16S Ribosomal RNA Sequencing Research Articles

Identification of phytoplasmas associated with Bunchy Top disease of papaya in Colima, Mexico

Phytoplasmas, rickettsiae and viruses have been detected in papaya plants with Bunchy Top disease (BT). In 2019, papaya plants with BT-like symptoms were observed in agroecosystems of Colima, Mexico. In order to determine the BT-associated phytoplasmas species or subgroups, asymptomatic and symptomatic plants were collected from papaya agroecosystems in four papaya producer municipalities, as well as papaya-associated weeds and insects. Phytoplasma detection and identification was conducted by PCR, sequencing and phylogenetics of translocase subunit SecA (secA) and 16S ribosomal RNA (16Sr) genes, and PCR-RFLPs in vitro and in silico for 16Sr gene. In papaya, phytoplasma groups 16SrI (subgroup AF), 16SrX, and 16SrXIII were identified in 2.08% (4 out of 192) symptomatic samples. The results of RFLPs in silico analysis showing the presence of 16SrX and 16SrXIII (sub)groups. In papaya-associated weeds and insects, phytoplasmas of group 16SrI (subgroups AF and B) were identified in 1.7% (3 out of 174) and 1.1% (2 out of 185) evaluated samples, respectively. Phytoplasma-carrying weeds were Amaranthus palmeri and Echinochloa colona; positive insects were Micrutalis calva and Balclutha mexicana. It is the first time that phytoplasmas 16SrI-AF, 16SrX y 16SrXIII are associated with Bunchy Top disease of papaya in agroecosystems from Colima, Mexico. Phytoplasmas 16SrX y 16SrXIII are first reported in papaya plants at the world level and in Mexico, respectively. Phytoplasma-carrying weeds and insects are new records as natural reservoirs and potential vectors.

Distinct gut microbiota signatures associated with progression of atherosclerosis in people living with HIV.

The relationship of microbiota composition dynamics and the progression of subclinical atherosclerosis in people with HIV (PWH) remains unknown. 96-week, prospective, longitudinal study in virologically-suppressed PWH. Carotid intima-media thickness (cIMT) measurements and stool samples were obtained at baseline, 48-week and 96-week visits. cIMT progression was defined as an increase >10% and/or detection of new carotid plaque. To profile the gut microbiome, amplification and sequencing of 16S ribosomal-RNA (V3-V4 variable regions) were carried out following the Illumina protocol. Sequencing was performed with MiSeq platform. 191, 190 and 167 patients had available fecal samples for microbiome analysis at the baseline, 48- and 96-week visits, respectively. 87 (43%) participants showed atherosclerosis progression, and 54 (26.7%) presented new carotid plaque. No significant differences were observed in adjusted α-diversity indices between groups defined by cIMT progression. Beta-diversity determined through principal coordinate analysis distances showed that the groups exhibited distinct microbial profiles (PERMANOVA p-value = 0.03). Longitudinal analysis with ANCOM-BC2 adjusted for traditional cardiovascular risk factors, MSM and nadir CD4 count revealed that cIMT progression was consistently associated with Agathobacter and Ruminococcus_2, while non-progression was consistently associated with Prevotella_7. Progression of atherosclerosis in PWH might be associated with distinctive signatures in the gut microbiota.

Helicobacter pylori causes gastric dysbacteriosis in chronic gastritis patients.

Gastric mucosal samples were procured and underwent the sequencing of 16S ribosomal RNA (16S rRNA) via Illumina high-throughput sequencing technology to explore the impact of Helicobacter pylori (H. pylori) infection on the composition of gastric flora in chronic gastritis (CG) patients. In the results, the operational taxonomic unit (OTU) analysis revealed an overlap of 5706 OTUs shared between the two groups. The top 5 abundance ranking (TOP5) phyla comprised Bacteroidetes, Proteobacteria, Firmicutes, Actinobacteria, and Epsilonbacteraeota, while the TOP5 genus was Lachnospiraceae_NK4A136_group, Helicobacter, Bacteroides, Klebsiella, and Pseudomonas. In the metabolic pathways at the Kyoto Encyclopedia of Genes and Genomes (KEGG)_L3 level, conspicuous variations across seven functions were observed between the H. pylori-positive (HP_Pos) and H. pylori-negative (HP_Neg) groups. Subsequently, functional gene enrichment in KEGG pathways was further validated through animal experimentation. In contrast to the mice in the HP_Neg group, those infected with H. pylori manifested an infiltration of inflammatory cells, an augmentation in gastric acid secretion, and conspicuously elevated scores regarding gastric activity, along with heightened levels of malondialdehyde. In conclusion, CG patients infected with H. pylori displayed a disorder in gastric flora, furnishing a theoretical basis for the prophylaxis of H. pylori infection and its associated pathogenic ramifications.

Oral and gut microbial profiling in periodontitis and Parkinson’s disease

ABSTRACT Objectives We tested the hypothesis that Parkinson’s disease (PA) alters the periodontitis-associated oral microbiome. Method Patients with periodontitis with Parkinson’s disease (PA+P) and without PA (P) and systemically and periodontally healthy individuals (HC) were enrolled. Clinical, periodontal and neurological parameters were recorded. The severity of PA motor functions was measured. Unstimulated saliva samples and stool samples were collected. Next-generation sequencing of 16S ribosomal RNA (V1-V3 regions) was performed. Results PA patients had mild-to-moderate motor dysfunction and comparable plaque scores as those without, indicating that oral hygiene was efficient in the PA+P group. In saliva, there were statistically significant differences in beta diversity between HC and PA+P (p = 0.001), HC and P (p = 0.001), and P and PA+P (p = 0.028). The microbial profiles of saliva and fecal samples were distinct. Mycoplasma faucium, Tannerella forsythia, Parvimonas micra, and Saccharibacteria (TM7) were increased in P; Prevotella pallens, Prevotella melaninogenica, Neisseria multispecies were more abundant in PA+P group, Ruthenibacterium lactatiformans, Dialister succinatiphilus, Butyrivibrio crossotus and Alloprevotella tannerae were detected in fecal samples in P groups compared to healthy controls. Conclusions No significant differences were detected between Parkinson’s and non-Parkinson’s gut microbiomes, suggesting that Parkinson’s disease modifies the oral microbiome in periodontitis subjects independent of the gut microbiome.

Characterization of bacterial diversity and screening of cellulose-degrading bacteria in the gut system of Glenea cantor (Fabricius) larvae.

The intestinal bacteria of longhorn beetles would be ideal targets for pest control and lignocellulosic resources by destroying or exploiting their cellulose-degrading function. This article aims to investigate the diversity and community structure of intestinal bacteria the oligophagous longhorn beetle Glenea cantor. Additionally, it seeks to identify the presence of lignocellulose-degrading bacteria in the gut, and explore their role in consuming host kapok trees Bombax malabaricum. In this study, the bacterial community from G. cantor was examined by Illumina sequencing of 16S ribosomal RNA (rRNA) targeting the V3 and V4 regions. A total of 563,201 valid sequences and 814 OTUs were obtained. The dominant phyla were Proteobacteria, and the dominant genera were Acinetobacter and Lactococcus. The analysis of microbial diversity revealed a high bacterial diversity in the samples, with the gut bacteria playing a crucial role in the physiological activities of the host, particularly, 9 genera of intestinal bacteria with cellulose degradation function were found, highlighting their vital role in cellulose degradation. Five strains of cellulose-degrading bacteria, belonging to the genus Pseudomonas, were obtained from the intestinal tract of G. cantor larvae using traditional isolation and culture techniques as well as 16S rDNA sequencing. Among these strains, A4 exhibited a cellulase activity of 94.42 ± 0.42U/mL, while A5 displayed the highest filter paper enzyme activity of 127.46 ± 3.54U/mL. These results offered valuable insights into potential targets for pest control through internal attack digestion and cellulose-degrading bacteria in longhorn beetles.

An improved and extended dual-index multiplexed 16S rRNA sequencing for the Illumina HiSeq and MiSeq platform.

Recent advancements in next-generation sequencing (NGS) technology have ushered in significant improvements in sequencing speed and data throughput, thereby enabling the simultaneous analysis of a greater number of samples within a single sequencing run. This technology has proven particularly valuable in the context of microbial community profiling, offering a powerful tool for characterizing the microbial composition at the species level within a given sample. This profiling process typically involves the sequencing of 16S ribosomal RNA (rRNA) gene fragments. By scaling up the analysis to accommodate a substantial number of samples, sometimes as many as 2,000, it becomes possible to achieve cost-efficiency and minimize the introduction of potential batch effects. Our study was designed with the primary objective of devising an approach capable of facilitating the comprehensive analysis of 1,711 samples sourced from diverse origins, including oropharyngeal swabs, mouth cavity swabs, dental swabs, and human fecal samples. This analysis was based on data obtained from 16S rRNA metagenomic sequencing conducted on the Illumina MiSeq and HiSeq sequencing platforms. We have designed a custom set of 10-base pair indices specifically tailored for the preparation of libraries from amplicons derived from the V3-V4 region of the 16S rRNA gene. These indices are instrumental in the analysis of the microbial composition in clinical samples through sequencing on the Illumina MiSeq and HiSeq platforms. The utilization of our custom index set enables the consolidation of a significant number of libraries, enabling the efficient sequencing of these libraries in a single run. The unique array of 10-base pair indices that we have developed, in conjunction with our sequencing methodology, will prove highly valuable to laboratories engaged in sequencing on Illumina platforms or utilizing Illumina-compatible kits.

Preliminary Analysis of Gut Microbiome and Gastrointestinal Symptom Burden in Breast Cancer Patients Receiving Chemotherapy Compared to Healthy Controls.

Alterations in the naturally occurring bacteria of the gut, known as the gastrointestinal (GI) microbiome, may influence GI symptoms in women with breast cancer. This work aims to describe GI symptom occurrence, duration, severity, and distress and measures of the GI microbiome among women with breast cancer receiving chemotherapy compared to age- and sex-matched healthy controls. 22 women with breast cancer receiving chemotherapy and 17 healthy control women provided stool specimens and GI symptom data using the modified Memorial Symptom Assessment Scale (MSAS). The fecal microbiome was profiled by metagenomic sequencing of 16S Ribosomal RNA (rRNA). GI microbiome was compared between groups using alpha-diversity (Observed OTU number and Shannon index), beta-diversity (UniFrac distances), and relative abundance of select genera. GI symptoms with high symptom reports among breast cancer patients included nausea, diarrhea, flatulence, dry mouth, taste change, and poor appetite. Indices of differential abundance (beta diversity) significantly distinguished between breast cancer patients and healthy controls. Unique bacterial features differentiating the 2 groups were Prevotella_9, Akkermansia, Lachnospira, Lachnospiraceae_NK4A136, Lachnoclostridium, and Oscillibacter. Gut bacteria are associated with GI inflammation and mucus degradation, suggesting the potential role of the GI microbiome in GI symptom burden. Understanding the influence of GI bacteria on gut health and symptoms will help harness the enormous potential of the GI microbiome as a future diagnostic and therapeutic agent to reduce the symptom burden associated with chemotherapy.

FRI076 Colchicine Treatment Effects On The Gut Microbiome In Adults With Metabolic Syndrome, Insulin Resistance, And High C-reactive Protein (CRP): A Secondary Analysis Of A Randomized, Placebo-controlled Clinical Trial

Abstract Disclosure: C.M. Kisimba: None. J.L. Donahue: None. K.K. Chivukula: None. P. Subramanian: None. S.D. Mistry: None. A. Wolska: None. A.T. Remaley: None. J.A. Yanovski: None. A.P. Demidowich: None. Background: Obesity-induced inflammation plays a substantial role in the development of insulin resistance and type 2 diabetes. The altered gut flora in obesity can also contribute to metabolic dysregulation and systemic inflammation. However, it remains unclear how dysregulation of systemic inflammation in obesity affects the gut microbiome. We hypothesized that colchicine’s systemic anti-inflammatory effects in obesity would be associated with improvements in gut microbial diversity. Methods: This study was a secondary analysis of a double-blind randomized placebo-controlled trial, in which 40 adults with obesity, high CRP (≥ 2.0 mg/L), insulin resistance (HOMA-IR ≥ 2.6 mg/L), and metabolic syndrome (MetS) were randomized to three months of colchicine 0.6mg or placebo tablets twice daily. Serum and stool samples were collected at baseline and final visit. Gut microbiota composition was characterized from stool DNA by dual-index amplification and sequencing of 16S ribosomal RNA. Results: Pre- and post-intervention stool samples were available for 15 colchicine- and 12 placebo-treated subjects. Circulating hsCRP, interleukin-6, resistin, white blood count, and neutrophils were significantly decreased in the colchicine arm as compared to placebo. However, changes in stool microbiome alpha diversity, as assessed by the Chao1, Shannon, and Pielou indices, were not significant between groups. Sequence variant counts were unchanged among all examined phyla or families. Oscillibacter was the only genus to demonstrate even a nominally significant change. Conclusion: Among adults with obesity and MetS, colchicine significantly improved systemic inflammation. However, this anti-inflammatory effect was not associated with significant changes in the gut microbiome. Further studies are warranted to investigate this relationship. Presentation: Friday, June 16, 2023

Automating microbial taxonomy workflows with PHANTASM: phylogenomic analyses for the taxonomy and systematics of microbes.

The nucleotide sequences of 16S ribosomal RNA (rRNA) genes have been used to inform the taxonomic placement of prokaryotes for several decades. Whole-genome approaches can better resolve evolutionary relationships of organisms, but these analyses often require computational proficiencies that are uncommon among microbiologists. PHANTASM is a new tool capable of automating these workflows. This tool was designed to work for a wide range of prokaryotes and is the first example of an automated reconciliation of NCBI's Taxonomy database with that of the List of Prokaryotic names with Standing in Nomenclature (LPSN). In this study, we describe the workflow of PHANTASM and provide several examples of results generated by it. The source code is freely-available on GitHub. In order to facilitate the ease-of-access for researchers, PHANTASM is also available as a Docker image. While other tools exist to facilitate starting points for these analyses, PHANTASM provides users with a greater degree of control and produces outputs that can be used to make publication-quality figures.

Investigation of bacterial and fungal population structure on environmental surfaces of three medical institutions during the COVID-19 pandemic.

To evaluate the population structure of environmental bacteria and fungi in three different types of medical institutions and the potential risks due to antibiotic resistance during the coronavirus disease 2019 (COVID-19) pandemic. One hundred twenty-six environmental surface samples were collected from three medical institutions during the COVID-19 pandemic. A total of 6,093 and 13,514 representative sequences of 16S and ITS ribosomal RNA (rRNA) were obtained by amplicon sequencing analysis. The functional prediction was performed using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States tool based on the Greengenes database and the FAPROTAX database. On environmental surfaces in three medical institutions during the COVID-19 pandemic, Firmicutes (51.6%) and Bacteroidetes (25%) were the dominant bacteria, while Ascomycota (39.4%) and Basidiomycota (14.2%) were the dominant fungi. A number of potential bacterial and fungal pathogens were successfully identified by the metagenomic approach. Furthermore, compared with the bacterial results, the fungi showed a generally closer Bray Curtis distance between samples. The overall ratio of Gram-negative bacteria to Gram-positive bacteria was about 3:7. The proportion of stress-tolerant bacteria in medical institutions A, B and C reached 88.9, 93.0 and 93.8%, respectively. Anaerobic bacteria accounted for 39.6% in outdoor environments, 77.7% in public areas, 87.9% in inpatient areas and 79.6% in restricted areas. Finally, the β-Lactam resistance pathway and polymyxin resistance pathway were revealed through functional prediction. We described the microbial population structure changes in three different types of medical institutions using the metagenomic approach during the COVID-19 pandemic. We found that the disinfection measures performed by three healthcare facilities may be effective on the "ESKAPE" pathogens, but less effective on fungal pathogens. Moreover, emphasis should be given to the prevention and control of β-lactam and polymyxin antibiotics resistance bacteria during the COVID-19 pandemic.

Clinical characteristics, susceptibility profiles, and treatment of nocardiosis: a multicenter retrospective study in 2015-2021

ObjectivesThis study aimed to investigate the microbiological characteristics, antimicrobial resistance profiles, antibiotic choice, and outcomes of Nocardia infection in various centers over a 7-year period (from 2015 to 2021). MethodsWe retrospectively analyzed the medical records of all hospitalized patients diagnosed with Nocardia between 2015 and 2021. The isolates were identified to the species level through the sequencing of 16S ribosomal RNA or secA1 or ropB genes. The susceptibility profiles were determined using the broth microdilution method. ResultsOf the 130 nocardiosis cases, 99 (76.2%) were established as pulmonary infection, of which the most common underlying disease was chronic lung disease (40.4%, 40/99), including bronchiectasis, chronic obstructive pulmonary disease, and chronic bronchitis. Among 130 isolates, 12 species were identified, with the most common species being Nocardia cyriacigeorgica (37.7%) and Nocardia farcinica (20.8%). All Nocardia strains were susceptible to linezolid and amikacin, and the susceptibility rate of trimethoprim-sulfamethoxazole (TMP-SMX) was 97.7%. Of the 130 patients, 86 (66.2%) received TMP-SMX monotherapy or multidrug regimen. Furthermore, 92.3% patients who were treated achieved clinical improvement. ConclusionTMP-SMX was the treatment of choice for nocardiosis, and other combination drugs with TMP-SMX therapy yielded even better results.

Colchicine effects on the gut microbiome in adults with metabolic syndrome.

Obesity-induced inflammation plays a substantial role in the development of insulin resistance and type 2 diabetes. The altered gut flora in obesity can also contribute to metabolic dysregulation and systemic inflammation. However, it remains unclear how dysregulation of systemic inflammation in obesity affects the gut microbiome. We hypothesized that colchicine's systemic anti-inflammatory effects in obesity would be associated with improvements in gut microbial diversity. We conducted a secondary analysis of a double-blind randomized placebo-controlled trial, in which 40 adults with obesity, high C-reactive protein (CRP) (≥2.0 mg/L), insulin resistance (homeostatic model of insulin resistance: HOMA-IR ≥2.6 mg/L), and metabolic syndrome (MetS) were randomized to three months of colchicine 0.6 mg or placebo tablets twice daily. Serum and stool samples were collected at baseline and final visit. Gut microbiota composition was characterized from stool DNA by dual-index amplification and sequencing of 16S ribosomal RNA. Pre- and post-intervention stool samples were available for 15 colchicine- and 12 placebo-treated subjects. Circulating high sensitivity CRP (hsCRP), interleukin-6, resistin, white blood count, and neutrophils were significantly decreased in the colchicine arm as compared to placebo. However, changes in stool microbiome alpha diversity, as assessed by the Chao1, Shannon, and Pielou indices, were not significant between groups. Amplicon sequence variant counts were unchanged among all examined phyla or families. Oscillibacter was the only genus to demonstrate even a nominally significant change. Among adults with obesity and MetS, colchicine significantly improved systemic inflammation. However, this anti-inflammatory effect was not associated with significant changes in the gut microbiome. Further studies are warranted to investigate this relationship.

Unlocking The Human Urobiome: Impact On Health and Disease- A Review

The urinary microbiome or the urobiome are the group of microbes present in the urinary tract. They came into the limelight in the last decade due to advances in diagnostic technologies. Two complementary assays are widely used for research in urobiomes. Next-generation sequencing (NGS) of 16S ribosomal RNA (rRNA) paired with enhanced urine culture techniques (EUCT) are widely employed for research. This has paved the way for investigations on sterile body sites such as urine thereby breaking the myth of urine being considered sterile. EUCT, such as expanded quantitative urine culture (EQUC) contributed to the evidence that the microbes detected by the NGS are still alive. EQUC has been employed in clinical laboratories since the last decade and is indicated only when there are unexplained clinical symptoms and conventional urine culture is negative. Our aim is to have a comprehensive review study on the urobiome concerning health, its association with urological pathologies. Our main objective is to collect review and research articles using databases and review them for obtaining in-depth knowledge of the urobiome as well as to identify possible alternate study areas. The urobiome is a new area with minimal information available. This review helps the researcher to comprehend this upcoming area easily. Investigations into urobiome research, however, could have a considerable impact on our understanding of the pathogenesis of urogenital disorders and even reveal novel possibilities. Thus, the forthcoming years will open a ripe ground for future research into diagnosis, treatment and prevention strategies for urological pathologies.

Disruption of the intestinal barrier exacerbates experimental autoimmune pancreatitis by promoting the translocation of Staphylococcus sciuri into the pancreas.

Autoimmune pancreatitis (AIP) and IgG4-related disease (IgG4-RD) are new disease entities characterized by enhanced IgG4 antibody responses and involvement of multiple organs, including the pancreas and salivary glands. Although the immunopathogenesis of AIP and IgG4-RD is poorly understood, we previously reported that intestinal dysbiosis mediates experimental AIP through the activation of IFN-α- and IL-33-producing plasmacytoid dendritic cells (pDCs). Because intestinal dysbiosis is linked to intestinal barrier dysfunction, we explored whether the latter affects the development of AIP and autoimmune sialadenitis in MRL/MpJ mice treated with repeated injections of polyinosinic-polycytidylic acid [poly (I:C)]. Epithelial barrier disruption was induced by the administration of dextran sodium sulfate (DSS) in the drinking water. Mice co-treated with poly (I:C) and DSS, but not those treated with either agent alone, developed severe AIP, but not autoimmune sialadenitis, which was accompanied by the increased accumulation of IFN-α- and IL-33-producing pDCs. Sequencing of 16S ribosomal RNA revealed that Staphylococcus sciuri translocation from the gut to the pancreas was preferentially observed in mice with severe AIP co-treated with DSS and poly (I:C). The degree of experimental AIP, but not of autoimmune sialadenitis, was greater in germ-free mice mono-colonized with S. sciuri and treated with poly (I:C) than in germ-free mice treated with poly (I:C) alone, which was accompanied by the increased accumulation of IFN-α- and IL-33-producing pDCs. Taken together, these data suggest that intestinal barrier dysfunction exacerbates AIP through the activation of pDCs and translocation of S. sciuri into the pancreas.

Nasal Dysbiosis in Cutaneous T-Cell Lymphoma Is Characterized by Shifts in Relative Abundances of Non-Staphylococcus Bacteria

The nasal microbiome of patients with cutaneous T-cell lymphoma (CTCL) remains unexplored despite growing evidence connecting nasal bacteria to skin health and disease. Nasal swabs from 45 patients with CTCL (40 with mycosis fungoides, 5 with Sézary syndrome) and 20 healthy controls from the same geographical region (Chicago Metropolitan Area, Chicago, IL) were analyzed using sequencing of 16S ribosomal RNA and tuf2 gene amplicons. Nasal α-diversity did not differ between mycosis fungoides/Sézary syndrome and healthy controls (Shannon index, genus level, P = 0.201), but distinct microbial communities were identified at the class (R2 = 0.104, P = 0.023) and order (R2 = 0.0904, P = 0.038) levels. Increased relative abundance of the genera Catenococcus, Vibrio, Roseomonas, Acinetobacter, and unclassified Clostridiales was associated with increased skin disease burden (P < 0.005, q < 0.05). Performed to accurately resolve nasal Staphylococcus at the species level, tuf2 gene amplicon sequencing revealed no significant differences between mycosis fungoides/Sézary syndrome and healthy controls. Although S. aureus has been shown to worsen CTCL through its toxins, no increase in the relative abundance of this taxon was observed in nasal samples. Despite the lack of differences in Staphylococcus, the CTCL nasal microbiome was characterized by shifts in numerous other bacterial taxa. These data add to our understanding of the greater CTCL microbiome and provide context for comprehending nasal-skin and host‒tumor‒microbial relationships.

The Negative Effects of Feces-Associated Microorganisms on the Fitness of the Stored Product Mite Tyrophagus putrescentiae.

Feces have been suggested as a major source of microorganisms for recolonization of the gut of stored product mites via coprophagy. The mites can host microorganisms that decrease their fitness, but their transmission is not known. To address the role of fecal microbiota on mite fitness, we performed an experimental study in which the surfaces of mite (Tyrophagus putrescentiae) eggs were sterilized. Mites eggs (15 per experimental box) were then hatched and grown on feedstock with and without feces. These experiments were conducted with four distinct T. putrescentiae populations (5L, 5K, 5N, and 5P), and mite population density after 21 day of cultivation was used to assess mite fitness and the impact of fecal microbiota on fitness. Population density was not affected by the presence of feces in two of the cultures (5L and 5K), while significant effects of feces were observed in the other cultures (5N and 5P). Mite culture microbial communities were analyzed using cultivation-independent next-generation amplicon sequencing of microbial 16S and 18S ribosomal RNA (rRNA) genes in the fitness influenced populations (5N and 5P). Several microbial taxa were associated with fecal treatments and reduced mite fitness, including Staphylococcus and Bartonella-like bacteria, and the fungal genera Yamadazyma, Candida, and Aspergillus. Although coprophagy is the transmission route mites used to obtain beneficial gut bacteria such as Bartonella-like organisms, the results of this study demonstrate that fecal-associated microorganisms can have negative effects on some populations of T. putrescentiae fitness, and this may counteract the positive effects of gut symbiont acquisition.

The impact of intestinal microbiota in antithymocyte globulin-based myeloablative allogeneic hematopoietic cell transplantation.

The correlation between intestinal microbiota and clinical outcomes after allogeneic hematopoietic stem cell transplantation (allo-HCT) has been reported in platforms with T-cell depletion or postcyclophosphamide-based graft-vs-host disease (GVHD) prophylaxis regimens. It is still unclear whether it is the same in platforms of antithymocyte globulin (ATG)-based myeloablative allo-HCT. A total of 603 fecal specimens from 100 consecutive patients receiving allo-HCT were collected between December 2018 and July 2020. Fetal samples were profiled with next-generation sequencing of bacterial 16S ribosomal RNA (rRNA) genes. The diversity decreased to the lowest level at approximately day 12 after allo-HCT and then increased over time. According to the diversity of 314 samples that were collected from 86 patients during the engraftment period, patients were grouped into the low- and high-diversity groups. Two-year overall survival in the high-diversity group was significantly longer than that in the low-diversity group (83.7% vs 60.6%, P=.026). Further analysis revealed that worse outcomes for patients with low diversity were associated with increased risk of worse outcomes for patients with low diversity (adjusted hazard ratio, 4.95; P=.046). Its association with relapse and GVHD was not found. Compositional analysis of fecal microbiota revealed that the abundance of bacteroides decreased greatly during allo-HCT, whereas that of Enterococcus, Klebsiella, and Escherichia was found to be increased. This study indicates that gut dysbiosis in platforms of ATG-based myeloablative allo-HCT featured loss of bacterial diversity. The diversity of the intestinal flora at the engraftment period was an independent predictor of longer survival. The correlation between intestinal microbiota and clinical outcomes after allogeneic hematopoietic stem cell transplantation (allo-HCT) is reported in platforms with T-cell depletion or postcyclophosphamide-based graft-vs-host disease (GVHD) prophylaxis regimens. It is still unclear whether it is the same pattern in platforms of antithymocyte globulin (ATG)-based T-cell repletion myeloablative allo-HCT. Our study indicated that gut dysbiosis in platforms of ATG-based myeloablative allo-HCT also features loss of bacterial diversity. The diversity of the intestinal flora at the engraftment period is an independent predictor of longer survival.

Dietary Lasia spinosa Thw. Improves Growth Performance in Broilers.

This study aimed to evaluate the effects of dietary Lasia spinosa Thw. (LST) powder supplementation on growth performance, blood metabolites, antioxidant status, intestinal morphology, and cecal microbiome in broiler chickens. A total of 400 1-day-old male Guangxi partridge broilers (initial body weight: 42.52 ± 0.06 g) were randomly allotted to 4 dietary treatments: LST0 group (a basal diet), LST1 group (a basal diet with 1% LST powder), LST2 group (a basal diet with 2% LST powder), LST4 group (a basal diet with 4% LST powder), 10 replicates for each treatment, and 10 broilers in each treatment group. Results indicated that the average daily feed intake of broilers during 22–42 days and the average daily gain of chickens during 1–42 days significantly increased by dietary supplementation of LST powder (p < 0.01), while the feed conversion ratio during the overall periods was decreased by dietary supplementation of LST powder (p < 0.01). Except for the levels of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) in liver (p > 0.05), the levels of SOD, catalase (CAT) and GSH-Px in serum, liver, and breast muscle were significantly increased in the LST supplemented groups (p < 0.05), while the levels of reactive oxygen species (ROS) and malondialdehyde (MDA) in serum, liver, and breast muscle were significantly decreased in the LST supplemented groups (p < 0.05). Furthermore, the levels of triglyceride (TG) and low-density lipoprotein cholesterol (LDL-C) were significantly decreased by the addition of dietary LST powder (p < 0.01), while the levels of HDL-C, Ca, Fe, Mg, and P were linearly increased by the addition of dietary LST powder (p < 0.01). With respect to the gut morphometric, crypt depth was significantly decreased by LST supplementation (p < 0.05), while villus height and the ratio of villus height to crypt depth were notably increased by LST supplementation (p < 0.05). Sequencing of 16S ribosomal RNA (16S rRNA) from the cecal contents of broilers revealed that the composition of the chicken gut microbiota was altered by LST supplementation. The α-diversity of microbiota in broilers was increased (p < 0.05) in the LST1 group, but was decreased (p < 0.05) in the LST2 and LST4 groups compared with the LST0 group. The differential genera enriched in the LST1 group, such as Bacillus, Odoribacter, Sutterella, Anaerofilum, Peptococcus, were closely related to the increased growth performance, antioxidant status, intestinal morphology, Ca, Mg, and reduced blood lipid in the treated broilers.

Learning, visualizing and exploring 16S rRNA structure using an attention-based deep neural network.

Recurrent neural networks with memory and attention mechanisms are widely used in natural language processing because they can capture short and long term sequential information for diverse tasks. We propose an integrated deep learning model for microbial DNA sequence data, which exploits convolutional neural networks, recurrent neural networks, and attention mechanisms to predict taxonomic classifications and sample-associated attributes, such as the relationship between the microbiome and host phenotype, on the read/sequence level. In this paper, we develop this novel deep learning approach and evaluate its application to amplicon sequences. We apply our approach to short DNA reads and full sequences of 16S ribosomal RNA (rRNA) marker genes, which identify the heterogeneity of a microbial community sample. We demonstrate that our implementation of a novel attention-based deep network architecture, Read2Pheno, achieves read-level phenotypic prediction. Training Read2Pheno models will encode sequences (reads) into dense, meaningful representations: learned embedded vectors output from the intermediate layer of the network model, which can provide biological insight when visualized. The attention layer of Read2Pheno models can also automatically identify nucleotide regions in reads/sequences which are particularly informative for classification. As such, this novel approach can avoid pre/post-processing and manual interpretation required with conventional approaches to microbiome sequence classification. We further show, as proof-of-concept, that aggregating read-level information can robustly predict microbial community properties, host phenotype, and taxonomic classification, with performance at least comparable to conventional approaches. An implementation of the attention-based deep learning network is available at https://github.com/EESI/sequence_attention (a python package) and https://github.com/EESI/seq2att (a command line tool).

Production and diversity of microorganisms associated with sinking particles in the subtropical North Pacific Ocean

AbstractSinking particulate organic matter controls the flux of carbon (C) from the surface ocean to the deep sea. Microorganisms actively colonize particles, but the extent to which microbial metabolism influences particle export remains uncertain. We conducted experiments to quantify rates of bacterial production (derived based on 3H‐leucine incorporation) and dark C‐fixation (based on 14C‐bicarbonate assimilation) associated with sinking particles collected from the base of the euphotic zone (175 m) in the subtropical North Pacific Ocean. Seawater was amended with sinking particles and rates of filter size‐fractionated (0.2, 2, and 20 μm) bacterial production and dark C‐fixation were measured. Sequencing of 16S ribosomal RNA (rRNA) gene amplicons revealed that microorganisms in the particle‐amended treatments differed from those in the unamended seawater controls, with the particle treatments enriched in putative copiotrophic bacteria. The addition of sinking particles increased rates of bacterial production (by 6‐ to 9‐fold), and to a lesser extent dark C‐fixation (by 1.7‐ to 4.6‐fold), relative to unamended controls, with most of the production associated with filter pore sizes &lt; 20 μm. Normalizing production to concentrations of particulate C yielded rates that were statistically indistinguishable between particle‐amended treatments and unamended controls. We then examined possible relationships between sinking particulate C flux attenuation and its supply to the mesopelagic waters, revealing that flux attenuation was positively related to increases in particulate C supply. Together with results from our experiments, we suggest processes that contribute to sinking particle disaggregation both increase flux attenuation and favor microbial mineralization of particle‐derived organic matter.