Replication Study: Intestinal inflammation targets cancer-inducing activity of the microbiota

A Prebiotic Diet Containing Galactooligosaccharides and Polydextrose Produces Dynamic and Reproducible Changes in the Gut Microbial Ecosystem in Male Rats

Despite substantial evidence supporting the efficacy of prebiotics for promoting host health and stress resilience, few experiments present evidence documenting the dynamic changes in microbial ecology and fecal microbially modified metabolites over time. Furthermore, the literature reports a lack of reproducible effects of prebiotics on specific bacteria and bacterial-modified metabolites. The current experiments examined whether consumption of diets enriched in prebiotics (galactooligosaccharides (GOS) and polydextrose (PDX)), compared to a control diet, would consistently impact the gut microbiome and microbially modified bile acids over time and between two research sites. Male Sprague Dawley rats were fed control or prebiotic diets for several weeks, and their gut microbiomes and metabolomes were examined using 16S rRNA gene sequencing and untargeted LC-MS/MS analysis. Dietary prebiotics altered the beta diversity, relative abundance of bacterial genera, and microbially modified bile acids over time. PICRUSt2 analyses identified four inferred functional metabolic pathways modified by the prebiotic diet. Correlational network analyses between inferred metabolic pathways and microbially modified bile acids revealed deoxycholic acid as a potential network hub. All these reported effects were consistent between the two research sites, supporting the conclusion that dietary prebiotics robustly changed the gut microbial ecosystem. Consistent with our previous work demonstrating that GOS/PDX reduces the negative impacts of stressor exposure, we propose that ingesting a diet enriched in prebiotics facilitates the development of a health-promoting gut microbial ecosystem.

Natural polysaccharides regulate intestinal microbiota for inhibiting colorectal cancer

The gastrointestinal tract is an important part of the human immune system. The gut microbiome, which constitutes a major component of the gastrointestinal tract, plays a crucial role in maintaining normal physiological functions and influences the development, diagnosis, and immunotherapy of colorectal cancer (CRC). Natural polysaccharides can be extracted from animals, plants, and traditional Chinese medicines. They serve as an essential energy source for the gut microbiome, promoting probiotic proliferation and regulating the intestinal microecological balance. Moreover, polysaccharides exhibit anti-tumor effects due to their immune regulatory functions and low toxicity. This review focuses on discussing these anti-tumor effects in CRC, along with improving gut microbiome dysbiosis and regulating the tumor immune microenvironment, providing evidence for effective therapeutic strategies against CRC.

Group authorship, an excellent opportunity laced with ethical, legal and technical challenges

Group authorship (also known as corporate authorship, team authorship, consortium authorship) refers to attribution practices that use the name of a collective (be it team, group, project, corporation, or consortium) in the authorship byline. Data shows that group authorships are on the rise but thus far, in scholarly discussions about authorship, they have not gained much specific attention. Group authorship can minimize tensions within the group about authorship order and the criteria used for inclusion/exclusion of individual authors. However, current use of group authorships has drawbacks, such as ethical challenges associated with the attribution of credit and responsibilities, legal challenges regarding how copyrights are handled, and technical challenges related to the lack of persistent identifiers (PIDs), such as ORCID, for groups. We offer two recommendations: 1) Journals should develop and share context-specific and unambiguous guidelines for group authorship, for which they can use the four baseline requirements offered in this paper; 2) Using persistent identifiers for groups and consistent reporting of members' contributions should be facilitated through devising PIDs for groups and linking these to the ORCIDs of their individual contributors and the Digital Object Identifier (DOI) of the published item.

The relationship between Clostridium butyricum and colorectal cancer

Gut microbiota dysbiosis is involved in intestinal diseases. The resident microorganisms in the digestive tract contribute to maintenance of gut homeostasis. Some bacterial species have been identified and are suspected to play a role in colorectal cancer (CRC). Many studies have found that Clostridium butyricum has a close relationship with CRC, and the mechanism is becoming increasingly clear. This review discusses the possible relationship between C. butyricum and CRC.

Challenges for assessing replicability in preclinical cancer biology

We conducted the Reproducibility Project: Cancer Biology to investigate the replicability of preclinical research in cancer biology. The initial aim of the project was to repeat 193 experiments from 53 high-impact papers, using an approach in which the experimental protocols and plans for data analysis had to be peer reviewed and accepted for publication before experimental work could begin. However, the various barriers and challenges we encountered while designing and conducting the experiments meant that we were only able to repeat 50 experiments from 23 papers. Here we report these barriers and challenges. First, many original papers failed to report key descriptive and inferential statistics: the data needed to compute effect sizes and conduct power analyses was publicly accessible for just 4 of 193 experiments. Moreover, despite contacting the authors of the original papers, we were unable to obtain these data for 68% of the experiments. Second, none of the 193 experiments were described in sufficient detail in the original paper to enable us to design protocols to repeat the experiments, so we had to seek clarifications from the original authors. While authors were extremely or very helpful for 41% of experiments, they were minimally helpful for 9% of experiments, and not at all helpful (or did not respond to us) for 32% of experiments. Third, once experimental work started, 67% of the peer-reviewed protocols required modifications to complete the research and just 41% of those modifications could be implemented. Cumulatively, these three factors limited the number of experiments that could be repeated. This experience draws attention to a basic and fundamental concern about replication – it is hard to assess whether reported findings are credible.

Challenges for assessing replicability in preclinical cancer biology

We conducted the Reproducibility Project: Cancer Biology to investigate the replicability of preclinical research in cancer biology. The initial aim of the project was to repeat 193 experiments from 53 high-impact papers, using an approach in which the experimental protocols and plans for data analysis had to be peer reviewed and accepted for publication before experimental work could begin. However, the various barriers and challenges we encountered while designing and conducting the experiments meant that we were only able to repeat 50 experiments from 23 papers. Here we report these barriers and challenges. First, many original papers failed to report key descriptive and inferential statistics: the data needed to compute effect sizes and conduct power analyses was publicly accessible for just 4 of 193 experiments. Moreover, despite contacting the authors of the original papers, we were unable to obtain these data for 68% of the experiments. Second, none of the 193 experiments were described in sufficient detail in the original paper to enable us to design protocols to repeat the experiments, so we had to seek clarifications from the original authors. While authors were extremely or very helpful for 41% of experiments, they were minimally helpful for 9% of experiments, and not at all helpful (or did not respond to us) for 32% of experiments. Third, once experimental work started, 67% of the peer-reviewed protocols required modifications to complete the research and just 41% of those modifications could be implemented. Cumulatively, these three factors limited the number of experiments that could be repeated. This experience draws attention to a basic and fundamental concern about replication - it is hard to assess whether reported findings are credible.

Interaction between intestinal microbiota and tumour immunity in the tumour microenvironment

In recent years, an increasing number of studies have reported that intestinal microbiota have an important effect on tumour immunity by affecting the tumour microenvironment (TME). The intestinal microbiota are closely associated with various immune cells, such as T lymphocytes, natural killer cells (NK cells) and macrophages. Some bacteria, such as Akkermansia muciniphila (A. muciniphila) and Lactobacillus reuteri (L. reuteri), have been shown to improve the effect of tumour immunity. Furthermore, microbial imbalance, such as the increased abundance of Fusobacterium nucleatum (F. nucleatum) and Helicobacter hepaticus (H. hepaticus), generally causes tumour formation and progression. In addition, some microbiota also play important roles in tumour immunotherapy, especially PD-L1-related therapies. Therefore, what is the relationship between these processes and how do they affect each other? In this review, we summarize the interactions and corresponding mechanisms among the intestinal microbiota, immune system and TME to facilitate the research and development of new targeted drugs and provide new approaches to tumour therapy.

'Author Contribution Details' and not 'Authorship Sequence' as a merit to determine credit: A need to relook at the current Indian practice

The Medical Council of India (MCI) has made research publications in indexed medical journals an obligatory requirement for promotion of medical teachers. In 2015, MCI guidelines said the first and the second author would receive credit for a research paper. In 2017, the amended guidelines provided credit to the first and the corresponding authors instead. We reviewed the common types of authorship order in medical publications from across the world and noted that before the 1990s, corresponding authors were rarely acknowledged and were not considered more important than any of the co-authors. By 2016, the corresponding author was usually the first or the last author. With an increase in collaborative research globally, more and more papers are published with multiple first, last or corresponding authors. Some journals have revised their Instructions to Authors to acknowledge co-first authors equally. Since 2017, PubMed also displays equal contributors in the author byline while still allowing searches for 'First author' and 'Last author' supporting the 'first and last author emphasis'. However, most guidelines mention that the authorship order is a collective decision of the authors. Any association between authorship sequence and credit for an article is debatable. Some journals allow or even insist on authorship statements to explain each contributor's role. Standardized vocabularies and taxonomies such as the Contributor Roles Taxonomy (CRediT) system can highlight contributions of individual authors. Some suggest doing away with the authorship order altogether. Readers and assessors should look at the 'author contribution details' rather than the 'authorship order' before drawing any conclusions about contributions of each author.

The protective role of short-chain fatty acids acting as signal molecules in chemotherapy- or radiation-induced intestinal inflammation

A compelling set of links between chemotherapy- or radiation-induced intestinal inflammation and microbial dysbiosis has emerged. It is the proportional imbalance between pathogenic and beneficial bacteria that aggravates intestinal mucositis. Bacteria that ferment fibers and produce short-chain fatty acids (SCFAs), (such as acetate, propionate, and butyrate) are typically reduced in the mucosa and feces of patients undergoing cancer therapy. In contrast, increasing lipopolysaccharide-producing bacteria result in proinflammatory events by interacting with Toll-like receptors. A collective acceptance is that bacterial metabolites are critical in recovering intestinal homeostasis. We herein review evidence supporting the positive roles carried out by SCFAs. SCFAs, acting as signaling molecules, directly activate G-coupled-receptors and inhibit histone deacetylases. Thus, SCFAs are able to strengthen the gut barrier and regulate immunomodulatory functions. Furthermore, it is possible to reverse intestinal microbial dysbiosis and subsequently suppress the secretion of proinflammatory cytokines by directly applying SCFA-producing bacteria. In addition, anticancer effects of SCFAs have proved in the colorectal cancer. In this review, we discuss microbial dysbiosis and its impact on chemotherapy- or radiation-induced intestinal mucositis. Moreover, we summarize the mechanisms of SCFA production and its effects on intestinal mucositis. This review suggests the therapeutic potential of SCFAs for the management of chemotherapy- or radiation-induced intestinal inflammation.

The microbiome in inflammatory bowel diseases: from pathogenesis to therapy

Inflammatory bowel disease (IBD) has become a global disease with accelerating incidence worldwide in the 21st century while its accurate etiology remains unclear. In the past decade, gut microbiota dysbiosis has consistently been associated with IBD. Although many IBD-associated dysbiosis have not been proven to be a cause or an effect of IBD, it is often hypothesized that at least some of alteration in microbiome is protective or causative. In this article, we selectively reviewed the hypothesis supported by both association studies in human and pathogenesis studies in biological models. Specifically, we reviewed the potential protective bacterial pathways and species against IBD, as well as the potential causative bacterial pathways and species of IBD. We also reviewed the potential roles of some members of mycobiome and virome in IBD. Lastly, we covered the current status of therapeutic approaches targeting microbiome, which is a promising strategy to alleviate and cure this inflammatory disease.

Understanding of researcher behavior is required to improve data reliability

BACKGROUND

A lack of data reproducibility ("reproducibility crisis") has been extensively debated across many academic disciplines.

RESULTS

Although a reproducibility crisis is widely perceived, conclusive data on the scale of the problem and the underlying reasons are largely lacking. The debate is primarily focused on methodological issues. However, examples such as the use of misidentified cell lines illustrate that the availability of reliable methods does not guarantee good practice. Moreover, research is often characterized by a lack of established methods. Despite the crucial importance of researcher conduct, research and conclusive data on the determinants of researcher behavior are widely missing.

CONCLUSION

Meta-research that establishes an understanding of the factors that determine researcher behavior is urgently needed. This knowledge can then be used to implement and iteratively improve measures that incentivize researchers to apply the highest standards, resulting in high-quality data.