Periodic Addition of Glucose Suppressed Cyanobacterial Abundance in Additive Lake Water Samples during the Entire Bloom Season.

Previously, we showed that prophylactic addition of glucose to Harsha Lake water samples could inhibit cyanobacteria growth, at least for a short period of time. The current study tested cyanobacterial control with glucose for the entire Harsha Lake bloom season. Water samples (1000 ml) were collected weekly from Harsha Lake during the algal-bloom season starting June 9 and lasting until August 24, 2022. To each of two 7-liter polypropylene containers, 500 ml of Harsha Lake water was added, and the containers were placed in a controlled environment chamber. To one container labeled "Treated," 0.15 g of glucose was added, and nothing was added to the container labeled "Control." After that, three 25 ml samples from each container were collected and used for 16S rRNA gene sequencing each week. Then 1000 ml of Harsha Lake water was newly collected each week, with 500 ml added to each container, along with the addition of 0.15 g glucose to the "Treated" container. Sequencing data were used to examine differences in the composition of bacterial communities between Treated and Control containers. Treatment with glucose altered the microbial communities by 1) reducing taxonomic diversity, 2) largely eliminating cyanobacterial taxa, and 3) increasing the relative abundance of subsets of non-cyanobacterial taxa (such as Proteobacteria and Actinobacteriota). These effects were observed across time despite weekly inputs derived directly from Lake water. The addition of glucose to a container receiving weekly additions of Lake water suppressed the cyanobacterial populations during the entire summer bloom season. The glucose appears to stimulate the diversity of certain bacterial taxa at the expense of the cyanobacteria.

Analysis of the nasopharyngeal microbiome and respiratory pathogens in COVID-19 patients from Saudi Arabia.

BACKGROUND: Infection with SARS-CoV-2 may perturb normal microbiota, leading to secondary infections that can complicate the viral disease. The aim of this study was to probe the alteration of nasopharyngeal (NP) microbiota in the context of SARS-CoV-2 infection and obesity and to identify other respiratory pathogens among COVID-19 cases that may affect patients' health. METHODS: A total of 107 NP swabs, including 22 from control subjects and 85 from COVID-19 patients, were processed for 6S amplicon sequencing. The respiratory pathogens causing secondary infections were identified by RT-PCR assay, using a kit that contained specific primers and probes combinations to amplify 33 known respiratory pathogens. RESULTS: No significant (p > 0.05) difference was observed in the alpha and beta diversity analysis, but specific taxa differed significantly between the control and COVID-19 patient groups. Genera of Sphingomonas, Kurthia, Microbacterium, Methylobacterium, Brevibacillus, Bacillus, Acinetobacter, Lactococcus, and Haemophilus was significantly abundant (p < 0.05) in COVID-19 patients compared with a healthy control group. Staphylococcus was found in relatively high abundance (35.7 %) in the COVID-19 patient groups, mainly those treated with antibiotics. A relatively high percentage of Streptococcus was detected in COVID-19 patient groups with obesity or other comorbidities. Respiratory pathogens, including Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Salmonella species, along with Pneumocystis jirovecii fungal species were detected by RT-PCR mainly in the COVID-19 patients. Klebsiella pneumoniae was commonly found in most of the samples from the control and COVID-19 patients. Four COVID-19 patients had viral coinfections with human adenovirus, human rhinovirus, enterovirus, and human parainfluenza virus 1. CONCLUSIONS: Overall, no substantial difference was observed in the predominant NP bacterial community, but specific taxa were significantly changed between the healthy control and COVID-19 patients. Comparatively, an increased number of respiratory pathogens were identified in COVID-19 patients, and NP colonization by K. pneumoniae was probably occurring in the local population.

Dietary Efficacy Evaluation by Applying a Prediction Model Using Clinical Fecal Microbiome Data of Colorectal Disease to a Controlled Animal Model from an Obesity Perspective.

Obesity associated with a Western diet such as a high-fat diet (HFD) is a known risk factor for inflammatory bowel disease (IBD) and colorectal cancer (CRC). In this study, we aimed to develop fecal microbiome data-based deep learning algorithms for the risk assessment of colorectal diseases. The effects of a HFD and a candidate food (Nypa fruticans, NF) on IBD and CRC risk reduction were also evaluated. Fecal microbiome data were obtained from 109 IBD patients, 111 CRC patients, and 395 healthy control (HC) subjects by 16S rDNA amplicon sequencing. IBD and CRC risk assessment prediction models were then constructed by deep learning algorithms. Dietary effects were evaluated based on fecal microbiome data from rats fed on a regular chow diet (RCD), HFD, and HFD plus ethanol extracts or water extracts of NF. There were significant differences in taxa when IBD and CRC were compared with HC. The diagnostic performance (area under curve, AUC) of the deep learning algorithm was 0.84 for IBD and 0.80 for CRC prediction. Based on the rat fecal microbiome data, IBD and CRC risks were increased in HFD-fed rats versus RCD-fed rats. Interestingly, in the HFD-induced obesity model, the IBD and CRC risk scores were significantly lowered by the administration of ethanol extracts of NF, but not by the administration of water extracts of NF. In conclusion, changes in the fecal microbiome of obesity by Western diet could be important risk factors for the development of IBD and CRC. The risk prediction model developed in this study could be used to evaluate dietary efficacy.

Gut microbial composition in developmental stages of gall inducing thrips Gynaikothrips uzeli and associated plant pathogenesis.

Gut bacteria play a crucial role in the several metabolic activity of the insects. In the present work, effort has been made to decipher the gut microbiota associated with the developmental stages of Gynaikothrips uzeli a gall inducing thrips along with their predicted functional role. Further, an effort has been made to correlate the bacterial communities with plant pathogenesis and thelytoky behaviour of G. uzeli. Findings obtained revealed that genus Arsenophonus dominated the total bacterial diversity and was transmitted vertically through the developmental stages. Further, it was observed that the high abundance of genus Arsenophonus promotes the thelytoky behaviour in G. uzeli and results in the killing of males. Furthermore, strong connecting link between Arsenophonus abundance and gall induction in F. benjamina was observed in the current dataset. G. uzeli being in the category of phloem sucking insect was known for the induction of galls and the current findings for the first time unveiled the facts that high abundance of genus Arsenophonus a well-known plant pathogen may be one of the major reason for inducing galls in F. benjamina. Moreover, PICRUSt2 analysis revealed that predicted functional pathways like biosynthesis of amino acids, and metabolism of carbon, nitrogen, carbohydrates and amino acids (e.g. Arginine, Alanine, Aspartate, Glutamate, Proline, Cysteine, Methionine, Glycine, Threonine, and Serine) were frequently noticed in profiles associated with all the developmental stages of G. uzeli. More to this, the high abundance of Arsenophonus in G. uzeli suggest that representatives of this genus may be resistant and/or tolerant to different antibacterial agents, alkaloids, flavonoids, and glycosides (e.g. quercetin). The correlation of bacterial diversity in pathogenicity can be extrapolated in different pest and vector species of other arthropods.

Meta-analysis defines predominant shared microbial responses in various diseases and a specific inflammatory bowel disease signal.

BACKGROUND: Gut microbial alteration is implicated in inflammatory bowel disease but is noted in other diseases. Systematic comparison to define similarities and specificities is hampered since most studies focus on a single disease. RESULTS: We develop a pipeline to compare between disease cohorts starting from the raw V4 16S amplicon sequence variants. Including 12,838 subjects, from 59 disease cohorts, we demonstrate a predominant shared signature across diseases, indicating a common bacterial response to different diseases. We show that classifiers trained on one disease cohort predict relatively well other diseases due to this shared signal, and hence, caution should be taken when using such classifiers in real-world scenarios, where diseases are intermixed. Based on this common signature across a large array of diseases, we develop a universal dysbiosis index that successfully differentiates between cases and controls across various diseases and can be used for prioritizing fecal donors and samples with lower disease probability. Finally, we identify a set of IBD-specific bacteria, which can direct mechanistic studies and design of IBD-specific microbial interventions. CONCLUSIONS: A robust non-specific general response of the gut microbiome is detected in a large array of diseases. Disease classifiers may confuse between different diseases due to this shared microbial response. Our universal dysbiosis index can be used as a tool to prioritize fecal samples and donors. Finally, the IBD-specific taxa may indicate a more direct association to gut inflammation and disease pathogenesis, and those can be further used as biomarkers and as future targets for interventions.

Changes in the gut microbiota of morbidly obese patients after laparoscopic sleeve gastrectomy.

Aims: Permanent treatment of morbid obesity with medication or diet is nearly impossible. Laparoscopic sleeve gastrectomy (LSG) is becoming a widely accepted treatment option. This study profiled and compared gut microbiota composition before and after LSG. Methods & results: A total of 54 stool samples were collected from 27 morbidly obese individuals before and after LSG. The gut microbiota was profiled with 16S amplicon sequencing. After LSG, patients demonstrated a significant decrease (p < 0.001) in BMI and an increase in bacterial diversity. An increased Firmicutes/Bacteroidetes ratio was also noticed after LSG. The families Prevotellaceae and Veillonellaceae predominated in preoperative samples but were markedly lowered after LSG. A marked increase in Akkermansia, Alistipes, Streptococcus, Ruminococcus and Parabacteroides was observed after LSG. Conclusion: In addition to lowering BMI, LSG remodeled gut microbiota composition.

Exploring Gut Microbiota in Patients with Colorectal Disease Based on 16S rRNA Gene Amplicon and Shallow Metagenomic Sequencing.

The gastrointestinal tract, the largest human microbial reservoir, is highly dynamic. The gut microbes play essential roles in causing colorectal diseases. In the present study, we explored potential keystone taxa during the development of colorectal diseases in central China. Fecal samples of some patients were collected and were allocated to the adenoma (Group A), colorectal cancer (Group C), and hemorrhoid (Group H) groups. The 16S rRNA amplicon and shallow metagenomic sequencing (SMS) strategies were used to recover the gut microbiota. Microbial diversities obtained from 16S rRNA amplicon and SMS data were similar. Group C had the highest diversity, although no significant difference in diversity was observed among the groups. The most dominant phyla in the gut microbiota of patients with colorectal diseases were Bacteroidetes, Firmicutes, and Proteobacteria, accounting for >95% of microbes in the samples. The most abundant genera in the samples were Bacteroides, Prevotella, and Escherichia/Shigella, and further species-level and network analyses identified certain potential keystone taxa in each group. Some of the dominant species, such as Prevotella copri, Bacteroides dorei, and Bacteroides vulgatus, could be responsible for causing colorectal diseases. The SMS data recovered diverse antibiotic resistance genes of tetracycline, macrolide, and beta-lactam, which could be a result of antibiotic overuse. This study explored the gut microbiota of patients with three different types of colorectal diseases, and the microbial diversity results obtained from 16S rRNA amplicon sequencing and SMS data were found to be similar. However, the findings of this study are based on a limited sample size, which warrants further large-scale studies. The recovery of gut microbiota profiles in patients with colorectal diseases could be beneficial for future diagnosis and treatment with modulation of the gut microbiota. Moreover, SMS data can provide accurate species- and gene-level information, and it is economical. It can therefore be widely applied in future clinical metagenomic studies.

Comparison Between Cultivation and Sequencing Based Approaches for Microbiota Analysis in Swabs and Biopsies of Chronic Wounds.

Chronic wounds are a prominent health concern affecting 0.2% of individuals in the Western population. Microbial colonization and the consequent infection contribute significantly to the healing process. We have compared two methods, cultivation and 16S amplicon sequencing (16S-AS), for the characterization of bacterial populations in both swabs and biopsy tissues obtained from 45 chronic wounds. Using cultivation approach, we detected a total of 39 bacterial species, on average 2.89 per sample (SD = 1.93), compared to 5.9 (SD = 7.1) operational taxonomic units per sample obtained with 16S-AS. The concordance in detected bacteria between swab and biopsy specimens obtained from the same CWs was greater when using cultivation (58.4%) as compared to 16S-AS (25%). In the entire group of 45 biopsy samples concordance in detected bacterial genera between 16S-AS and cultivation-based approach was 36.4% and in swab samples 28.7%. Sequencing proved advantageous in comparison to the cultivation mainly in case of highly diverse microbial communities, where we could additionally detect numerous obligate and facultative anaerobic bacteria from genera Anaerococcus, Finegoldia, Porphyromonas, Morganella, and Providencia. Comparing swabs and biopsy tissues we concluded, that neither sampling method shows significant advantage over the other regardless of the method used (16S-AS or cultivation). In this study, chronic wound microbiota could be distributed into three groups based on the bacterial community diversity. The chronic wound surface area was positively correlated with bacterial diversity in swab specimens but not in biopsy tissues. Larger chronic wound surface area was also associated with the presence of Pseudomonas in both biopsy and swab specimens. The presence of Corynebacterium species at the initial visit was the microbial marker most predictive of the unfavorable clinical outcome after one-year follow-up visit.

Impact of Processed Food (Canteen and Oil Wastes) on the Development of Black Soldier Fly (Hermetia illucens) Larvae and Their Gut Microbiome Functions.

Canteens represent an essential food supply hub for educational institutions, companies, and business parks. Many people in these locations rely on a guaranteed service with consistent quality. It is an ongoing challenge to satisfy the demand for sufficient serving numbers, portion sizes, and menu variations to cover food intolerances and different palates of customers. However, overestimating this demand or fluctuating quality of dishes leads to an inevitable loss of unconsumed food due to leftovers. In this study, the food waste fraction of canteen leftovers was identified as an optimal diet for black soldier fly (Hermetia illucens) larvae based on 50% higher consumption and 15% higher waste reduction indices compared with control chicken feed diet. Although the digestibility of food waste was nearly twice as high, the conversion efficiency of ingested and digested chicken feed remains unparalleled (17.9 ± 0.6 and 37.5 ± 0.9 in CFD and 7.9 ± 0.9 and 9.6 ± 1.0 in FWD, respectively). The oil separator waste fraction, however, inhibited biomass gain by at least 85% and ultimately led to a larval mortality of up to 96%. In addition to monitoring larval development, we characterized physicochemical properties of pre- and post-process food waste substrates. High-throughput amplicon sequencing identified Firmicutes, Proteobacteria, and Bacteroidota as the most abundant phyla, and Morganella, Acinetobacter, and certain Lactobacillales species were identified as indicator species. By using metagenome imputation, we additionally gained insights into the functional spectrum of gut microbial communities. We anticipate that the results will contribute to the development of decentralized waste-management sites that make use of larvae to process food waste as it has become common practice for biogas plants.

Far infrared radiation induces changes in gut microbiota and activates GPCRs in mice.

Far infrared radiation (FIR) has been widely used to treat chronic diseases and symptoms; however, the underlying mechanism remains unclear. As gut microbiota (GM) markedly impact the host's physiology, making GM a potential target for the therapeutic evaluation of FIR. C57BL/6J mice were exposed to five times of 2 min-FIR exposure on the abdomen, with a two-hour interval of each exposure within one day. Fecal samples were collected on day one and day 25 after the FIR/control treatment, and the extracted fecal DNAs were evaluated using ERIC-PCR and 16S amplicon sequencing. Host's G-protein coupled receptors (GPCR) were analyzed using qRT-PCR. FIR induced immediate changes in the GM composition. A prompt and significant (p < 0.05) reduction in the abundance of phylum Deferribacteres (comprised of several pathogens) was observed in the FIR-irradiated mice compared to the control group. Contrarily, FIR exposure induced beneficial genera such as Alistipes, Barnesiella, and Prevotella. The gut of FIR-irradiated mice was predominated by short-chain fatty acids (SCFAs) producers. Also, FIR stimulated the expression of SCFAs-sensing receptors, GPCR 41, 43, and 109 in the gut epithelial barrier. These findings provide the first-hand evidence in which the beneficial effects of FIR radiation might be partially through the modulation of GM.

Unveiling hákarl: A study of the microbiota of the traditional Icelandic fermented fish.

Hákarl is produced by curing of the Greenland shark (Somniosus microcephalus) flesh, which before fermentation is toxic due to the high content of trimethylamine (TMA) or trimethylamine N-oxide (TMAO). Despite its long history of consumption, little knowledge is available on the microbial consortia involved in the fermentation of this fish. In the present study, a polyphasic approach based on both culturing and DNA-based techniques was adopted to gain insight into the microbial species present in ready-to-eat hákarl. To this aim, samples of ready-to-eat hákarl were subjected to viable counting on different selective growth media. The DNA directly extracted from the samples was further subjected to Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) and 16S amplicon-based sequencing. Moreover, the presence of Shiga toxin-producing Escherichia coli (STEC) and Pseudomonas aeruginosa was assessed via qualitative real-time PCR assays. pH values measured in the analyzed samples ranged from between 8.07 ±â€¯0.06 and 8.76 ±â€¯0.00. Viable counts revealed the presence of total mesophilic aerobes, lactic acid bacteria and Pseudomonadaceae. Regarding bacteria, PCR-DGGE analysis highlighted the dominance of close relatives of Tissierella creatinophila. For amplicon sequencing, the main operational taxonomic units (OTUs) shared among the data set were Tissierella, Pseudomonas, Oceanobacillus, Abyssivirga and Lactococcus. The presence of Pseudomonas in the analyzed samples supports the hypothesis of a possible role of this microorganism on the detoxification of shark meat from TMAO or TMA during fermentation. Several minor OTUs (<1%) were also detected, including Alkalibacterium, Staphylococcus, Proteiniclasticum, Acinetobacter, Erysipelothrix, Anaerobacillus, Ochrobactrum, Listeria and Photobacterium. Analysis of the yeast and filamentous fungi community composition by PCR-DGGE revealed the presence of close relatives of Candida tropicalis, Candida glabrata, Candida parapsilosis, Candida zeylanoides, Saccharomyces cerevisiae, Debaryomyces, Torulaspora, Yamadazyma, Sporobolomyces, Alternaria, Cladosporium tenuissimum, Moristroma quercinum and Phoma/Epicoccum, and some of these species probably play key roles in the development of the sensory qualities of the end product. Finally, qualitative real-time PCR assays revealed the absence of STEC and Pseudomonas aeruginosa in all of the analyzed samples.

Glucocorticosteroids and ciclosporin do not significantly impact canine cutaneous microbiota.

BACKGROUND: As prednisone and ciclosporin can have immunosuppressive effects and have been considered potential predisposing factors for skin infections, we investigated the impact of these drugs on the diversity of the cutaneous microbiota, the abundance of Malassezia and infection with Papillomaviruses. RESULTS: Six atopic, asymptomatic Maltese-beagle dogs were treated with ciclosporin for one month and then with prednisone for another month, with a one-month wash-out between treatments. The dogs were sampled on the abdomen and pinna before and after each treatment using a swab. Samples for Papillomavirus detection were obtained with cytobrush sticks. The bacterial microbiota was characterized using 16S amplicon high-throughput sequencing. Malassezia populations were quantified with nested real-time PCR targeting the ribosomal internal transcribed spacer 1. The diversity and composition of cutaneous microbiota was not impacted in a detectable manner by any of the treatments. As observed for the bacterial microbiota, Malassezia populations were not affected by treatment. Three dogs were positive for Papillomavirus at more than one timepoint, but an association with treatment was not apparent. CONCLUSIONS: Ciclosporin and prednisone at doses used for the treatment of atopic dermatitis do not impact the canine cutaneous microbiota in a detectable manner.

Environmental Pollutant Benzo[a]Pyrene Impacts the Volatile Metabolome and Transcriptome of the Human Gut Microbiota.

Benzo[a]pyrene (B[a]P) is a ubiquitous, persistent, and carcinogenic pollutant that belongs to the large family of polycyclic aromatic hydrocarbons. Population exposure primarily occurs via contaminated food products, which introduces the pollutant to the digestive tract. Although the metabolism of B[a]P by host cells is well known, its impacts on the human gut microbiota, which plays a key role in health and disease, remain unexplored. We performed an in vitro assay using 16S barcoding, metatranscriptomics and volatile metabolomics to study the impact of B[a]P on two distinct human fecal microbiota. B[a]P exposure did not induce a significant change in the microbial structure; however, it altered the microbial volatolome in a dose-dependent manner. The transcript levels related to several metabolic pathways, such as vitamin and cofactor metabolism, cell wall compound metabolism, DNA repair and replication systems, and aromatic compound metabolism, were upregulated, whereas the transcript levels related to the glycolysis-gluconeogenesis pathway and bacterial chemotaxis toward simple carbohydrates were downregulated. These primary findings show that food pollutants, such as B[a]P, alter human gut microbiota activity. The observed shift in the volatolome demonstrates that B[a]P induces a specific deviation in the microbial metabolism.

Microbiota bacteriana asociada al papel moneda de circulación en Colombia / Bacterial microbiota on circulating Colombian banknotes

Diariamente los seres humanos están en interacción con objetos de uso continuo, como el papel moneda, sin el conocimiento de que estos almacenan microorganismos y de que nos exponemos al contacto con potenciales patógenos. La composición de la comunidad bacteriana en un billete colombiano fue determinada mediante el secuenciamiento profundo de librerías de amplicones 16S. Se encontraron 233 géneros bacterianos; 12 de estos géneros corresponden a especies con potencial patogénico. El género más abundante fue Propionibacterium, seguido de Streptococcus, Staphylococcus Pseudomonas . Este es el primer reporte de la diversidad bacteriana que puede ser alojada en este objeto de alta circulación en Colombia. Pocos estudios en el mundo han mostrado este nivel de detalle de la microbiota en billetes de circulación y ofrece un panorama mucho más amplio de la exposición diaria a microorganismos al utilizar papel moneda en las condiciones en las que se utiliza en Colombia.

Commonly used objects such as currency paper can be colonised by bacteria and can serve as carriers of microbes. This colonisation might expose us to unnoticed pathogenic bacteria. In this study, the researchers obtained a detailed panorama of the microbes that can be carried on currency notes in Colombia by using 454 next-generation deep sequencing of 16S amplicón libraries. A total of 233 bacterial genera were detected and classified, 12 of which are potential human pathogens. The most abundant genera were Propionibacterium, Streptococcus, Staphylococcus and Pseudomonas. To date, this is the first in-depth analysis of the microbiota carried by circulating banknotes in our continent and it offers insights into daily exposure to microbes when using banknotes in Colombia.