The lung microbiome, peripheral gene expression, and recurrence-free survival after resection of stage II non-small cell lung cancer

Genome Medicine, Journal Year: 2022, Volume and Issue: 14(1)

Published: Oct. 27, 2022

Cancer recurrence after tumor resection in early-stage non-small cell lung cancer (NSCLC) is common, yet difficult to predict. The microbiota and systemic immunity may be important modulators of risk for recurrence, biomarkers from the microbiome peripheral immune environment are understudied. Such markers hold promise prediction as well improved etiologic understanding recurrence.

Language: Английский

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Computational methods and challenges in analyzing intratumoral microbiome data

Trends in Microbiology, Journal Year: 2023, Volume and Issue: 31(7), P. 707 - 722

Published: Feb. 23, 2023

Language: Английский

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Soil microbial communities are sensitive to differences in fertilization intensity in organic and conventional farming systems

FEMS Microbiology Ecology, Journal Year: 2023, Volume and Issue: 99(6)

Published: May 9, 2023

Abstract Intensive agriculture has increased global food production, but also impaired ecosystem services and soil biodiversity. Organic fertilization, essential to organic integrated farming, can provide numerous benefits for quality compromise the environment by polluting soils producing greenhouse gases through animal husbandry. The need reduced stocking density is inevitably accompanied lower FYM inputs, little research available on impact of these effects microbiome. We collected samples from winter wheat plots a 42-year-old long-term trial comparing different farming systems receiving farmyard manure at two intensities measured parameters microbial community diversity DNA metabarcoding. High-input corresponding 1.4 livestock units (LU) improved soil’s nutritional status biomass respiration when compared low-input 0.7 LU. Bacterial fungal α-diversity was largely unaffected fertilization intensity, whereas their structure changed consistently, an increase in bacterial copiotroph-to-oligotroph ratio high-input more copiotrophic indicator OTUs associated with high than low-input. This study shows that nutrient availability under selects oligotrophic microbes efficiently obtaining nutrients various carbon sources; potentially beneficial trait considering future agroecosystems.

Language: Английский

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Gut microbiota alterations in schizophrenia might be related to stress exposure: Findings from the machine learning analysis

Psychoneuroendocrinology, Journal Year: 2023, Volume and Issue: 155, P. 106335 - 106335

Published: July 13, 2023

Specific mechanisms underlying gut microbiota alterations in schizophrenia remain unknown. We aimed to compare between patients with and controls, taking into consideration exposure stress across lifespan, dietary habits, metabolic parameters clinical manifestation. A total of 142 participants, including 89 52 were recruited. Gut analyzed using the 16 S rRNA sequencing. Additionally, biochemical related glucose homeostasis, lipid profile inflammation assessed. Increased abundance Lactobacillus Limosilactobacillus as well decreased Faecalibacterium Paraprevotella found schizophrenia. The machine learning analysis demonstrated that between-group differences associated psychosocial (a history childhood trauma, greater cumulative lifespan higher level perceived stress), poor nutrition (lower consumption vegetables fish products), levels high-density lipoproteins) cognitive impairment (worse performance attention). Our findings indicate schizophrenia, increased lactic acid bacteria (Lactobacillus Limosilactobacillus) producing short-chain fatty acids (Faecalibacterium Paraprevotella) might be stress, impairment.

Language: Английский

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Gut microbiota composition links to variation in functional domains across psychiatric disorders

Brain Behavior and Immunity, Journal Year: 2024, Volume and Issue: 120, P. 275 - 287

Published: May 28, 2024

Language: Английский

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Sequencing introduced false positive rare taxa lead to biased microbial community diversity, assembly, and interaction interpretation in amplicon studies

Environmental Microbiome, Journal Year: 2022, Volume and Issue: 17(1)

Published: Aug. 17, 2022

Increasing studies have demonstrated potential disproportionate functional and ecological contributions of rare taxa in a microbial community. However, the study biosphere is hampered by their inherent scarcity deficiency currently available techniques. Sample-wise cross contaminations might be introduced sample index misassignment most widely used metabarcoding amplicon sequencing approach. Although downstream bioinformatic quality control clustering or denoising algorithms could remove errors non-biological artifact reads, no algorithm eliminate high reads from sample-wise misassignment, making it difficult to distinguish between bona fide false positives studies.We thoroughly evaluated rate NovaSeq 6000 DNBSEQ-G400 platforms using both commercial customized mock communities, observed significant lower (0.08% vs. 5.68%) fraction positive for as compared 6000. Significant batch effects caused stochastically negative taxa. These detections also lead inflated alpha diversity relatively simple communities underestimated that complex ones. Further test set cow rumen samples reported differential different platforms. Correlation analysis detected each platform identified had much higher possibility correlated with physiochemical properties fluid platform. Community assembly mechanism network correlation indicated detection biased community identification fake keystone species community.We highly suggest proper positive/negative/blank controls, technical replicate settings, selection future studies, especially when would focused.

Language: Английский

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Bacterial communities of Aedes aegypti mosquitoes differ between crop and midgut tissues

PLoS neglected tropical diseases, Journal Year: 2023, Volume and Issue: 17(3), P. e0011218 - e0011218

Published: March 29, 2023

Microbiota studies of Aedes aegypti and other mosquitoes generally focus on the bacterial communities found in adult female midguts. However, compartments digestive tract maintain bacteria which remain almost entirely unstudied. For example, Dipteran crop is a food storage organ, but few have looked at microbiome crops mosquitoes, only single previous study has investigated Ae . In this study, we used both culture-dependent culture-independent methods to compare midguts laboratory reared Both revealed trend towards higher abundance, also variability, midgut than crop. When present, from genus Elizabethkingia (family Weeksellaceae) dominated communities. crops, diversity bacteria, these were by acetic acid Acetobacteriaceae) genera Tanticharoenia Asaia These three taxa drove significant community structure differences between tissues. We FAPROTAX predict metabolic functions that significantly more likely contain capable methanol oxidation methylotrophy. presence (which commonly catabolize sugar produce acid) functional profile includes correlated with natural sources like nectar) may relate sugar, stored mosquito A better understanding what are present how assemble will inform microbiota impacts physiology full spectrum provided microbiota. It facilitate engineering for vector control or prevention disease transmission.

Language: Английский

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Combined DNA Methylation and Gastric Microbiome Marker Predicts Helicobacter pylori-Negative Gastric Cancer

Gut and Liver, Journal Year: 2024, Volume and Issue: 18(4), P. 611 - 620

Published: March 21, 2024

While DNA methylation and gastric microbiome are each associated with cancer (GC), their combined role in predicting GC remains unclear. This study investigated the potential of a signature to predict

Language: Английский

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synDNA—a Synthetic DNA Spike-in Method for Absolute Quantification of Shotgun Metagenomic Sequencing

mSystems, Journal Year: 2022, Volume and Issue: 7(6)

Published: Nov. 1, 2022

Microbiome studies have the common goal of determining which microbial taxa are present, respond to specific conditions, or promote phenotypic changes in host. Most these rely on relative abundance measurements drive conclusions. Inherent limitations values inability determine whether an individual taxon is more less abundant and magnitude this change between two samples. These can be overcome by using absolute quantifications, allow for a complete understanding community dynamics measuring variations total loads. Obtaining still technically challenging. Here, we developed synthetic DNA (synDNA) spike-ins that enable precise cost-effective quantification microbiome data adding defined amounts synDNAs We designed 10 with following features: 2,000-bp length, variable GC content (26, 36, 46, 56, 66% GC), negligible identity sequences found NCBI database. Dilution pools were generated mixing at different concentrations. Shotgun metagenomic sequencing showed percentages efficiently reproduced serial dilution, showing high correlation (r = 0.96; R2 ≥ 0.94) significance (P < 0.01). Furthermore, demonstrated used as generate linear models predict accuracy number bacterial cells complex communities. IMPORTANCE The study accurate reproducible amount fold species method proposed here versatile promising it applied communities genomic features like genes operons, addition being easily adaptable other research groups low cost. also made synDNAs' plasmids available encourage future application

Language: Английский

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Meta-analysis of microbiome association networks reveal patterns of dysbiosis in diseased microbiomes

Scientific Reports, Journal Year: 2022, Volume and Issue: 12(1)

Published: Oct. 19, 2022

Abstract The human gut microbiome is composed of a diverse and dynamic population microbial species which play key roles in modulating host health physiology. While individual have been found to be associated with certain disease states, increasing evidence suggests that higher-order interactions may an equal or greater contribution fitness. To better understand community dynamics, we utilize networks study through meta-analysis association between healthy microbiomes. Taking advantage the large number metagenomes derived from individuals patients various diseases, together recent advances network inference can deal sparse compositional data, inferred based on co-occurrence made publicly available as resource (GitHub repository named GutNet). Through our networks, were able identify network-associated features help stratify states such differentiation bacterial phyla enrichment Proteobacteria diseased networks. Additionally, findings show contributions taxa associations are disproportionate their abundances rarer integral part shaping dynamics interactions. Network-based revealed valuable insights into phenotypes. We anticipate will become important for human-related research.

Language: Английский

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