Effect of Biofloc Technology Enriches the Growth of Litopenaeus vannamei (Boone, 1931)

The use of probiotics in shrimp farms has expanded as an alternative to antibiotics, improving shrimp health, growth, disease control and water quality. However, the efficacy of probiotics in intensive systems using biofloc remains uncertain. This study investigated bioremediation and biocontrol of commercial probiotics using biofloc, analysing water quality and bacterial groups influencing shrimp performance. Thirteen microbial colonies were observed in the biofloc samples, and their evolutionary history was inferred using the neighbour-joining method. Analysis using MEGA6 software revealed 99.6% similarity between colony 1P1 and Virgibacillus sp. and 99.8% similarity between colony 2P2 and Bacillus kochii. The study analysed the biochemical and amino acid content of shrimp cultured using biofloc technology for 85 days. The study found that biofloc-cultured L. Vannamei flesh had higher levels of moisture (31%), ash (15.2%), protein (34%) and lipid (12.6%). No seasonal variations were observed between biofloc samples in winter and summer seasons. Protein levels were found to be appropriate for shrimp growth in both ex situ and in situ biofloc systems. The average growth rate (kg/m2) of biofloc-cultured shrimp was significantly greater than in normal pond shrimp in both samples. The feed conversion ratio in the biofloc tank was lower than in the usual pond-cultured shrimp, possibly due to lower growth rate, lower feeding frequency (2 times per day) and higher density. The growth of L. vannamei shrimp is influenced by stocking density, with higher stocking density affecting the average weight. The study also examined the growth biochemical and amino acid content of shrimp cultured using biofloc technology.

From the Gut to the Brain: Is Microbiota a New Paradigm in Parkinson's Disease Treatment?

Parkinson's disease (PD) is recognized as the second most prevalent primary chronic neurodegenerative disorder of the central nervous system. Clinically, PD is characterized as a movement disorder, exhibiting an incidence and mortality rate that is increasing faster than any other neurological condition. In recent years, there has been a growing interest concerning the role of the gut microbiota in the etiology and pathophysiology of PD. The establishment of a brain-gut microbiota axis is now real, with evidence denoting a bidirectional communication between the brain and the gut microbiota through metabolic, immune, neuronal, and endocrine mechanisms and pathways. Among these, the vagus nerve represents the most direct form of communication between the brain and the gut. Given the potential interactions between bacteria and drugs, it has been observed that the therapies for PD can have an impact on the composition of the microbiota. Therefore, in the scope of the present review, we will discuss the current understanding of gut microbiota on PD and whether this may be a new paradigm for treating this devastating disease.

The Interplay between Mycobacterium tuberculosis and Human Microbiome

Tuberculosis (TB), a respiratory disease caused by Mycobacterium tuberculosis (Mtb), is a significant cause of mortality worldwide. The lung, a breeding ground for Mtb, was once thought to be a sterile environment, but has now been found to host its own profile of microbes. These microbes are critical in the development of the host immune system and can produce metabolites that aid in host defense against various pathogens. Mtb infection as well as antibiotics can shift the microbial profile, causing dysbiosis and dampening the host immune response. Additionally, increasing cases of drug resistant TB have impacted the success rates of the traditional therapies of isoniazid, rifampin, pyrazinamide, and ethambutol. Recent years have produced tremendous research into the human microbiome and its role in contributing to or attenuating disease processes. Potential treatments aimed at altering the gut-lung bacterial axis may offer promising results against drug resistant TB and help mitigate the effects of TB.

Tuning Expectations to Reality: Don't Expect Increased Gut Microbiota Diversity with Dietary Fiber

Dietary approaches, particularly those including fiber supplementation, can be used to promote health benefits by shaping gut microbial communities. Whereas community diversity measures, such as richness and evenness, are often used in microbial ecology to make sense of these complex and vast microbial ecosystems, it is less clear how these concepts apply when dietary fiber supplementation is given. In this perspective, we summarize and demonstrate how factors including experimental approach, number of bacteria sharing a dietary fiber, and initial relative abundances of bacteria that use a fiber can significantly affect diversity outcomes in fiber fermentation studies. We also show that a reduction in alpha diversity is possible, and perhaps expected, for most approaches that use fermentable fibers to beneficially shape the gut microbial community while still achieving health-related improvements.

Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis

The multi-batch reanalysis approach of jointly reevaluating gene/genome sequences from different works has gained particular relevance in the literature in recent years. The large amount of 16S ribosomal ribonucleic acid (rRNA) gene sequence data stored in public repositories and information in taxonomic databases of the same gene far exceeds that related to complete genomes. This review is intended to guide researchers new to studying microbiota, particularly the oral microbiota, using 16S rRNA gene sequencing and those who want to expand and update their knowledge to optimise their decision-making and improve their research results. First, we describe the advantages and disadvantages of using the 16S rRNA gene as a phylogenetic marker and the latest findings on the impact of primer pair selection on diversity and taxonomic assignment outcomes in oral microbiome studies. Strategies for primer selection based on these results are introduced. Second, we identified the key factors to consider in selecting the sequencing technology and platform. The process and particularities of the main steps for processing 16S rRNA gene-derived data are described in detail to enable researchers to choose the most appropriate bioinformatics pipeline and analysis methods based on the available evidence. We then produce an overview of the different types of advanced analyses, both the most widely used in the literature and the most recent approaches. Several indices, metrics and software for studying microbial communities are included, highlighting their advantages and disadvantages. Considering the principles of clinical metagenomics, we conclude that future research should focus on rigorous analytical approaches, such as developing predictive models to identify microbiome-based biomarkers to classify health and disease states. Finally, we address the batch effect concept and the microbiome-specific methods for accounting for or correcting them.

Unveiling the Pharmacological Significance of Marine Streptomyces violaceusniger KS20: Isolation, Characterization, and Assessment of Its Biomedical Applications

Marine actinomycetes represent a highly favorable source of bioactive compounds and have been the mainstay of much research in recent years. Recent reports have shown that marine Streptomyces sp. can produce compounds with diverse and potent biological activities. Therefore, the key objective of the study was to isolate and screen a potential actinomycete from marine ecosystems of Devbagh and Tilmati beaches, Karwar. Streptomyces sp. KS20 was characterized and the ethyl acetate extract (EtOAc-Ex) was screened for biomedical applications. Streptomyces sp. KS20 produced grayish-white aerial and pale-yellow substrate mycelia and revealed an ancestral relationship with Streptomyces violaceusniger. Optimum growth of the organism was recorded at 30 °C and pH 7.0. The metabolite profiling of EtOAc-Ex expressed the existence of several bioactive metabolites, whereas the functional groups were indicated by Fourier transform infrared (FTIR) spectroscopy. A considerable antioxidant activity was shown for EtOAc-Ex with IC50 of 92.56 μg/mL. In addition to this, Streptomyces sp. KS20 exhibited significant antimicrobial properties, particularly against Escherichia coli, where a zone of inhibition measuring 36 ± 0.83 mm and a minimum inhibitory concentration (MIC) of 3.12 µg/mL were observed. The EtOAc-Ex even revealed significant antimycobacterial potency with IC50 of 6.25 μg/mL. Finally, the antiproliferative potentiality of EtOAc-Ex against A549 and PC-3 cell lines revealed a constant decline in cell viability while raising the concentration of EtOAc-Ex from 12.5 to 200 μg/mL. The IC50 values were determined as 94.73 μg/mL and 121.12 μg/mL for A549 and PC-3 cell lines, respectively. Overall, the exploration of secondary metabolites from marine Streptomyces sp. KS20 represents an exciting area of further research with the potential to discover novel bioactive compounds that could be developed into therapeutics for various medical applications.

Isolation, Characterization of Pyraclostrobin Derived from Soil Actinomycete Streptomyces sp. HSN-01 and Its Antimicrobial and Anticancer Activity

The present study demonstrated the isolation, characterization, and antimicrobial and anticancer activity of active metabolite produced from mining-soil-derived actinomycetes. Among the 21 actinomycete isolates, the isolate HSN-01 exhibited significant antimicrobial activity in primary screening and was identified as Streptomyces sp. through 16S rRNA gene sequencing. The active metabolite was separated, purified, and confirmed through UV-Vis spectroscopy, FTIR, HR-ESI-MS, and NMR analysis and identified as pyraclostrobin. Further, the active metabolite pyraclostrobin was tested for antimicrobial and anticancer activity against the hepatocellular carcinoma (HepG2) cell line. The metabolite exhibited maximum antimicrobial potential with 17.0, 13.33, 17.66, 15.66, 14.66, and 14.0 mm of inhibition against B. cereus, S. aureus, E. coli, P. aeruginosa, S. flexneri, and C. glabrata. The active metabolite exhibited dose-dependent anticancer potential against the hepatocellular carcinoma (HepG2) cell line with the IC₅₀ 56.76 µg/mL. This study suggests that Streptomyces sp. HSN-01 is an excellent source of active secondary metabolites with various biological activities.

Antimicrobial Efficacy of 7-Hydroxyflavone Derived from Amycolatopsis sp. HSN-02 and Its Biocontrol Potential on Cercospora Leaf Spot Disease in Tomato Plants

The actinomycete strain HSN-02 was isolated from the soil of a mining field in the Sandur region, Bellary, Karnataka, India. According to the morphological, cultural, physiological, and biochemical characteristics and the 16S rDNA sequence analysis, the strain HSN-02 was identified as Amycolatopsis sp. The antimicrobial activity strain HSN-02 presented stable and moderate inhibitory activity against human pathogens. In pot experiments in the greenhouse, the development of Cercospora leaf spot was markedly suppressed by treatment with the purified compound from the strain HSN-02, and the control efficacy was 45.04 ± 1.30% in Septoria lycopersici-infected tomato plants. A prominent compound was obtained from the fermentation broth of the strain HSN-02 using column chromatography and HPLC. The chemical structural analyses using UV, FTIR, HR-ESI-MS, and NMR confirmed that the compound produced by the strain HSN-02 is 7-hydroxyflavone. This investigation showed the role which the actinomycete strain can play in controlling leaf spots caused by S. lycopersici to reduce treatments with chemical fungicides.

Esophageal microflora in esophageal diseases

With the development of endoscopic technology, an increasing number of patients with esophageal disease are being diagnosed, although the underlying pathogenesis of many esophageal diseases remains unclear. In recent years, a large number of studies have demonstrated that the occurrence and development of various intestinal diseases were related to intestinal flora. As a result, researchers have shifted their focus towards investigating esophageal flora to better understand the pathogenesis, early diagnosis, and treatment of esophageal diseases. This paper reviewed the normal esophageal flora and the changes of esophageal flora under different esophageal disease states. It was observed that there are distinct differences in the composition of esophageal microflora among Gastroesophageal Reflux, Barrett's esophagus, eosinophilic esophagitis and normal esophagus. The normal esophageal flora was dominated by gram-positive bacteria, particularly Streptococcus, while the esophageal flora under esophagitis was dominated by gram-negative bacteria. Furthermore, the diversity of esophageal flora is significantly decreased in patients with esophageal cancer. Several potential microbial biomarkers for esophageal cancer have been identified, among which Fusobacterium nucleatum showed a close association with esophageal squamous cell carcinoma's pathological stage and clinical stage.

A bibliometric analysis of microbial forensics from 1984 to 2022: progress and research trends

Microbial forensics is a rapidly evolving discipline that has gained significant momentum in recent years. The study evaluated relevant results over the last four decades from 1984 to 2022 all over the world, aiming to analyze the growing trends and research orientations of microbial forensics. Using "microbial forensics" as the search topic in the Web of Science Core Collection, the systematic retrieval identified 579 documents relevant to the field and draw many statistical tables and maps to make the retrieval results visible. According to further bibliometric analysis, there are an increasing number of publications related to microbial forensics from the overall trend, with the highest number of publications recorded in 2021. In terms of the total number of articles, the USA and China were both the leading contributors to the field among 40 countries. The field has developed rapidly in recent years based on the development of next-generation sequencing. Over the course of its development, there are rich keywords in the research of scholars, which focus on diversity and identification. Moreover, despite the early hot topic being PCR (the use of PCR to probe microorganisms), in recent years, the topics, markers, and the potential application of microorganisms in forensic practice have become hot, which also indicates the future research directions of microbial forensic.

Role of Surgical Pathologist for the Detection of Immuno-oncologic Predictive Factors in Non-small Cell Lung Cancers

Until very recently, surgery, chemotherapy, and radiation therapy have been the mainstay of treatment in non-small cell carcinomas (NSCLCs). However, recent advances in molecular immunology have unveiled some of the complexity of the mechanisms regulating cellular immune responses and led to the successful targeting of immune checkpoints in attempts to enhance antitumor T-cell responses. Immune checkpoint molecules such as cytotoxic T-lymphocyte associated protein-4, programmed cell death protein-1, and programmed death ligand (PD-L) 1 have been shown to play central roles in evading cancer immunity. Thus, these molecules have been targeted by inhibitors for the management of cancers forming the basis of immunotherapy. Advanced NSCLC has been the paradigm for the benefits of immunotherapy in any cancer. Treatment decisions are made based on the expression of PD-L1 on the tumor cells and the presence or absence of driver mutations. Patients with high PD-L1 expression (≥50%) and no driver mutations are treated with single-agent immunotherapy whereas, for all other patients with a lower level of PD-L1 expression, a combination of chemotherapy and immunotherapy is preferred. Thus, PD-L1 blockers are the only immunotherapeutic agents approved in advanced NSCLC without any oncogenic driver mutations. PD-L1 immunohistochemistry, however, may not be the best biomarker in view of its dynamic nature in time and space, and the benefits may be seen regardless of PD -L1 expression. Each immunotherapy molecule is prescribed based on the levels of PD-L1 expression as assessed by a Food and Drug Administration-approved companion diagnostic assay. Other biomarkers that have been studied include tumor mutational burden, the T-effector signature, tumor-infiltrating lymphocytes, radiomic assays, inflammation index, presence or absence of immune-related adverse events and specific driver mutations, and gut as well as local microbiome. At the current time, none of these biomarkers are routinely used in the clinical decision-making process for immunotherapy in NSCLC. However, in individual cases, they can be useful adjuncts to conventional therapy. This review describes our current understanding of the role of biomarkers as predictors of response to immune checkpoint molecules. To begin with a brief on cancer immunology in general and in NSCLC, in particular, is discussed. In the end, recent advancements in laboratory techniques for refining biomarker assays are described.

Involvement of the human microbiome in frequent cancers, current knowledge and carcinogenesis mechanisms

The human body is home to a complex microbial community, living in symbiosis. However, when an imbalance occurs, known as dysbiosis, it can lead to organic diseases such as cancers. Helicobacter pylori is commonly recognized as the causative agent of gastric cancer. Numerous studies have explored the potential role of other microorganisms in cancers. For example, the role of intestinal microbiota in the hepatocellular carcinoma formation and progression, the microbiota in breast cancer and the interaction between the microbiome and TP53 in human lung carcinogenesis. In this review, we highlight the latest findings on the microbiome involved in the most common cancers and the suggested mechanisms of carcinogenesis.

Role of microbiota and microbiota-derived short-chain fatty acids in PDAC

Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive lethal diseases among other cancer types. Gut microbiome and its metabolic regulation play a crucial role in PDAC. Metabolic regulation in the gut is a complex process that involves microbiome and microbiome-derived short-chain fatty acids (SCFAs). SCFAs regulate inflammation, as well as lipid and glucose metabolism, through different pathways. This review aims to summarize recent developments in PDAC in the context of gut and oral microbiota and their associations with short-chain fatty acid (SCFA). In addition to this, we discuss possible therapeutic applications using microbiota in PDAC.

Validation of 16S rRNA Gene Sequencing of the Periocular Microbiome and Lack of Alteration by Topical Eyedrops

Purpose

Genomic techniques for characterizing the ocular microbiome require further validation. We compared the microbiome of patients' eyelids through both conventional culture and 16S rRNA analysis and analyzed the impact of eyedrop use on microbiome diversity.

Methods

Ninety-eight patients followed for management of glaucoma or suspicion of glaucoma had eyelid swabs performed with Isohelix MS Mini DNA Swabs (98 participants) and ESwabs (49 participants) for 16S rRNA analysis and conventional culture, respectively. The effect of preservative-containing eyedrops on the microbiomes detected using these two techniques were analyzed and compared across techniques.

Results

Forty-five of the 50 (non-unique) genera (90%) identified by conventional culture were also identified by each individual's 16S rRNA analysis within the top 14 most abundant organisms present based on operational taxonomic unit. All conventional cultures performed had at least one or more genera also identified by each participant's 16S rRNA analysis. There was no difference in the conventional culture positivity rate or proportion of participants with a particular genus present on conventional culture based on whether preservative-containing eyedrops were regularly used. Similarly, in eyes using versus not using eyedrops, no differences were observed in the proportions of participants with a particular genus present or the Shannon index as determined by 16S rRNA analysis.

Conclusions

16S rRNA analysis correlates well with conventional culture results for the eyelid microbiome, with results from neither technique demonstrating an association of microbiome composition and eyedrop use. The clinical relevance of the large numbers of microbes detected via 16S rRNA analysis requires further study.

Translational Relevance

16S rRNA analysis of the periocular microbiome is consistent with conventional culture and enables further study of physiologic and pathologic ocular processes possibly related to microbiome diversity.

Genomic diversity, pathogenicity and antimicrobial resistance of Escherichia coli isolated from poultry in the southern United States

Escherichia coli (E. coli) are typically present as commensal bacteria in the gastro-intestinal tract of most animals including poultry species, but some avian pathogenic E. coli (APEC) strains can cause localized and even systematic infections in domestic poultry. Emergence and re-emergence of antimicrobial resistant isolates (AMR) constrain antibiotics usage in poultry production, and development of an effective vaccination program remains one of the primary options in E. coli disease prevention and control for domestic poultry. Thus, understanding genetic and pathogenic diversity of the enzootic E. coli isolates, particularly APEC, in poultry farms is the key to designing an optimal vaccine candidate and to developing an effective vaccination program. This study explored the genomic and pathogenic diversity among E. coli isolates in southern United States poultry. A total of nine isolates were recovered from sick broilers from Mississippi, and one from Georgia, with epidemiological variations among clinical signs, type of housing, and bird age. The genomes of these isolates were sequenced by using both Illumina short-reads and Oxford Nanopore long-reads, and our comparative analyses suggested data from both platforms were highly consistent. The 16 s rRNA based phylogenetic analyses showed that the 10 bacteria strains are genetically closer to each other than those in the public database. However, whole genome analyses showed that these 10 isolates encoded a diverse set of reported virulence and AMR genes, belonging to at least nine O:H serotypes, and are genetically clustered with at least five different groups of E. coli isolates reported by other states in the United States. Despite the small sample size, this study suggested that there was a large extent of genomic and serological diversity among E. coli isolates in southern United States poultry. A large-scale comprehensive study is needed to understand the overall genomic diversity and the associated virulence, and such a study will be important to develop a broadly protective E. coli vaccine.

Exploring the Cystic Fibrosis Lung Microbiome: Making the Most of a Sticky Situation

Chronic lower respiratory tract infections are a leading contributor to morbidity and mortality in persons with cystic fibrosis (pwCF). Traditional respiratory tract surveillance culturing has focused on a limited range of classic pathogens; however, comprehensive culture and culture-independent molecular approaches have demonstrated complex communities highly unique to each individual. Microbial community structure evolves through the lifetime of pwCF and is associated with baseline disease state and rates of disease progression including occurrence of pulmonary exacerbations. While molecular analysis of the airway microbiome has provided insight into these dynamics, challenges remain including discerning not only "who is there" but "what they are doing" in relation to disease progression. Moreover, the microbiome can be leveraged as a multi-modal biomarker for both disease activity and prognostication. In this article, we review our evolving understanding of the role these communities play in pwCF and identify challenges in translating microbiome data to clinical practice.

Interplay between natural environment, human microbiota and immune system: A scoping review of interventions and future perspectives towards allergy prevention

BACKGROUND

Urbanization and biodiversity loss are linked to chronic disorders, in particular allergic diseases. The aim of this scoping review was to provide a synopsis of intervention studies specifically examining the influence of exposure to natural environments on human microbiota as well as immunological markers as suggested interlink between natural environment and the development of allergic diseases.

METHODS

We searched PubMed (MEDLINE®) and all references cited in the included studies following the PRISMA statement guidelines. No restrictions regarding age and sex of study participants, language or publication date were made. The protocol was registered at OSF REGISTRIES (https://osf.io/musgr).

RESULTS

After screening, eight intervention studies were included. The interventions reported were mainly of pilot character and various, ranging from nature-related educational programs, biodiversity interventions in day-cares to short-term contact with soil- and sand-preparations. Most of the studied interventions appeared to increase human microbiota richness and diversity in specific taxa groups in the short-time. Immunological markers were assessed in only two studies. In these, their associations with human microbiota richness were pre-dominantly reported.

CONCLUSION

There is some evidence that the so-called biodiversity interventions have the potential to diversify human microbiota, at least over a short period. Adequately powered randomized controlled trials with long term follow-up are required to examine sustainable effects on microbiota and immune system.

Bladder Microbiome in the Context of Urological Disorders—Is There a Biomarker Potential for Interstitial Cystitis?

Since the development of modern cultivation and sequencing techniques, the human microbiome has increasingly become the focus of scientific attention. Even in the bladder, long considered to be a sterile niche, a highly variable and complex microbial colonization has now been demonstrated. Especially in the context of diseases such as interstitial cystitis, whose etiopathogenesis is largely unknown, and whose diagnosis is based on a process of exclusion of confusable diseases, science hopes to gain far-reaching insights for etiology and diagnosis, including the identification of potential biomarkers. While for functional disorders such as urge urinary incontinence and overactive bladder syndrome, initial associations have been demonstrated between reduced microbial diversity and increased symptomatology, as well as shifts in the abundance of specific microorganisms such as Lactobacillus or Proteus, studies in interstitial cystitis show conflicting results and have failed to identify a putative organism or urotype that clearly distinguishes the urinary microbiome of patients with IC/BPS from that of healthy controls. At the present time, therefore, the new insights into the bladder microbiome and its potential influence on urologic disease cannot yet be used in the context of elucidating possible etiopathogenetic causes, as well as in the use of a biomarker for diagnostic or prognostic purposes. Further studies should focus primarily on uniform procedures and detection methods to achieve better comparability of results and increase the likelihood of detecting hidden patterns.

Gut Microbial Changes and their Contribution to Post-Burn Pathology

ABSTRACT

Burn injuries are a common form of traumatic injury that leads to significant morbidity and mortality worldwide. Burn injuries are characterized by inflammatory processes and alterations in numerous organ systems and functions. Recently, it has become apparent that the gastrointestinal bacterial microbiome is a key component of regulating the immune response and recovery from burn and can also contribute to significant detrimental sequelae after injury, such as sepsis and multiple organ failure. Microbial dysbiosis has been linked to multiple disease states; however, its role in exacerbating acute traumatic injuries, such as burn, is poorly understood. In this article, we review studies that document changes in the intestinal microbiome after burn injury, assess the implications in post-burn pathogenesis, and the potential for further discovery and research.

To understand the reproductive tract microbiome associated with infertility through metagenomics analysis

Background

Knowledge of the microbiome is in its infancy in health and human illness, especially concerning human reproduction. We will be better able to treat dysbiosis of the reproductive tract clinically if it is better explained and understood. It has been shown that altered vaginal microbiota affects parturition, and its function is uncertain in assisted reproductive technologies. However, the effects of recognized microbes such as Mycoplasma tuberculosis, Chlamydia trachomatis, and Neisseria gonorrhoeae are well established, resulting in subclinical changes which are considered to be risk factors for infertility and poor reproductive outcomes.

Main body

Recent studies indicate that the vaginal tract comprises several different organisms of the microbiome. Some microbiota can play an important role not only in the reproductive tract but also in overall health. The microbiome of the female reproductive tract has been identified mainly based on studies that examine vaginal samples across many reproductive technologies, using a metagenomics approach.

Conclusion

Alteration of reproductive tract microbiota or presence of certain microbiota irrespective of the level of pathogenicity may interfere with fertilization, implantation, and subsequent embryo development. This may lead to failed fertility treatments and reduced live birth rate (LBR).

Elucidating biofilm diversity on water lily leaves through 16S rRNA amplicon analysis: Comparison of four DNA extraction kits

PREMISE

Within a broader study on leaf fossilization in freshwater environments, a long-term study on the development and microbiome composition of biofilms on the foliage of aquatic plants has been initiated to understand how microbes and biofilms contribute to leaf decay and preservation. Here, water lily leaves are employed as a study model to investigate the relationship between bacterial microbiomes, biodegradation, and fossilization. We compare four DNA extraction kits to reduce biases in interpretation and to identify the most suitable kit for the extraction of DNA from bacteria associated with biofilms on decaying water lily leaves for 16S rRNA amplicon analysis.

METHODS

We extracted surface-associated DNA from Nymphaea leaves in early stages of decay at two water depth levels using four commercially available kits to identify the most suitable protocol for bacterial extraction, applying a mock microbial community standard to enable a reliable comparison of the kits.

RESULTS

Kit 4, the FastDNA Spin Kit for Soil, resulted in high DNA concentrations with better quality and yielded the most accurate depiction of the mock community. Comparison of the leaves at two water depths showed no significant differences in community composition.

DISCUSSION

The success of Kit 4 may be attributed to its use of bead beating with a homogenizer, which was more efficient in the lysis of Gram-positive bacteria than the manual vortexing protocols used by the other kits. Our results show that microbial composition on leaves during early decay remains comparable and may change only in later stages of decomposition.

A rarefaction-based extension of the LDM for testing presence-absence associations in the microbiome

MOTIVATION

Many methods for testing association between the microbiome and covariates of interest (e.g., clinical outcomes, environmental factors) assume that these associations are driven by changes in the relative abundance of taxa. However, these associations may also result from changes in which taxa are present and which are absent. Analyses of such presence-absence associations face a unique challenge: confounding by library size (total sample read count), which occurs when library size is associated with covariates in the analysis. It is known that rarefaction (subsampling to a common library size) controls this bias, but at the potential cost of information loss as well as the introduction of a stochastic component into the analysis. Currently, there is a need for robust and efficient methods for testing presence-absence associations in the presence of such confounding, both at the community level and at the individual-taxon level, that avoid the drawbacks of rarefaction.

RESULTS

We have previously developed the linear decomposition model (LDM) that unifies the community-level and taxon-level tests into one framework. Here we present an extension of the LDM for testing presence-absence associations. The extended LDM is a non-stochastic approach that repeatedly applies the LDM to all rarefied taxa count tables, averages the residual sum-of-squares (RSS) terms over the rarefaction replicates, and then forms an F-statistic based on these average RSS terms. We show that this approach compares favorably to averaging the F-statistic from R rarefaction replicates, which can only be calculated stochastically. The flexible nature of the LDM allows discrete or continuous traits or interactions to be tested while allowing confounding covariates to be adjusted for. Our simulations indicate that our proposed method is robust to any systematic differences in library size and has better power than alternative approaches. We illustrate our method using an analysis of data on inflammatory bowel disease (IBD) in which cases have systematically smaller library sizes than controls.

AVAILABILITY

The R package LDM is available on GitHub at https://github.com/yijuanhu/LDM in formats appropriate for Macintosh or Windows.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Synbiotics Alleviate the Gut Indole Load and Dysbiosis in Chronic Kidney Disease

Chronic kidney disease (CKD) has long been known to cause significant digestive tract pathology. Of note, indoxyl sulfate is a gut microbe-derived uremic toxin that accumulates in CKD patients. Nevertheless, the relationship between gut microbiota, fecal indole content, and blood indoxyl sulfate level remains unknown. In our study, we established an adenine-induced CKD rat model, which recapitulates human CKD-related gut dysbiosis. Synbiotic treatment in CKD rats showed a significant reduction in both the indole-producing bacterium Clostridium and fecal indole amount. Furthermore, gut microbiota diversity was reduced in CKD rats but was restored after synbiotic treatment. Intriguingly, in our end-stage kidney disease (ESKD) patients, the abundance of indole-producing bacteria, Bacteroides, Prevotella, and Clostridium, is similar to that of healthy controls. Consistently, the fecal indole tends to be higher in the ESKD patients, but the difference did not achieve statistical significance. However, the blood level of indoxyl sulfate was significantly higher than that of healthy controls, implicating that under an equivalent indole production rate, the impaired renal excretion contributes to the accumulation of this notorious uremic toxin. On the other hand, we did identify two short-chain fatty acid-producing bacteria, Faecalibacterium and Roseburia, were reduced in ESKD patients as compared to the healthy controls. This may contribute to gut dysbiosis. We also identified that three genera Fusobacterium, Shewanella, and Erwinia, in the ESKD patients but not in the healthy controls. Building up gut symbiosis to treat CKD is a novel concept, but once proved effective, it will provide an additional treatment strategy for CKD patients.

Do we have the guts to go? The abdominal compartment, intra-abdominal hypertension, the human microbiome and exploration class space missions

Humans are destined to explore space, yet critical illness and injury may be catastrophically limiting for extraterrestrial travel. Humans are superorganisms living in symbiosis with their microbiomes, whose genetic diversity dwarfs that of humans. Symbiosis is critical and imbalances are associated with disease, occurring within hours of serious illness and injury. There are many characteristics of space flight that negatively influence the microbiome, especially deep space itself, with its increased radiation and absence of gravity. Prolonged weightlessness causes many physiologic changes that are detrimental; some resemble aging and will adversely affect the ability to tolerate critical illness or injury and subsequent treatment. Critical illness-induced intra-abdominal hypertension (IAH) may induce malperfusion of both the viscera and microbiome, with potentially catastrophic effects. Evidence from animal models confirms profound IAH effects on the gut, namely ischemia and disruption of barrier function, mechanistically linking IAH to resultant organ dysfunction. Therefore, a pathologic dysbiome, space-induced immune dysfunction and a diminished cardiorespiratory reserve with exacerbated susceptibility to IAH, imply that a space-deconditioned astronaut will be vulnerable to IAH-induced gut malperfusion. This sets the stage for severe gut ischemia and massive biomediator generation in an astronaut with reduced cardiorespiratory/immunological capacity. Fortunately, experiments in weightless analogue environments suggest that IAH may be ameliorated by conformational abdominal wall changes and a resetting of thoracoabdominal mechanics. Thus, review of the interactions of physiologic changes with prolonged weightlessness and IAH is required to identify appropriate questions for planning exploration class space surgical care.

Biosynthesis, characterization, and in vitro assessment on cytotoxicity of actinomycete-synthesized silver nanoparticles on Allium cepa root tip cells

Background

The industrial production of silver nanoparticles (AgNPs) and its commercial applications are being considerably increased in recent times, resulting in the release of AgNPs in the environment and enhanced probability of contaminations and their adverse effects on living systems. Based on this, the present study was conducted to evaluate the in vitro cytotoxicity of actinomycete-synthesized AgNPs on Allium cepa (A. cepa) root tip cells. A green synthesis method was employed for biosynthesis of AgNPs from Streptomyces sp. NS-33. However, morphological, physiological, biochemical, and molecular analysis were carried out to characterize the strain NS-33. Later, the synthesized AgNPs were characterized and antibacterial activity was also carried out against pathogenic bacteria. Finally, cytotoxic activity was evaluated on A. cepa root tip cells.

Results

Results showed the synthesis of spherical and polydispersed AgNPs with a characteristic UV-visible (UV-Vis.) spectral peak at 397 nm and average size was 32.40 nm. Energy dispersive spectroscopy (EDS) depicted the presence of silver, whereas Fourier transform infrared (FTIR) studies indicated the presence of various functional groups. The phylogenetic relatedness of Streptomyces sp. NS-33 was found with Streptomyces luteosporeus through gene sequencing. A good antibacterial potential of AgNPs was observed against two pathogenic bacteria. Concerning cytotoxicity, a gradually decreased mitotic index (MI) and increased chromosomal aberrations were observed along with the successive increase of AgNPs concentration.

Conclusions

Therefore, the release of AgNPs into the environment must be prevented, so that it cannot harm plants and other beneficial microorganisms.

Impact of the microbiome on checkpoint inhibitor treatment in patients with non-small cell lung cancer and melanoma

The microbiome is increasingly recognized for its role in multiple aspects of cancer development and treatment, specifically in response to checkpoint inhibitors. While checkpoint inhibitors have revolutionized cancer treatment by producing durable anti-tumor responses, only a minority of patients respond to the available immunotherapy drugs and accurate, sensitive and specific microbiome predictors of response to treatment remain elusive. Additionally, the specific mechanisms linking the microbiome and host immunological responses remain unclear. In this review, we examine the evidence for the gut microbiome's association with anti-tumor responses to checkpoint inhibitors in the treatment of melanoma, non-small cell lung cancer, and renal cell carcinoma. Furthermore, we discuss the current evidence available from murine models seeking to explain the immunological mechanisms that may drive this process. While this work is promising in defining the impact of gut microbiota in cancer treatment, many unanswered questions indicate the need for additional human and experimental studies.

Current evidence on the relation between gut microbiota and intestinal anastomotic leak in colorectal surgery

BACKGROUND

Anastomotic leak (AL) is a major complication in colorectal surgery. It worsens morbidity, mortality and oncological outcomes in colorectal cancer. Some evidence suggests a potential effect of the intestinal microbiome on wound healing. This review aims to provide a comprehensive review on historical and current evidence regarding the relation between the gastrointestinal microbiota and AL in colorectal surgery, and the potential microbiota-modifying effect of some perioperative commonly used measures.

DATA SOURCES

A comprehensive search was conducted in Pubmed, Medline and Embase for historical and current clinical and animal studies addressing perioperative intestinal microbiota evaluation, intestinal healing and AL.

CONCLUSIONS

Evidence on microbes' role in AL is mainly derived from animal experiments. The microbiota's composition and implications are poorly understood in surgical patients. Elaborate microbiota sequencing is required in colorectal surgery to identify potentially beneficial microbial profiles that could lead to specific perioperative microbiome-altering measures and improve surgical and oncological outcomes.

Compositional Analysis of the Human Microbiome in Cancer Research

Gut microbial composition has shown to be associated with obesity, diabetes mellitus, inflammatory bowel disease, colitis, autoimmune disorders, and cancer, among other diseases. Microbiome research has significantly evolved through the years and continues to advance as we develop new and better strategies to more accurately measure its composition and function. Careful selection of study design, inclusion and exclusion criteria of participants, and methodology are paramount to accurately analyze microbial structure. Here we present the most up-to-date available information on methods for gut microbial collection and analysis.

The interplay between oral microbiome, lifestyle factors and genetic polymorphisms in the risk of oral squamous cell carcinoma

Poor oral hygiene may lead to overgrowth of pathogenic oral bacteria, which may induce chronic inflammation to promote the oncogenesis of oral squamous cell carcinoma (OSCC). This study investigated the association between oral bacterial profile and OSCC risk in a case-control study of 138 OSCC cases and 151 controls (88 cases and 90 controls for the discovery group and 50 cases and 61 controls for the validation group). Oral bacterial profiles were characterized by targeted sequencing of the 16S rRNA gene. Three species of periodontopathogenic bacteria, Prevotella tannerae, Fusobacterium nucleatum, and Prevotella intermedia, were associated with an increased OSCC risk. This association was modified by the genetic polymorphisms of TLR2 and TLR4. Use of alcohol, betel quids and cigarettes and poor oral hygiene were associated with a higher percentage of oral periodontopathogenic bacteria. The association between alcohol and periodontopathogenic bacteria was modified by the genetic polymorphism of ALDH2, with a stronger positive association observed among the ALDH2-deficient individuals. The percentage of periodontopathogenic bacteria was positively correlated with the level of salivary IL1β, an inflammatory cytokine. Overall, our results showed a positive association between periodontopathogenic bacteria and OSCC risk and this relationship may be influenced by lifestyle and genetic factors. Our results provided further biological support for the established association between poor oral hygiene and OSCC risk. This suggested that improving oral hygiene may reduce OSCC risk and should be part of a public health campaign to prevent the occurrence of OSCC.

MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data

Background

With the advent of the age of big data in bioinformatics, large volumes of data and high-performance computing power enable researchers to perform re-analyses of publicly available datasets at an unprecedented scale. Ever more studies imply the microbiome in both normal human physiology and a wide range of diseases. RNA sequencing technology (RNA-seq) is commonly used to infer global eukaryotic gene expression patterns under defined conditions, including human disease-related contexts; however, its generic nature also enables the detection of microbial and viral transcripts.

Findings

We developed a bioinformatic pipeline to screen existing human RNA-seq datasets for the presence of microbial and viral reads by re-inspecting the non-human-mapping read fraction. We validated this approach by recapitulating outcomes from six independent, controlled infection experiments of cell line models and compared them with an alternative metatranscriptomic mapping strategy. We then applied the pipeline to close to 150 terabytes of publicly available raw RNA-seq data from  more than 17,000 samples from more than 400 studies relevant to human disease using state-of-the-art high-performance computing systems. The resulting data from this large-scale re-analysis are made available in the presented MetaMap resource.

Conclusions

Our results demonstrate that common human RNA-seq data, including those archived in public repositories, might contain valuable information to correlate microbial and viral detection patterns with diverse diseases. The presented MetaMap database thus provides a rich resource for hypothesis generation toward the role of the microbiome in human disease. Additionally, codes to process new datasets and perform statistical analyses are made available.

Diabetic gut microbiota dysbiosis as an inflammaging and immunosenescence condition that fosters progression of retinopathy and nephropathy

The increased prevalence of type 2 diabetes mellitus (T2DM) and life expectancy of diabetic patients fosters the worldwide prevalence of retinopathy and nephropathy, two major microvascular complications that have been difficult to treat with contemporary glucose-lowering medications. The gut microbiota (GM) has become a lively field research in the last years; there is a growing recognition that altered intestinal microbiota composition and function can directly impact the phenomenon of ageing and age-related disorders. In fact, human GM, envisaged as a potential source of novel therapeutics, strongly modulates host immunity and metabolism. It is now clear that gut dysbiosis and their products (e.g. p-cresyl sulfate, trimethylamine‑N‑oxide) dictate a secretory associated senescence phenotype and chronic low-grade inflammation, features shared in the physiological process of ageing ("inflammaging") as well as in T2DM ("metaflammation") and in its microvascular complications. This review provides an in-depth look on the crosstalk between GM, host immunity and metabolism. Further, it characterizes human GM signatures of elderly and T2DM patients. Finally, a comprehensive scrutiny of recent molecular findings (e.g. epigenetic changes) underlying causal relationships between GM dysbiosis and diabetic retinopathy/nephropathy complications is pinpointed, with the ultimate goal to unravel potential pathophysiological mechanisms that may be explored, in a near future, as personalized disease-modifying therapeutic approaches.

16S rRNA Gene Sequencing for Deciphering the Colorectal Cancer Gut Microbiome: Current Protocols and Workflows

The human gut holds the densest microbiome ecosystem essential in maintaining a healthy host physiology, whereby disruption of this ecosystem has been linked to the development of colorectal cancer (CRC). The advent of next-generation sequencing technologies such as the 16S rRNA gene sequencing has enabled characterization of the CRC gut microbiome architecture in an affordable and culture-free approach. Nevertheless, the lack of standardization in handling and storage of biospecimens, nucleic acid extraction, 16S rRNA gene primer selection, length, and depth of sequencing and bioinformatics analyses have contributed to discrepancies found in various published studies of this field. Accurate characterization of the CRC microbiome found in different stages of CRC has the potential to be developed into a screening tool in the clinical setting. This mini review aims to concisely compile all available CRC microbiome studies performed till end of 2016 and to suggest standardized protocols that are crucial in developing a gut microbiome screening panel for CRC.

A Method for Targeted 16S Sequencing of Human Milk Samples

Studies of microbial communities have become widespread with the development of relatively inexpensive, rapid, and high throughput sequencing. However, as with all these technologies, reproducible results depend on a laboratory workflow that incorporates appropriate precautions and controls. This is particularly important with low-biomass samples where contaminating bacterial DNA can generate misleading results. This article details a semi-automated workflow to identify microbes from human breast milk samples using targeted sequencing of the 16S ribosomal RNA (rRNA) V4 region on a low- to mid-throughput scale. The protocol describes sample preparation from whole milk including: sample lysis, nucleic acid extraction, amplification of the V4 region of the 16S rRNA gene, and library preparation with quality control measures. Importantly, the protocol and discussion consider issues that are salient to the preparation and analysis of low-biomass samples including appropriate positive and negative controls, PCR inhibitor removal, sample contamination by environmental, reagent, or experimental sources, and experimental best practices designed to ensure reproducibility. While the protocol as described is specific to human milk samples, it is adaptable to numerous low- and high-biomass sample types, including samples collected on swabs, frozen neat, or stabilized in a preservation buffer.

Gut microbiota and its implications in small bowel transplantation

The gut microbiota is mainly composed of a diverse population of commensal bacterial species and plays a pivotal role in the maintenance of intestinal homeostasis, immune modulation and metabolism. The influence of the gut microbiota on solid organ transplantation has recently been recognized. In fact, several studies indicated that acute and chronic allograft rejection in small bowel transplantation (SBT) is closely associated with the alterations in microbial patterns in the gut. In this review, we focused on the recent findings regarding alterations in the microbiota following SBTand the potential roles of these alterations in the development of acute and chronic allograft rejection. We also reviewed important advances with respect to the interplays between the microbiota and host immune systems in SBT. Furthermore, we explored the potential of the gut microbiota as a microbial marker and/or therapeutic target for the predication and intervention of allograft rejection and chronic dysfunction. Given that current research on the gut microbiota has become increasingly sophisticated and comprehensive, large cohort studies employing metagenomic analysis and multivariate linkage should be designed for the characterization of host-microbe interaction and causality between microbiota alterations and clinical outcomes in SBT. The findings are expected to provide valuable insights into the role of gut microbiota in the development of allograft rejection and other transplant-related complications and introduce novel therapeutic targets and treatment approaches in clinical practice.

Bacterial alterations in salivary microbiota and their association in oral cancer

Oral squamous cell carcinoma (OSCC) is the most common malignant neoplasm of the oral cavity and the fourth leading malignancy and cause of cancer-related death in the male population of Taiwan. Most cases are detected at advanced stages, resulting in poor prognosis. Therefore, improved detection of early oral health disorders is indispensable. The involvement of oral bacteria in inflammation and their association with OSCC progression provide a feasible target for diagnosis. Due to the nature of oral neoplasms, the diagnosis of epithelial precursor lesions is relatively easy compared with that of other types of cancer. However, the transition from an epithelial precursor lesion to cancer is slow and requires further and continuous follow-up. In this study, we investigated microbiota differences between normal individuals, epithelial precursor lesion patients, and cancer patients with different lifestyle habits, such as betel chewing and smoking, using next-generation sequencing. Overall, the oral microbiome compositions of five genera, Bacillus, Enterococcus, Parvimonas, Peptostreptococcus, and Slackia, revealed significant differences between epithelial precursor lesion and cancer patients and correlated with their classification into two clusters. These composition changes might have the potential to constitute a biomarker to help in monitoring the oral carcinogenesis transition from epithelial precursor lesion to cancer.

Mechanisms and consequences of intestinal dysbiosis

The composition of the gut microbiota is in constant flow under the influence of factors such as the diet, ingested drugs, the intestinal mucosa, the immune system, and the microbiota itself. Natural variations in the gut microbiota can deteriorate to a state of dysbiosis when stress conditions rapidly decrease microbial diversity and promote the expansion of specific bacterial taxa. The mechanisms underlying intestinal dysbiosis often remain unclear given that combinations of natural variations and stress factors mediate cascades of destabilizing events. Oxidative stress, bacteriophages induction and the secretion of bacterial toxins can trigger rapid shifts among intestinal microbial groups thereby yielding dysbiosis. A multitude of diseases including inflammatory bowel diseases but also metabolic disorders such as obesity and diabetes type II are associated with intestinal dysbiosis. The characterization of the changes leading to intestinal dysbiosis and the identification of the microbial taxa contributing to pathological effects are essential prerequisites to better understand the impact of the microbiota on health and disease.

Molecular and genetic inflammation networks in major human diseases

It has been well-recognized that inflammation alongside tissue repair and damage maintaining tissue homeostasis determines the initiation and progression of complex diseases. Albeit with the accomplishment of having captured the most critical inflammation-involved molecules, genetic susceptibilities, epigenetic factors, and environmental factors, our schemata on the role of inflammation in complex diseases remain largely patchy, in part due to the success of reductionism in terms of research methodology per se. Omics data alongside the advances in data integration technologies have enabled reconstruction of molecular and genetic inflammation networks which shed light on the underlying pathophysiology of complex diseases or clinical conditions. Given the proven beneficial role of anti-inflammation in coronary heart disease as well as other complex diseases and immunotherapy as a revolutionary transition in oncology, it becomes timely to review our current understanding of the molecular and genetic inflammation networks underlying major human diseases. In this review, we first briefly discuss the complexity of infectious diseases and then highlight recently uncovered molecular and genetic inflammation networks in other major human diseases including obesity, type II diabetes, coronary heart disease, late onset Alzheimer's disease, Parkinson's disease, and sporadic cancer. The commonality and specificity of these molecular networks are addressed in the context of genetics based on genome-wide association study (GWAS). The double-sword role of inflammation, such as how the aberrant type 1 and/or type 2 immunity leads to chronic and severe clinical conditions, remains open in terms of the inflammasome and the core inflammatome network features. Increasingly available large Omics and clinical data in tandem with systems biology approaches have offered an exciting yet challenging opportunity toward reconstruction of more comprehensive and dynamic molecular and genetic inflammation networks, which hold great promise in transiting network snapshots to video-style multi-scale interplays of disease mechanisms, in turn leading to effective clinical intervention.

[The lung microbiota. Review]

In the last 20years, culture-independent DNA-based techniques ("shotgun sequencing") demonstrated that complex microbial communities reside on most epithelial surfaces, including the lower airways. Until the amniotic sac ruptures, a fetus is considered to be essentially sterile. Many factors affect the composition of the lung microbiota: inheritance, mode of delivery, diet, and age-related changes in adults. It interacts with the digestive and oropharyngeal microbiotas. Animal models show that these interactions play a role in innate pulmonary immunity and modulation of the inflammatory response. The microbial composition of the airway microbiota differs between healthy children and those with chronic lung disease. The advances in the comprehension of microbiome changes have resulted in new approaches concerning the microbiota for treatment and prevention of disease.

The emerging landscape of salivary diagnostics

Saliva contains a variety of biomolecules, including DNA, coding and noncoding RNA, proteins, metabolites and microbiota. The changes in the salivary levels of these molecular constituents can be used to develop markers for disease detection and risk assessment. Use of saliva as an early-detection tool is a promising approach because collection of saliva is easy and noninvasive. Here, we review recent developments in salivary diagnostics, accomplished using salivaomics approaches, including genomic, transcriptomic, proteomic, metabolomic and microbiomic technologies. Additionally, we illustrate the mechanisms of how diseases distal from the oral cavity can lead to the appearance of discriminatory biomarkers in saliva, and discuss the relevance of these markers for translational and clinical applications.

Addressing unmet needs in understanding asthma mechanisms: From the European Asthma Research and Innovation Partnership (EARIP) Work Package (WP)2 collaborators

Asthma is a heterogeneous, complex disease with clinical phenotypes that incorporate persistent symptoms and acute exacerbations. It affects many millions of Europeans throughout their education and working lives and puts a heavy cost on European productivity. There is a wide spectrum of disease severity and control. Therapeutic advances have been slow despite greater understanding of basic mechanisms and the lack of satisfactory preventative and disease modifying management for asthma constitutes a significant unmet clinical need. Preventing, treating and ultimately curing asthma requires co-ordinated research and innovation across Europe. The European Asthma Research and Innovation Partnership (EARIP) is an FP7-funded programme which has taken a co-ordinated and integrated approach to analysing the future of asthma research and development. This report aims to identify the mechanistic areas in which investment is required to bring about significant improvements in asthma outcomes.

Colorectal Carcinoma: A General Overview and Future Perspectives in Colorectal Cancer

Colorectal cancer (CRC) is the third most common cancer and the fourth most common cause of cancer-related death. Most cases of CRC are detected in Western countries, with its incidence increasing year by year. The probability of suffering from colorectal cancer is about 4%–5% and the risk for developing CRC is associated with personal features or habits such as age, chronic disease history and lifestyle. In this context, the gut microbiota has a relevant role, and dysbiosis situations can induce colonic carcinogenesis through a chronic inflammation mechanism. Some of the bacteria responsible for this multiphase process include Fusobacterium spp, Bacteroides fragilis and enteropathogenic Escherichia coli. CRC is caused by mutations that target oncogenes, tumour suppressor genes and genes related to DNA repair mechanisms. Depending on the origin of the mutation, colorectal carcinomas can be classified as sporadic (70%); inherited (5%) and familial (25%). The pathogenic mechanisms leading to this situation can be included in three types, namely chromosomal instability (CIN), microsatellite instability (MSI) and CpG island methylator phenotype (CIMP). Within these types of CRC, common mutations, chromosomal changes and translocations have been reported to affect important pathways (WNT, MAPK/PI3K, TGF-β, TP53), and mutations; in particular, genes such as c-MYC, KRAS, BRAF, PIK3CA, PTEN, SMAD2 and SMAD4 can be used as predictive markers for patient outcome. In addition to gene mutations, alterations in ncRNAs, such as lncRNA or miRNA, can also contribute to different steps of the carcinogenesis process and have a predictive value when used as biomarkers. In consequence, different panels of genes and mRNA are being developed to improve prognosis and treatment selection. The choice of first-line treatment in CRC follows a multimodal approach based on tumour-related characteristics and usually comprises surgical resection followed by chemotherapy combined with monoclonal antibodies or proteins against vascular endothelial growth factor (VEGF) and epidermal growth receptor (EGFR). Besides traditional chemotherapy, alternative therapies (such as agarose tumour macrobeads, anti-inflammatory drugs, probiotics, and gold-based drugs) are currently being studied to increase treatment effectiveness and reduce side effects.

Molecular Testing in Emerging Infectious Diseases

It was widely believed in the late 1960s that infectious diseases had been conquered by vaccines and antibiotics and humans were no longer under threat by microbial pathogens. Yet, since that time more than 60 pathogens have been discovered that can cause serious emerging infectious diseases. Molecular methods have played critical roles in the discovery, monitoring, and clinical diagnostics of emerging pathogens. In this chapter, we present well-recognized emerging pathogens. We provide examples of the utility of molecular assays in research and clinical care of emerging infectious diseases. We also discuss some theoretical and practical limitations of molecular tests and the future prospects of expanding molecular diagnostics for emerging pathogens based on new advances of knowledge and technologies.

Salivary biomarkers in cancer detection

Cancer is the second most common cause of death in the USA. Its symptoms are often not specific and absent, until the tumors have already metastasized. Therefore, there is an urgent demand for developing rapid, highly accurate and noninvasive tools for cancer screening, early detection, diagnostics, staging and prognostics. Saliva as a multi-constituent oral fluid comprises secretions from the major and minor salivary glands, extensively supplied by blood. Molecules such as DNAs, RNAs, proteins, metabolites, and microbiota, present in blood, could be also found in saliva. Recently, salivary diagnostics has drawn significant attention for the detection of specific biomarkers, since the sample collection and processing are simple, cost-effective, and precise and do not cause patient discomfort. Here, we review recent salivary candidate biomarkers for systemic cancers by dividing them according to their origin into: genomic, transcriptomic, proteomic, metabolomic and microbial types.

The lung microbiome and exacerbations of COPD

PURPOSE OF REVIEW

Traditional culture methods have identified airway bacterial pathogens that cause acute exacerbations of chronic obstructive pulmonary disease (COPD), and contribute to airway inflammation and COPD progression. However, conventional microbiology is limited by low sensitivity and bias toward predetermined and predominant pathogens. Highly sensitive, unbiased microbiome techniques overcome these limitations. Here, we present recent lung microbiome data, specifically in the context of smoking, COPD, and exacerbations.

RECENT FINDINGS

In contrast to the sterile lung environment found with conventional microbiology, microbiome techniques demonstrate a lower respiratory tract microbiome in health. Alterations in the lung microbiome with smoking and COPD have been clearly demonstrated by culture techniques, however, the findings in microbiome studies are limited and controversial. Increasing COPD disease severity is associated with a reduction in microbial diversity. Though microbial community structure does not change with exacerbation, there are notable changes in its composition. Antibiotic and corticosteroid treatment of acute exacerbations of COPD have significant but opposing effects on microbiome composition.

SUMMARY

The composition of the lung microbiome changes with smoking, the severity of COPD, during acute exacerbations and with the use of steroids and/or antibiotics. Understanding the role of the microbiome in disease progression and development of exacerbations will lead to novel therapies.

Impact of micro-environmental changes on respiratory tract infections with intracellular bacteria

Community-acquired pneumonia is caused by intra- and extracellular bacteria, with some of these bacteria also being linked to the pathogenesis of chronic lung diseases, including asthma and chronic obstructive pulmonary disease. Chlamydia pneumoniae is an obligate intracellular pathogen that is highly sensitive to micro-environmental conditions controlling both pathogen growth and host immune responses. The availability of nutrients, as well as changes in oxygen, pH and interferon-γ levels, have been shown to directly influence the chlamydial life cycle and clearance. Although the lung has been traditionally regarded as a sterile environment, sequencing approaches have enabled the identification of a large number of bacteria in healthy and diseased lungs. The influence of the lung microbiota on respiratory infections has not been extensively studied so far and data on chlamydial infections are currently unavailable. In the present study, we speculate on how lung microbiota might interfere with acute and chronic infections by focusing exemplarily on the obligate intracellular C. pneumoniae. Furthermore, we consider changes in the gut microbiota as an additional player in the control of lung infections, especially in view the increasing evidence suggesting the involvement of the gut microbiota in various immunological processes throughout the human body.

Microbiome Changes during Tuberculosis and Antituberculous Therapy

The critical role of commensal microbiota in the human body has been increasingly recognized, and our understanding of its implications in human health and disease has expanded rapidly. The lower respiratory tract contains diverse communities of microbes known as lung microbiota, which are present in healthy individuals and in individuals with respiratory diseases. The dysbiosis of the airway microbiota in pulmonary tuberculosis (TB) may play a role in the pathophysiological processes associated with TB disease. Recent studies of the lung microbiome have pointed out changes in lung microbial communities associated with TB and other lung diseases and have also begun to elucidate the profound effects that antituberculous drug therapy can have on the human lung microbiome composition. In this review, the potential role of the human microbiome in TB pathogenesis and the changes in the human microbiome with Mycobacterium tuberculosis infection and TB therapy are presented and discussed.

The New Role of Biomedical Informatics in the Age of Digital Medicine

OBJECTIVES

To reflect on the recent rise of Digital Medicine, as well as to analyse main research opportunities in this area. Through the use of several examples, this article aims to highlight the new role that Biomedical Informatics (BMI) can play to facilitate progress in research fields such as participatory and precision medicine. This paper also examines the potential impact and associated risks for BMI due to the development of digital medicine and other recent trends. Lastly, possible strategies to place BMI in a better position to face these challenges are suggested.

METHODS

The core content of this article is based on a recent invited keynote lecture delivered by one of the authors (Martin-Sanchez) at the Medical Informatics Europe conference (MIE 2015) held in Madrid in May 2015. Both authors (Lopez-Campos and Martin-Sanchez) have collaborated during the last four years in projects such as the ones described in section 3 and have also worked in reviewing relevant articles and initiatives to prepare this talk.

RESULTS AND CONCLUSIONS

Challenges for BMI posed by the rise of technologically driven fields such as Digital Medicine are explored. New opportunities for BMI, in the context of two main avenues for biomedical and clinical research (participatory and precision medicine) are also emphasised. Several examples of current research illustrate that BMI plays a key role in the new area of Digital Medicine. Embracing these opportunities will allow academic groups in BMI to maintain their leadership, identify new research funding opportunities and design new educational programs to train the next generation of BMI scientists.