNA sequencing data. An Illumina high-throughput sequencing platform was used to analyze 16S rRNA variable (V) regions V3 and V4 in stool samples.ResultsIn the control group, the proportion ofEscherichia/Shigella(genus level) in the gut microbiome (64.67%) was significantly higher than that of the BMJ group. However, the prevalence ofBifidobacteriumorEnterococcusin the gut microbiome of the two groups was similar. The Simpson index indicated that the diversity of the bacterial population in the BMJ infants was significantly narrower than in the normal infants.ConclusionThe prevalence ofEscherichia/Shigellain the gut of breastfed infants is important for lowering BMJ development.

scholarly journals Dynamic Associations of Milk Components With the Infant Gut Microbiome and Fecal Metabolites in a Mother–Infant Model by Microbiome, NMR Metabolomic, and Time-Series Clustering Analyses

2022 ◽  
Vol 8 ◽  
Author(s):  
Yosuke Komatsu ◽  
Daiki Kumakura ◽  
Namiko Seto ◽  
Hirohisa Izumi ◽  
Yasuhiro Takeda ◽  
...  
Keyword(s):  
Breast Milk ◽  
Gut Microbiome ◽  
Lactation Period ◽  
Bioactive Components ◽  
Fecal Microbiome ◽  
Breastfed Infants ◽  
H Nmr ◽  
Milk Components ◽  
Infant Gut Microbiome ◽  
Infant Feces

Background: The gut microbiome and fecal metabolites of breastfed infants changes during lactation, and are influenced by breast milk components. This study aimed to investigate dynamic associations of milk components with the infant gut microbiome and fecal metabolites throughout the lactation period in a mother–infant model.Methods: One month after delivery, breast milk and subsequent infant feces were collected in a pair for 5 months from a mother and an exclusively breastfed infant. Composition of the fecal microbiome was determined with 16S rRNA sequencing. Low-molecular-weight metabolites, including human milk oligosaccharides (HMOs), and antibacterial proteins were measured in feces and milk using 1H NMR metabolomics and enzyme-linked immunosorbent assays. The association of milk bioactive components with the infant gut microbiome and fecal metabolites was determined with Python clustering and correlation analyses.Results: The HMOs in milk did not fluctuate throughout the lactation period. However, they began to disappear in infant feces at the beginning of month 4. Notably, at this time-point, a bifidobacterium species switching (from B. breve to B. longum subsp. infantis) occurred, accompanied by fluctuations in several metabolites including acetate and butyrate in infant feces.Conclusions: Milk bioactive components, such as HMOs, might play different roles in the exclusively breastfed infants depending on the lactation period.

scholarly journals Inferring species compositions of complex fungal communities from long- and short-read sequence data

2021 ◽  
Author(s):  
Yiheng Hu ◽  
Laszlo Irinyi ◽  
Minh Thuy Vi Hoang ◽  
Tavish Eenjes ◽  
Abigail Graetz ◽  
...  
Keyword(s):  
Community Composition ◽  
Pathogen Detection ◽  
High Throughput Sequencing ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Composition Analysis ◽  
Sequencing Data ◽  
Species Classification ◽  
Shotgun Metagenomics ◽  
Query Coverage

Background: The kingdom fungi is crucial for life on earth and is highly diverse. Yet fungi are challenging to characterize. They can be difficult to culture and may be morphologically indistinct in culture. They can have complex genomes of over 1 Gb in size and are still underrepresented in whole genome sequence databases. Overall their description and analysis lags far behind other microbes such as bacteria. At the same time, classification of species via high throughput sequencing without prior purification is increasingly becoming the norm for pathogen detection, microbiome studies, and environmental monitoring. However, standardized procedures for characterizing unknown fungi from complex sequencing data have not yet been established. Results: We compared different metagenomics sequencing and analysis strategies for the identification of fungal species. Using two fungal mock communities of 44 phylogenetically diverse species, we compared species classification and community composition analysis pipelines using shotgun metagenomics and amplicon sequencing data generated from both short and long read sequencing technologies. We show that regardless of the sequencing methodology used, the highest accuracy of species identification was achieved by sequence alignment against a fungi-specific database. During the assessment of classification algorithms, we found that applying cut-offs to the query coverage of each read or contig significantly improved the classification accuracy and community composition analysis without significant data loss. Conclusion: Overall, our study expands the toolkit for identifying fungi by improving sequence-based fungal classification, and provides a practical guide for the design of metagenomics analyses.

scholarly journals Hi-C chromosome conformation capture sequencing of avian genomes using the BGISEQ-500 platform

GigaScience ◽  
2020 ◽  
Vol 9 (8) ◽  
Author(s):  
Marcela Sandoval-Velasco ◽  
Juan Antonio Rodríguez ◽  
Cynthia Perez Estrada ◽  
Guojie Zhang ◽  
Erez Lieberman Aiden ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
High Throughput Sequencing ◽  
Data Generation ◽  
Next Generation ◽  
Sequencing Data ◽  
Yield Data ◽  
Chromosome Conformation ◽  
Sequencing Platform ◽  
Sequencing Platforms ◽  
Generation Sequencing

Abstract Background Hi-C experiments couple DNA-DNA proximity with next-generation sequencing to yield an unbiased description of genome-wide interactions. Previous methods describing Hi-C experiments have focused on the industry-standard Illumina sequencing. With new next-generation sequencing platforms such as BGISEQ-500 becoming more widely available, protocol adaptations to fit platform-specific requirements are useful to give increased choice to researchers who routinely generate sequencing data. Results We describe an in situ Hi-C protocol adapted to be compatible with the BGISEQ-500 high-throughput sequencing platform. Using zebra finch (Taeniopygia guttata) as a biological sample, we demonstrate how Hi-C libraries can be constructed to generate informative data using the BGISEQ-500 platform, following circularization and DNA nanoball generation. Our protocol is a modification of an Illumina-compatible method, based around blunt-end ligations in library construction, using un-barcoded, distally overhanging double-stranded adapters, followed by amplification using indexed primers. The resulting libraries are ready for circularization and subsequent sequencing on the BGISEQ series of platforms and yield data similar to what can be expected using Illumina-compatible approaches. Conclusions Our straightforward modification to an Illumina-compatible in situHi-C protocol enables data generation on the BGISEQ series of platforms, thus expanding the options available for researchers who wish to utilize the powerful Hi-C techniques in their research.

scholarly journals DNA extraction and sequencing of the Mawangdui ancient cadaver protected by formalin

2020 ◽  
Author(s):  
Hua-Lin Huang ◽  
Shikui Yin ◽  
Huifang Zhao ◽  
Chao Tian ◽  
Jufang Huang ◽  
...  
Keyword(s):  
Dna Extraction ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Pcr Amplification ◽  
Magnetic Bead ◽  
Sequencing Data ◽  
Sequencing Library ◽  
Bead Method ◽  
Formalin Fixed ◽  
Better Than

AbstractMawangdui ancient Cadaver is the first wet corpse found in the world, which is famous for being immortal for over two thousands of years. After being unearthed, the female corpse was immersed in the formalin protective solution for more than 40 years. We used magnetic bead method and formalin fixed paraffing (FFPE) method to extract the DNA of the female corpse, respectively. PCR amplification, sanger sequencing, library building, high throughput sequencing (testing) and data processing were carried out on the DNA samples, and about 0.5% of the whole genome coverage sequencing data was obtained. Comparing the results of DNA trough two extraction and sequencing methods. We found that the FFPE and high throughput sequencing methods is better than others for DNA extraction of the ancient samples which were preserved in formalin, providing a guidance for dealing with formalin preserved ancient samples in the future.

scholarly journals Metagenomic analysis of the gut microbiome composition associated with vitamin D supplementation in Taiwanese infants

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wei-Te Lei ◽  
Kai-Yao Huang ◽  
Jhih-Hua Jhong ◽  
Chia-Hung Chen ◽  
Shun-Long Weng
Keyword(s):  
Vitamin D ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Infant Health ◽  
Bone Mineralization ◽  
Vitamin D Supplementation ◽  
Metagenomic Analysis ◽  
Control Group ◽  
Microbiome Composition ◽  
Breastfed Infants

AbstractEarly childhood is a critical stage for the foundation and development of the gut microbiome, large amounts of essential nutrients are required such as vitamin D. Vitamin D plays an important role in regulating calcium homeostasis, and deficiency can impair bone mineralization. In addition, most people know that breastfeeding is advocated to be the best thing for a newborn; however, exclusively breastfeeding infants are not easily able to absorb an adequate amount of vitamin D from breast milk. Understanding the effects of vitamin D supplementation on gut microbiome can improve the knowledge of infant health and development. A total of 62 fecal sample from healthy infants were collected in Taiwan. Of the 62 infants, 31 were exclusively breastfed infants and 31 were mixed- or formula-fed infants. For each feeding type, one subgroup of infants received 400 IU of vitamin D per day, and the remaining infants received a placebo. In total, there are 15 breastfed and 20 formula-fed infants with additional vitamin D supplementation, and 16 breastfed and 11 formula-fed infants belong to control group, respectively. We performed a comparative metagenomic analysis to investigate the distribution and diversity of infant gut microbiota among different types of feeding regimes with and without vitamin D supplementation. Our results reveal that the characteristics of infant gut microbiota not only depend on the feeding types but also on nutrients intake, and demonstrated that the vitamin D plays an important role in modulating the infant gut microbiota, especially increase the proportion of probiotics in breast-fed infants.

scholarly journals Early probiotic supplementation with B. infantis in breastfed infants leads to persistent colonization at 1 year

2021 ◽  
Author(s):  
Claire E. O’Brien ◽  
Anna K. Meier ◽  
Karina Cernioglo ◽  
Ryan D. Mitchell ◽  
Giorgio Casaburi ◽  
...  
Keyword(s):  
Breast Milk ◽  
Gut Microbiome ◽  
Controlled Trial ◽  
Bifidobacterium Longum ◽  
List Type ◽  
Probiotic Supplementation ◽  
Breastfed Infants ◽  
Follow Up Study ◽  
Increased Risk

Abstract Background Recent studies have reported a dysfunctional gut microbiome in breastfed infants. Probiotics have been used in an attempt to restore the gut microbiome; however, colonization has been transient, inconsistent among individuals, or has not positively impacted the host’s gut. Methods This is a 2-year follow-up study to a randomized controlled trial wherein 7-day-old infants received 1.8 × 1010 colony-forming unit Bifidobacterium longum subsp. infantis (B. infantis) EVC001 (EVC) daily for 21 days or breast milk alone (unsupplemented (UNS)). In the follow-up study, mothers (n = 48) collected infant stool at 4, 6, 8, 10, and 12 months postnatal and completed the health-diet questionnaires. Results Fecal B. infantis was 2.5–3.5 log units higher at 6–12 months in the EVC group compared with the UNS group (P < 0.01) and this relationship strengthened with the exclusion of infants who consumed infant formula and antibiotics. Infants in the EVC group had significantly higher Bifidobacteriaceae and lower Bacteroidaceae and Lachnospiraceae (P < 0.05). There were no differences in any health conditions between the two groups. Conclusions Probiotic supplementation with B. infantis within the first month postnatal, in combination with breast milk, resulted in stable colonization that persisted until at least 1 year postnatal. Impact A dysfunctional gut microbiome in breastfed infants is common in resource-rich nations and associated with an increased risk of immune diseases. Probiotics only transiently exist in the gut without persistent colonization or altering the gut microbiome. This is the first study to show that early probiotic supplementation with B. infantis with breast milk results in stable colonization of B. infantis and improvements to the gut microbiome 1 year postnatal. This study addresses a key gap in the literature whereby probiotics can restore the gut microbiome if biologically selected microorganisms are matched with their specific food in an open ecological niche.

scholarly journals Highly comparable metabarcoding results from MGI-Tech and Illumina sequencing platforms

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12254
Author(s):  
Sten Anslan ◽  
Vladimir Mikryukov ◽  
Kęstutis Armolaitis ◽  
Jelena Ankuda ◽  
Dagnija Lazdina ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Coi Gene ◽  
Synthesis Methods ◽  
Sequence Variant ◽  
Sequencing Data ◽  
Data Set ◽  
Soil Dna ◽  
Sequencing Platform ◽  
Sequencing By Synthesis ◽  
Sequencing Platforms

With the developments in DNA nanoball sequencing technologies and the emergence of new platforms, there is an increasing interest in their performance in comparison with the widely used sequencing-by-synthesis methods. Here, we test the consistency of metabarcoding results from DNBSEQ-G400RS (DNA nanoball sequencing platform by MGI-Tech) and NovaSeq 6000 (sequencing-by-synthesis platform by Illumina) platforms using technical replicates of DNA libraries that consist of COI gene amplicons from 120 soil DNA samples. By subjecting raw sequencing data from both platforms to a uniform bioinformatics processing, we found that the proportion of high-quality reads passing through the filtering steps was similar in both datasets. Per-sample operational taxonomic unit (OTU) and amplicon sequence variant (ASV) richness patterns were highly correlated, but sequencing data from DNBSEQ-G400RS harbored a higher number of OTUs. This may be related to the lower dominance of most common OTUs in DNBSEQ data set (thus revealing higher richness by detecting rare taxa) and/or to a lower effective read quality leading to generation of spurious OTUs. However, there was no statistical difference in the ASV and post-clustered ASV richness between platforms, suggesting that additional denoising step in the ASV workflow had effectively removed the ‘noisy’ reads. Both OTU-based and ASV-based composition were strongly correlated between the sequencing platforms, with essentially interchangeable results. Therefore, we conclude that DNBSEQ-G400RS and NovaSeq 6000 are both equally efficient high-throughput sequencing platforms to be utilized in studies aiming to apply the metabarcoding approach, but the main benefit of the former is related to lower sequencing cost.

scholarly journals Evaluation on the characteristics of gut microbiome in polycystic ovary syndrome rats induced by dihydrotestosterone or letrozole

2020 ◽  
Author(s):  
Zheng Yanhua ◽  
Ying Xu ◽  
Hongxia Ma ◽  
Chengjie Liang ◽  
Tong Yang
Keyword(s):  
Polycystic Ovary Syndrome ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
High Throughput Sequencing ◽  
Polycystic Ovary ◽  
Molecular Ecology ◽  
Control Group ◽  
Polycystic Ovaries ◽  
Ovary Syndrome ◽  
And Function

Abstract Background: Etiology of polycystic ovary syndrome (PCOS) is unclear. Recent reports indicated that gut microbiota regulates metabolism and plays a major role in the development of PCOS.Methods: We used dihydrotestosterone (DHT) or letrozole (LET) to induce PCOS model rat. At the end of the experiment, ovarian morphology, hormonal and metabolic status were investigated in all rats. The molecular ecology of the fecal gut microbiota was analyzed by 16S rDNA high-throughput sequencing.Result: Rats induced by letrozole exhibited endocrine and reproductive characteristics, such as hyperandrogenism, abnormal oestrus cycles or complete acyclic, polycystic ovaries, and obesity. DHT-induced rats were showed obesity, irregular oestrus cycles, polycystic ovaries, lower level of HDL-C and lower activity of SOD than controls. Our study found that DHT can reduce the microbial richness in rats. PCoA plots confirmed that DHT group was statistically significantly separated from C group and LET group. LEfSe analysis showed that the family of Bacteroidales_S24_7_group, and genus Peptococcus and Turicibacter may play vital roles in the health and function of control group. Genus of Bifidobacteriales and Vibro may play roles in the letrozole induced PCOS rats. And genus of Lachnospiraceae_NK4A136_group, Ruminococcus_1, Ruminiclostridium, Treponema_2, Anaerotruncus, Acetatifactor and Anaeroplasma may play vital roles in the intestine of DHT induced PCOS rats.Conclusion: DHT affected the composition and diversity of gut microbial community, and leads to the gut dysbiosis. Letrozole may benefit to the gut microbiome in some aspects, but it also may have a trend of inhibiting the expression of some anti-inflammatory genera in intestinal tract.

scholarly journals Intestinal Enterococcus abundance correlates inversely with excessive weight gain and increased plasma leptin in breastfed infants

2020 ◽  
Vol 96 (5) ◽  
Author(s):  
Martin Frederik Laursen ◽  
Melanie Wange Larsson ◽  
Mads Vendelbo Lind ◽  
Anni Larnkjær ◽  
Christian Mølgaard ◽  
...  
Keyword(s):  
Weight Gain ◽  
Breast Milk ◽  
Large Body ◽  
Normal Weight ◽  
Control Group ◽  
Excessive Weight Gain ◽  
Breastfed Infants ◽  
Excessive Weight ◽  
Small Subgroup ◽  
Plasma Leptin

ABSTRACT Epidemiological evidence indicates that breastfeeding provides protection against development of overweight/obesity. Nonetheless, a small subgroup of infants undergo excessive weight gain during exclusive breastfeeding, a phenomenon that remains unexplained. Breast milk contains both gut-seeding microbes and substrates for microbial growth in the gut of infants, and a large body of evidence suggests a role for gut microbes in host metabolism. Based on the recently established SKOT III cohort, we investigated the role of the infant gut microbiota in excessive infant weight gain during breastfeeding, including 30 exclusively breastfed infants, 13 of which exhibited excessive weight gain and 17 controls which exhibited normal weight gain during infancy. Infants undergoing excessive weight gain during breastfeeding had a reduced abundance of gut Enterococcus as compared with that observed in the controls. Within the complete cohort, Enterococcus abundance correlated inversely with age/gender-adjusted body-weight, body-mass index and waist circumference, body fat and levels of plasma leptin. The reduced abundance of Enterococcus in infants with excessive weight gain was coupled to a lower content of Enterococcus in breast milk samples of their mothers than seen for mothers in the control group. Together, this suggests that lack of breast milk-derived gut-seeding Enterococci may contribute to excessive weight gain in breastfed infants.

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